Daily Papers

Low latent prediction error does not establish that a world model distinguishes the consequences of its actions. We introduce an evaluation protocol that traces the same intervention through simulator state, raster observations, target embeddings, and predictor outputs. Exact simulator-state forks in a controlled deformable-physics testbed reveal distinct bottlenecks. Changed commands alter particle motion, yet 41.5% of one-step raster pairs are identical. Observation loss is not the whole explanation: among 579 high-visibility counterfactuals, median predictor-to-target response is 0.0051 and 0.0217 across two seeds, falling to 0.0027 and 0.0116 after variance normalization. An isotropic state perturbation matched to the target counterfactual embedding shift produces 190x and 53x larger predictor changes on the same visible pairs, isolating action-path under-use rather than a dead or globally shrunk predictor. MSE-only training gives 8.36x lower 10-step latent error in matched seeds, but in spectrally concentrated spaces; one VICReg target encoder is also strongly concentrated, so neither error nor rank alone certifies physical state. Finally, stiffness remains near chance even from full-resolution rasters and mechanical state while privileged material parameters decode perfectly, indicating weak identifiability under this excitation rather than encoder discard. These results motivate auditing physical effect, observation visibility, representation geometry, and action dependence separately.

We present Δ-UQ -- a novel, general-purpose uncertainty estimator using the concept of anchoring in predictive models. Anchoring works by first transforming the input into a tuple consisting of an anchor point drawn from a prior distribution, and a combination of the input sample with the anchor using a pretext encoding scheme. This encoding is such that the original input can be perfectly recovered from the tuple -- regardless of the choice of the anchor. Therefore, any predictive model should be able to predict the target response from the tuple alone (since it implicitly represents the input). Moreover, by varying the anchors for a fixed sample, we can estimate uncertainty in the prediction even using only a single predictive model. We find this uncertainty is deeply connected to improper sampling of the input data, and inherent noise, enabling us to estimate the total uncertainty in any system. With extensive empirical studies on a variety of use-cases, we demonstrate that Δ-UQ outperforms several competitive baselines. Specifically, we study model fitting, sequential model optimization, model based inversion in the regression setting and out of distribution detection, & calibration under distribution shifts for classification.

Vision Transformers (ViTs) have significantly advanced computer vision, demonstrating strong performance across various tasks. However, the attention mechanism in ViTs makes each layer function as a low-pass filter, and the stacked-layer architecture in existing transformers suffers from frequency vanishing. This leads to the loss of critical details and textures. We propose a novel, circuit-theory-inspired strategy called Frequency-Dynamic Attention Modulation (FDAM), which can be easily plugged into ViTs. FDAM directly modulates the overall frequency response of ViTs and consists of two techniques: Attention Inversion (AttInv) and Frequency Dynamic Scaling (FreqScale). Since circuit theory uses low-pass filters as fundamental elements, we introduce AttInv, a method that generates complementary high-pass filtering by inverting the low-pass filter in the attention matrix, and dynamically combining the two. We further design FreqScale to weight different frequency components for fine-grained adjustments to the target response function. Through feature similarity analysis and effective rank evaluation, we demonstrate that our approach avoids representation collapse, leading to consistent performance improvements across various models, including SegFormer, DeiT, and MaskDINO. These improvements are evident in tasks such as semantic segmentation, object detection, and instance segmentation. Additionally, we apply our method to remote sensing detection, achieving state-of-the-art results in single-scale settings. The code is available at https://github.com/Linwei-Chen/FDAM.

When communicating with elders with cognitive impairment, cognitive stimulation (CS) help to maintain the cognitive health of elders. Data sparsity is the main challenge in building CS-based dialogue systems, particularly in the Chinese language. To fill this gap, we construct a Chinese CS conversation (CSConv) dataset, which contains about 2.6K groups of dialogues with CS principles and emotional support strategy labels. Making chit chat while providing emotional support is overlooked by the majority of existing cognitive dialogue systems. In this paper, we propose a multi-source knowledge fusion method for CS dialogue (CSD), to generate open-ended responses guided by the CS principle and emotional support strategy. We first use a progressive mask method based on external knowledge to learn encoders as effective classifiers, which is the prerequisite to predict the CS principle and emotional support strategy of the target response. Then a decoder interacts with the perceived CS principle and emotional support strategy to generate responses. Extensive experiments conducted on the CSConv dataset demonstrate the effectiveness of the proposed method, while there is still a large space for improvement compared to human performance.

Identifying which brain regions represent a visual concept in the human brain is a central challenge in neuroscience. Existing approaches have localized coarse functional regions (e.g., faces, places) through activation maximization, identifying regions that activate strongly for a target concept relative to other concepts. Yet strong activation alone does not establish that a region represents the concept itself, as responses may instead be driven by correlated visual or semantic cues. We introduce BrainCause, an automated framework that combines generative and brain models to synthesize controlled stimuli and validate neural representations through targeted causal testing. Given a query specifying a concept of interest, our framework constructs targeted stimulus sets comprising concept images, counterfactual edits that remove the target concept while preserving other image content, and images with candidate correlated distractors. It then uses an image-to-fMRI encoding model to predict brain responses and searches for representations that respond specifically to the target concept over correlated alternatives. BrainCause returns validated candidate representations and proposes follow-up fMRI experiments to further test or extend its discoveries. Our approach successfully recovers known functional localizations and identifies new candidate representations across dozens of concepts, validated on both predicted and measured fMRI data. Critically, we show that without causal validation, a large fraction of localizations would be false positives, confirming that activation alone is insufficient evidence of representation.

Prompt-tuning, which freezes pretrained language models (PLMs) and only fine-tunes few parameters of additional soft prompt, shows competitive performance against full-parameter fine-tuning (i.e.model-tuning) when the PLM has billions of parameters, but still performs poorly in the case of smaller PLMs. Hence, prompt transfer (PoT), which initializes the target prompt with the trained prompt of similar source tasks, is recently proposed to improve over prompt-tuning. However, such a vanilla PoT approach usually achieves sub-optimal performance, as (i) the PoT is sensitive to the similarity of source-target pair and (ii) directly fine-tuning the prompt initialized with source prompt on target task might lead to catastrophic forgetting of source knowledge. In response to these problems, we propose a new metric to accurately predict the prompt transferability (regarding (i)), and a novel PoT approach (namely PANDA) that leverages the knowledge distillation technique to transfer the "knowledge" from the source prompt to the target prompt in a subtle manner and alleviate the catastrophic forgetting effectively (regarding (ii)). Furthermore, to achieve adaptive prompt transfer for each source-target pair, we use our metric to control the knowledge transfer in our PANDA approach. Extensive and systematic experiments on 189 combinations of 21 source and 9 target datasets across 5 scales of PLMs demonstrate that: 1) our proposed metric works well to predict the prompt transferability; 2) our PANDA consistently outperforms the vanilla PoT approach by 2.3% average score (up to 24.1%) among all tasks and model sizes; 3) with our PANDA approach, prompt-tuning can achieve competitive and even better performance than model-tuning in various PLM scales scenarios. Code and models will be released upon acceptance.

With model weights fixed, we measure how much of an entity-replacement response transfers between English factual questions, beyond whether answers change. We add the hidden-state change from two source questions to a target question about the same entity, comparing the predicted log-probability shift between two relations' published answers, given known answer prefixes, with the measured one. Hidden reuse injects the aligned change at 50% depth before the target's remaining layers; direct reuse adds source output-score changes. With other-relation sources, hidden reuse removes 45% and 49% of no-change error on 0.5-1B Qwen and Llama. Gemma-2-2B removes 22% and passes one of three comparisons in plain text without its default beginning-of-sequence (BOS) token. A later protocol restoring it yields 58-68%, passing every comparison on three cohorts. Larger checkpoints, chat format and new entities show replication and format- or cohort-dependent failures. On small plain-format checkpoints, other-relation hidden reuse mainly reproduces the shift both relations' questions share, without reliably lowering relation-selective error. With target-relation sources, hidden reuse's post hoc advantage over direct reuse is 0.2-0.9 nats outside chat format, unconfirmed and not replacement-specific. The same relation-neutral change at both questions' entity tokens lowers relation-selective error more than random or other-replacement changes, indicating receiving-question dependence.

Destructive single-cell measurements provide unpaired population snapshots rather than observations of the same cells across conditions. Local cell states and transition requests may also be insufficient to distinguish responses across source populations. We introduce TempoBridge, a common source-conditioned transport formulation for temporal, genetic, and chemical population transitions. Source cells initialize latent transport and provide a fixed empirical population summary. The velocity field receives this summary alongside the evolving cell state, flow time, and a structured transition descriptor. Minibatch optimal transport (OT) supplies couplings only for conditional flow-matching training paths; inference requires neither target expression nor OT computation. On held-out donors, TempoBridge achieves an Energy distance of 0.129 versus 0.144 for scGen. Genetic mean-expression L_2 error is 2.261 versus 3.156 for scGPT-scratch under Seen 2/2. On held-out compounds, condition-averaged drug-effect correlation is 0.598 versus 0.561 for the CellFlow adapter. Temporal ablations show higher mean distributional error after removing source context, replacing optimal transport with random pairing, or replacing flow matching with static residual regression. Together, these results demonstrate the predictive utility of a common source-conditioned transport formulation across held-out donors, gene combinations, and compounds.

Predicting transcriptional responses to genetic perturbations is central to understanding gene function. Existing predictors primarily rely on transcriptomic measurements, although chromatin accessibility provides complementary information about the cellular context in which perturbations act. Using this information requires linking chromatin context to specific perturbations and accounting for baseline differences between independently sampled control and perturbed populations. We propose ChromaPert, a chromatin-informed framework for predicting state-dependent perturbation responses. ChromaPert combines molecular and DNA-informed locus priors with paired control RNA--ATAC features to jointly represent target identity and measured cellular context. Its Chromatin-Guided Response Router (CGRR) builds a source bank of control-derived expression offsets and retrieves relevant sources using perturbation/locus or control-ATAC similarity. These offsets account for baseline differences, while conditional transport flow learns the remaining response. Across three unseen-target and held-out-state settings on K562 CAT-ATAC and Perturb-Multiome, ChromaPert achieves the highest all-gene response correlation among evaluated methods. When transferring known perturbations to held-out states, it improves correlation by 23.2% across all genes and 46.2% for the twenty most responsive genes over the strongest respective baselines. Correct RNA--ATAC pairing improves recovery of chromatin-associated response slopes over shuffled pairing, while cross-state predictions retain state-specific responses to the same perturbation.

Dialogue models falter in noisy, multi-speaker environments, often producing irrelevant responses and awkward turn-taking. We present AV-Dialog, the first multimodal dialog framework that uses both audio and visual cues to track the target speaker, predict turn-taking, and generate coherent responses. By combining acoustic tokenization with multi-task, multi-stage training on monadic, synthetic, and real audio-visual dialogue datasets, AV-Dialog achieves robust streaming transcription, semantically grounded turn-boundary detection and accurate responses, resulting in a natural conversational flow. Experiments show that AV-Dialog outperforms audio-only models under interference, reducing transcription errors, improving turn-taking prediction, and enhancing human-rated dialogue quality. These results highlight the power of seeing as well as hearing for speaker-aware interaction, paving the way for {spoken} dialogue agents that perform {robustly} in real-world, noisy environments.

User response prediction is essential in industrial recommendation systems, such as online display advertising. Among all the features in recommendation models, user behaviors are among the most critical. Many works have revealed that a user's behavior reflects her interest in the candidate item, owing to the semantic or temporal correlation between behaviors and the candidate. While the literature has individually examined each of these correlations, researchers have yet to analyze them in combination, that is, the semantic-temporal correlation. We empirically measure this correlation and observe intuitive yet robust patterns. We then examine several popular user interest models and find that, surprisingly, none of them learn such correlation well. To fill this gap, we propose a Temporal Interest Network (TIN) to capture the semantic-temporal correlation simultaneously between behaviors and the target. We achieve this by incorporating target-aware temporal encoding, in addition to semantic encoding, to represent behaviors and the target. Furthermore, we conduct explicit 4-way interaction by deploying target-aware attention and target-aware representation to capture both semantic and temporal correlation. We conduct comprehensive evaluations on two popular public datasets, and our proposed TIN outperforms the best-performing baselines by 0.43% and 0.29% on GAUC, respectively. During online A/B testing in Tencent's advertising platform, TIN achieves 1.65% cost lift and 1.93% GMV lift over the base model. It has been successfully deployed in production since October 2023, serving the WeChat Moments traffic. We have released our code at https://github.com/zhouxy1003/TIN.

Predicting cellular responses to genetic perturbations helps prioritize experiments in single-cell genomics, where exhaustive measurement is infeasible. While computational models increasingly predict these responses, three evaluation deficiencies obscure what their scores demonstrate. First, absolute metrics cannot separate target-specific predictions from a shared background response. Second, common metrics remain high under gene shuffling, so gene-level accuracy is never verified. Third, a score at one training size says nothing about coverage, which depends on representation-space proximity and response-constraining power. We propose AmbiModBench, a specificity-aware, gene-resolved and coverage-aware benchmark. It pairs every score with a training-mean reference fitted on the same split, screens each readout by gene-coordinate permutation, and links embedding distance to response variation. Across K562, RPE1 and Norman, strong absolute scores largely reflect shared background rather than target-specific learning. Widely used readouts track response magnitude distributions rather than the affected genes. Detectable gain follows representation-space coverage rather than training-set size. Nonetheless, on RPE1 the protocol yields a reproducible target-specific gain across five additional splits and three gene selections, which absolute scores alone cannot distinguish from shared background.

In this work, we present a network-specific approach for predicting brain responses to complex multimodal movies, leveraging the Yeo 7-network parcellation of the Schaefer atlas. Rather than treating the brain as a homogeneous system, we grouped the seven functional networks into four clusters and trained separate multi-subject, multi-layer perceptron (MLP) models for each. This architecture supports cluster-specific optimization and adaptive memory modeling, allowing each model to adjust temporal dynamics and modality weighting based on the functional role of its target network. Our results demonstrate that this clustered strategy significantly enhances prediction accuracy across the 1,000 cortical regions of the Schaefer atlas. The final model achieved an eighth-place ranking in the Algonauts Project 2025 Challenge, with out-of-distribution (OOD) correlation scores nearly double those of the baseline model used in the selection phase. Code is available at https://github.com/Corsi01/algo2025.

Predicting transcriptomic responses to small-molecule perturbations across cell lines is central to drug discovery, but exhaustive profiling of drug-cell combinations is infeasible. We frame molecular perturbation prediction as retrieve-and-aggregate: approximate an unmeasured drug's response in a cell line by aggregating measured responses of a small set of biologically related compounds. We propose LLM-Guided Retrieval (LGR), where a large language model (LLM) ranks candidate neighbor drugs (restricted to those profiled in the target cell line); after which a fixed mean aggregator combines their observed expression deltas to form the prediction. We evaluate on the Tahoe-100M single-cell perturbation atlas under unseen-drug, unseen-cell-line, and open-world regimes. LGR consistently improves over drug mean, ChemCPA, and chemistry-based kNN baselines, with the strongest gains for unseen cell-line generalization, where it achieves higher correlation and lower error than mean baselines. Across settings, LGR improves directional (sign) accuracy of gene regulation, indicating better recovery of biologically meaningful perturbation effects even when magnitude-based metrics are similar. These results suggest that retrieval quality, rather than predictor complexity, is a key driver of zero-shot molecular perturbation prediction, and that LLMs can provide a useful biological prior when used as constrained retrieval modules.

Auto-bidding systems aim to maximize advertiser value over long horizons under budget constraints and ratio targets such as cost-per-acquisition, yet future traffic and auction dynamics are non-stationary and uncertain. Existing approaches face distinct limitations: control-based pacing reacts to deviations but cannot anticipate future conditions, while RL and generative methods fold constraints into reward signals, obscuring violations and degrading under distribution shift. We shift the learning target from actions to responses with the Generative Response Model (GRM), a history-conditioned sequence model that jointly predicts future traffic volume and horizon-aggregate cost/value curves as functions of a single bid multiplier. We show that under mild monotonicity conditions, the optimality gap relative to full per-tick control is bounded by the dispersion of per-tick marginal value-per-cost. Given predicted responses, a lightweight analytic controller enforces each active constraint via a 1D root-finding step. We prove this controller is exact for the single-multiplier problem and bound constraint violations under receding-horizon replanning in terms of prediction error. Experiments on AuctionNet show that GRM improves constraint stability and overall score compared to existing baselines.

Large vision-language models (VLMs) commonly process images at native or high resolution to remain effective across tasks. This inflates visual tokens ofter to 97-99% of total tokens, resulting in high compute and latency, even when low-resolution images would suffice. We introduce CARES-a Context-Aware Resolution Selector, a lightweight preprocessing module that, given an image-query pair, predicts the minimal sufficient input resolution. CARES uses a compact VLM (350M) to extract features and predict when a target pretrained VLM's response converges to its peak ability to answer correctly. Though trained as a discrete classifier over a set of optional resolutions, CARES interpolates continuous resolutions at inference for fine-grained control. Across five multimodal benchmarks spanning documents and natural images, as well as diverse target VLMs, CARES preserves task performance while reducing compute by up to 80%.

Foundation-model predictors of perturbation response are evaluated primarily by aggregate accuracy. Using their predictions to prioritize experiments requires assessing each prediction's reliability. We audit the state-transition (ST) decoder used in STATE across three encoders (SE-600M, scGPT, and Tahoe-x1) and four cell lines under CRISPRi. The decoder's first attention layer has a low-rank output. Projecting this output onto 4-32 fixed directions estimated from training activations preserves mean per-perturbation Pearson delta correlation (PDC). This low-rank attention bottleneck bounds the decoder's reliability by distance to training responses: PDC declines as the cosine distance from a perturbation's observed response to its nearest training response increases. We propose predicted-NN-distance, the cosine distance from a predicted response to its nearest training response, as a per-prediction confidence score. The score has a mean absolute Spearman correlation of 0.81 with PDC, close to the 0.88 obtained with the observed response. Thresholds calibrated on this score transfer across encoders and cell lines, and the score remains predictive of PDC for drug perturbations.

We develop a method to generate predictive regions that cover a multivariate response variable with a user-specified probability. Our work is composed of two components. First, we use a deep generative model to learn a representation of the response that has a unimodal distribution. Existing multiple-output quantile regression approaches are effective in such cases, so we apply them on the learned representation, and then transform the solution to the original space of the response. This process results in a flexible and informative region that can have an arbitrary shape, a property that existing methods lack. Second, we propose an extension of conformal prediction to the multivariate response setting that modifies any method to return sets with a pre-specified coverage level. The desired coverage is theoretically guaranteed in the finite-sample case for any distribution. Experiments conducted on both real and synthetic data show that our method constructs regions that are significantly smaller compared to existing techniques.

Given an algorithmic predictor that is accurate on some source population consisting of strategic human decision subjects, will it remain accurate if the population respond to it? In our setting, an agent or a user corresponds to a sample (X,Y) drawn from a distribution D and will face a model h and its classification result h(X). Agents can modify X to adapt to h, which will incur a distribution shift on (X,Y). Our formulation is motivated by applications where the deployed machine learning models are subjected to human agents, and will ultimately face responsive and interactive data distributions. We formalize the discussions of the transferability of a model by studying how the performance of the model trained on the available source distribution (data) would translate to the performance on its induced domain. We provide both upper bounds for the performance gap due to the induced domain shift, as well as lower bounds for the trade-offs that a classifier has to suffer on either the source training distribution or the induced target distribution. We provide further instantiated analysis for two popular domain adaptation settings, including covariate shift and target shift.

We post-train Qwen3.8-27B for Korean response style -- verbosity, list and markdown usage, discourse structure and register -- and measure two behaviours the objective never targets: abstention on ambiguous social questions in KoBBQ, where the benchmark-correct answer is UNKNOWN, and unprompted disclosure in securities guidance. Both move, and the changes are expressed primarily through the model's emission policy: how often it answers and how much it says. Matched target-form controls show that answer propensity depends on the training target, not the prompt set or recipe alone. Holding prompts, recipe, data volume and serving fixed and changing only the target text, three style seeds give positive answer-rate point estimates (mean +0.82 pp) and three neutral seeds negative ones (mean -1.53 pp); the observed seed ranges do not overlap and the means differ by 2.34 pp. A length-matched arm lies between them, and a fourth arm that stays short while preserving hedging is unstable across seeds, so which feature of the form is responsible is unresolved. For absolute stereotyped exposure the decomposition into an answer-propensity term and a conditional-composition term is an algebraic identity, not a finding; its empirical content is where the movement went. Across the trained checkpoints the changes are dominated by answer propensity while the composition term stays small, and because that term is evaluated on treatment-dependent answered subsets we do not read it as evidence about latent preference. Two measurement results follow. A between-arm contrast in conditional stereotyped share does not identify a change in conditional content preference when answer status is treatment-dependent. And agreement between two rule detectors for the same construct runs from 0.44 to 0.99 depending on which checkpoint produced the text -- observable without any reference labels.

We introduce a transfer learning framework for regression that leverages heterogeneous source domains to improve predictive performance in a data-scarce target domain. Our approach fits a conditional generative model to each source domain and calibrates a shared linear combination of the generated responses via conditional quantile matching at the observed target covariates. The calibration aligns the conditional response distributions while accommodating simultaneous shifts in both the covariate and conditional response distributions. The calibrated responses then serve as pseudo-labels to augment the target data for a broad class of downstream learning tasks. Theoretically, we derive an excess risk bound for an empirical risk minimizer (ERM) trained on the augmented data, separating the benefit of an enlarged training sample from errors due to density ratio estimation, source generator estimation, conditional calibration, and irreducible transfer bias. Empirically, simulations and real-data applications show that the proposed method can improve target-domain prediction when the transfer bias is small.

The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells. Here we propose a vision of leveraging advances in AI to construct virtual cells, high-fidelity simulations of cells and cellular systems under different conditions that are directly learned from biological data across measurements and scales. We discuss desired capabilities of such AI Virtual Cells, including generating universal representations of biological entities across scales, and facilitating interpretable in silico experiments to predict and understand their behavior using virtual instruments. We further address the challenges, opportunities and requirements to realize this vision including data needs, evaluation strategies, and community standards and engagement to ensure biological accuracy and broad utility. We envision a future where AI Virtual Cells help identify new drug targets, predict cellular responses to perturbations, as well as scale hypothesis exploration. With open science collaborations across the biomedical ecosystem that includes academia, philanthropy, and the biopharma and AI industries, a comprehensive predictive understanding of cell mechanisms and interactions has come into reach.

The presence of distribution shifts poses a significant challenge for deploying modern machine learning models in real-world applications. This work focuses on the target shift problem in a regression setting (Zhang et al., 2013; Nguyen et al., 2016). More specifically, the target variable y (also known as the response variable), which is continuous, has different marginal distributions in the training source and testing domain, while the conditional distribution of features x given y remains the same. While most literature focuses on classification tasks with finite target space, the regression problem has an infinite dimensional target space, which makes many of the existing methods inapplicable. In this work, we show that the continuous target shift problem can be addressed by estimating the importance weight function from an ill-posed integral equation. We propose a nonparametric regularized approach named ReTaSA to solve the ill-posed integral equation and provide theoretical justification for the estimated importance weight function. The effectiveness of the proposed method has been demonstrated with extensive numerical studies on synthetic and real-world datasets.

Predicting cellular responses to unseen chemical perturbations is challenging due to unknown targets and mechanisms, high-dimensional expression responses, and limited experimental coverage of the large small-molecule design space. We propose PerturbPFN, a PFN-style amortized model for unknown-target perturbation prediction under a hierarchical synthetic structural prior. Instead of directly regressing high-dimensional expression responses, PerturbPFN infers a latent system graph, sparse atomic intervention targets, and intervention strengths, then propagates their effects through an SCM decoder. The model is trained entirely on prior-predictive synthetic episodes generated from biologically motivated graph and expression simulators, enabling structured in-context learning without test-time gradient updates. We evaluate PerturbPFN on both real single-cell perturbation data and synthetic benchmarks, covering effect prediction, target identification, and regulatory structure discovery. Our results show that PerturbPFN offers a complementary trade-off to specialized baselines, achieving competitive perturbation prediction with low inference cost while exposing interpretable intermediate estimates of targets, strengths, and system structure.

Machine learning models routinely automate decisions in applications like lending and hiring. In such settings, consumer protection rules require companies that deploy models to explain predictions to decision subjects. These rules are motivated, in part, by the belief that explanations can promote recourse by revealing information that individuals can use to contest or improve their outcomes. In practice, many companies comply with these rules by providing individuals with a list of the most important features for their prediction, which they identify based on feature importance scores from feature attribution methods such as SHAP or LIME. In this work, we show how these practices can undermine consumers by highlighting features that would not lead to an improved outcome and by explaining predictions that cannot be changed. We propose to address these issues by highlighting features based on their responsiveness score -- i.e., the probability that an individual can attain a target prediction by changing a specific feature. We develop efficient methods to compute responsiveness scores for any model and any dataset. We conduct an extensive empirical study on the responsiveness of explanations in lending. Our results show that standard practices in consumer finance can backfire by presenting consumers with reasons without recourse, and demonstrate how our approach improves consumer protection by highlighting responsive features and identifying fixed predictions.

Scarce data and tumor heterogeneity limit patient-level cancer treatment-response prediction. Existing approaches predict response from pretreatment molecular profiles and drug representations, without explicitly modeling the molecular changes expected under treatment. We propose PerturbRx, a treatment-conditioned representation learning framework that learns intervention-induced latent transitions and uses them as patient-drug response features. PerturbRx trains a drug- and dose-conditioned transition predictor from context-matched but cell-unpaired control and treated single-cell populations, then freezes and transfers the predictor to pretreatment patient profiles without requiring post-treatment measurements. The transition is combined with patient and drug representations to predict response. Across TCGA and patient-derived xenograft benchmarks, PerturbRx achieves the strongest aggregate predictive performance among the evaluated methods. These results support perturbation-pretrained latent transitions as useful representations for patient-level drug-response prediction.

Training data attribution (TDA) aims to identify training examples that shape model behavior, but its intervention value depends on both which examples are selected and how they are modified. Influence functions (IF) estimate behavioral changes under infinitesimal reweighting, yet IF-selected examples often show limited advantages over random selection under conventional weight-based interventions. This raises the question of whether influential examples lack intervention value or whether reweighting fails to realize their behavioral leverage.We introduce influence-guided response rewriting, which uses IF to identify intervention targets and replaces their responses with behavior-aligned or behavior-opposed supervision while keeping instructions fixed. Across four open-weight LLMs, we compare rewriting and reweighting on the same influence-selected examples using epistemic abstention as our primary testbed. Response rewriting produces stronger, more persistent, and bidirectional behavioral shifts, while reweighting the same examples yields weak and inconsistent effects. Further analyses show that influence-selected examples provide greater rewriting leverage than alternative selectors, with changes remaining concentrated on target-relevant behaviors. The same qualitative contrast extends to safety refusal. These results distinguish the local reweighting effects captured by influence estimates from the broader intervention leverage of the examples they identify, motivating intervention-aware evaluation of TDA methods.

Large Language Models (LLMs) often expend significant computational resources generating boilerplate responses, such as refusals, simple acknowledgements and casual greetings, which adds unnecessary cost and latency. To address this inefficiency, we propose a simple yet highly effective method for detecting such responses after only a single generation step. We demonstrate that the log-probability distribution of the first generated token serves as a powerful signal for classifying the nature of the entire subsequent response. Our experiments, conducted across a diverse range of small, large, and reasoning-specialized models, show that the first-token log-probability vectors form distinctly separable clusters for different response types. Using a lightweight k-NN classifier, we achieve high accuracy in predicting whether a response will be a substantive answer or a form of boilerplate response, including user-specified refusals. The primary implication is a practical, computationally trivial technique, optimizing LLM inference by enabling early termination or redirection to a smaller model, thereby yielding significant savings in computational cost. This work presents a direct path toward more efficient and sustainable LLM deployment.

Longitudinal single cell atlases now capture matched pre treatment and post treatment states from responders and non responders, presenting an opportunity to mechanistically explain why two patients on the same drug diverge. We introduce scDEFT (single cell Drug EFfect Transducer), which treats a drug as a conditioning operator on cell representations, enabling prediction and explanation. In scDEFT, feature wise linear modulation produces drug conditioned cell latents, learned under abundant per cell supervision and then frozen. Two independent heads aggregate those latents over shared transcriptional neighborhoods to predict drug induced state change and responder status. A backward stage ranks the latent dimensions by how strongly they separate responders from non responders and maps them to genes under a cell composition control. On a harmonized inflammatory bowel disease atlas of 1.16 million cells, three cohorts and two drug classes, scDEFT predicts state change at 45% of the baseline to reproducibility ceiling headroom and stratifies responders before treatment at AUROC 0.70, where standard predictors remain at chance. These predictions and the drivers behind them support target and co target nomination, patient stratification, and counterfactual prediction of unseen drug cohort effects.

AI evaluation can support the wrong inference when an in-domain benchmark success does not survive distribution shift, or when the benchmark endpoint is entangled with a design factor. We study this problem in CRISPRi perturbation-effect prediction, evaluating a frozen Geneformer representation under a locked, pre-registered protocol: heads and model selection were frozen before test evaluation; the protocol required external outcome labels to remain withheld until final unblinding; and analysis-governing decisions were fixed before the evaluations they govern. In-distribution on the Virtual Cell Challenge (VCC), the frozen representation carries measurable predictive information beyond a dimension-matched random-feature control (Delta R^2 = +0.1645, 95% CI [+0.1375, +0.1920]), satisfying the pre-registered informativeness gate required before interpreting transfer. It then fails zero-shot transfer on both external screens (Spearman rho = -0.139 and -0.267), lying below that control on each. Adding a predefined magnitude block improves the representation externally (Delta rho = +0.032 and +0.143) but, under the frozen primary head, does not rescue transfer: both remain negative. A pre-registered, count-adjusted max-response secondary is positively associated with the outcome on both screens; we report it as correlational and secondary, not as a recovered magnitude signal. Finally, the VCC endpoint is strongly sample-size associated: a count-only linear model reaches R^2 = +0.4325, versus +0.2589 for the four magnitude scalars; adding those scalars to cell count improves R^2 by only +0.0017, so much of the aggregate-magnitude signal overlaps with cell count. This case study shows how locking the evaluation, harmonizing the measured endpoint, and separating primary from secondary evidence can change the inference supported by an AI benchmark.

Open-weights reasoning language models generate long chains-of-thought (CoTs) before producing a final response, which improves performance but introduces additional alignment risks, with harmful content often appearing in both the CoTs and the final outputs. In this work, we investigate if we can use CoTs to predict final response misalignment. We evaluate a range of monitoring approaches, including humans, highly-capable large language models, and text classifiers, using either CoT text or activations. First, we find that a simple linear probe trained on CoT activations can significantly outperform all text-based methods in predicting whether a final response will be safe or unsafe. CoT texts are often unfaithful and can mislead humans and classifiers, while model latents (i.e., CoT activations) offer a more reliable predictive signal. Second, the probe makes accurate predictions before reasoning completes, achieving strong performance even when applied to early CoT segments. These findings generalize across model sizes, families, and safety benchmarks, suggesting that lightweight probes could enable real-time safety monitoring and early intervention during generation.

Complete orthogonal predictive coordinates do not by themselves bind a latent direction to a named intervention. We present a mathematical and synthetic audit motivated by vascular device-vessel suitcordance. Capacity-matched least-squares predictors were exactly equivalent under complete fixed output transforms, whereas an anchor-only observer recovered interpretations only within the span of known perturbation signatures. Six three-dimensional configurations across 64 seeds gave a maximum paired prediction discrepancy of 6.7e-15 but a median untransported edit error of 1.513. Coordinate transport removed that error. Noisy and weak anchors constrained calibration stability, and changing the representation basis required recalibration or verified transport. Across 256 additional fits in dimensions 3-24, prediction equivalence persisted within 4.0e-15. We then evaluated nine deliberate runnable fault classes across 64 seeds. All 576 faulty executions completed, but each violated at least one reconstruction, prediction, delivered-edit or scope contract; all 320 valid control records passed. Repeating a faulty implementation gave exact self-agreement despite error against the separately computed simulator expectation. For one omitted-direction defect, probe coverage followed its analytic law, and rank-aware abstention protected unsupported interpretations. Scalar-noise experiments exposed both missed weak faults and excessive rejection under narrow relative tolerances. These controls provide an executable separation of prediction, semantic support and scientific acceptance. They are synthetic numerical audits, not clinical validation, neural JEPA-Anything replication, agent learning or patient treatment-effect estimation.

World models construct latent states that support prediction, planning, and reasoning about an underlying system. Joint-embedding predictive architectures (JEPAs) offer a direct way to learn such states by predicting targets in representation space instead of reconstructing every detail of the observation. Standard JEPAs, however, organize all predictable content through one target embedding and one prediction pathway. In complex systems, this monolithic state can allocate redundant capacity to dominant signals while providing weak or conflicting gradients to less dominant predictive structure. We introduce \method, a latent world-modeling framework based on orthogonal predictive factorization. Learned basis matrices analyze each target state into multiple components, and a dedicated prediction branch estimates each component from a shared context representation. Predictive regression preserves the factor magnitudes required for state synthesis, an orthogonality objective discourages repeated directions, factor-activity regularization maintains variation in projected targets, and online variance regularization discourages coordinate-wise encoder collapse. Predicted components are synthesized into a complete latent state that can be used by a readout, decoder, planner, or autoregressive rollout. The same predictive-state mechanism applies when the target is temporally future, spatially hidden, or another partial observation of the same system. Experiments on controlled vision, single-cell transcriptomics, longitudinal health records, continuous control, and molecular dynamics evaluate representation quality, forecasting, planning, and long-horizon stability.

Speech foundation models, such as HuBERT and its variants, are pre-trained on large amounts of unlabeled speech data and then used for a range of downstream tasks. These models use a masked prediction objective, where the model learns to predict information about masked input segments from the unmasked context. The choice of prediction targets in this framework impacts their performance on downstream tasks. For instance, models pre-trained with targets that capture prosody learn representations suited for speaker-related tasks, while those pre-trained with targets that capture phonetics learn representations suited for content-related tasks. Moreover, prediction targets can differ in the level of detail they capture. Models pre-trained with targets that encode fine-grained acoustic features perform better on tasks like denoising, while those pre-trained with targets focused on higher-level abstractions are more effective for content-related tasks. Despite the importance of prediction targets, the design choices that affect them have not been thoroughly studied. This work explores the design choices and their impact on downstream task performance. Our results indicate that the commonly used design choices for HuBERT can be suboptimal. We propose approaches to create more informative prediction targets and demonstrate their effectiveness through improvements across various downstream tasks.

We consider the problem of conformal prediction under covariate shift. Given labeled data from a source domain and unlabeled data from a covariate shifted target domain, we seek to construct prediction sets with valid marginal coverage in the target domain. Most existing methods require estimating the unknown likelihood ratio function, which can be prohibitive for high-dimensional data such as images. To address this challenge, we introduce the likelihood ratio regularized quantile regression (LR-QR) algorithm, which combines the pinball loss with a novel choice of regularization in order to construct a threshold function without directly estimating the unknown likelihood ratio. We show that the LR-QR method has coverage at the desired level in the target domain, up to a small error term that we can control. Our proofs draw on a novel analysis of coverage via stability bounds from learning theory. Our experiments demonstrate that the LR-QR algorithm outperforms existing methods on high-dimensional prediction tasks, including a regression task for the Communities and Crime dataset, an image classification task from the WILDS repository, and an LLM question-answering task on the MMLU benchmark.

Predicting how a patient's vital signs respond to an intervention is a central question in intensive care. World models can do so by learning dynamics as a function of prior actions. However, such models tend to be brittle outside of training data. Clinicians choose drug dosages based on the patient's state, so the association a model learns between dose and outcome runs opposite to the drug's effect, generalizing poorly to out-of-distribution (OOD) dosing practices. Yet, pharmacological information provides the directional effects of different drugs, which are invariant to OOD shifts. To resolve the OOD sensitivity of current ICU world models, we introduce PHYSIO WORLD, which isolates an intervention's effect by evaluating a forward pass twice: once under recorded doses, and once with those doses set to zero. The difference is projected onto pharmacologically admissible effect directions stated by 70 rules over 28 drugs, leaving the magnitude to be learned from data. Across five distribution-shift parameters over cohorts from three intensive-care databases, and against forecasters, counterfactual models, and invariance objectives, PHYSIO WORLD attains the lowest OOD RMSE in every setting, improving on the strongest external baseline by 8-12%, while matching the in-distribution error of its backbone. Reversing the pharmacological directions degrades accuracy below the backbone, and data-mined directions recover almost no gain, indicating the improvement derives from the content of the pharmacological knowledge. The construction may extend to other settings where the sign of an effect is known in advance and its magnitude is confounded by treatment assignment.

We study a self-supervised generation task for single-cell gene expression vectors: given a set of vectors from a cell type, we aim to generate additional gene expression vectors of that cell type. For this task we characterize both the biological fidelity of the generated gene expression vectors and the scaling behavior of the pretraining loss. The model is a causal transformer paired with a learned quantized VAE tokenizer, trained with a cross-entropy loss. To evaluate the model, we condition it on held-out gene expression vectors of a cell type and generate vectors of gene expression, comparing the resulting distribution over gene expression vectors to the ground truth distribution of that cell type. We study the scaling properties of the proposed architecture by varying the number of trained parameters and the amount of training data. To our knowledge, we find the first jointly-fit two-exponent scaling law and compute-optimal frontier for a single-cell foundation model. Finally, we discuss how this pretrained model could be finetuned for perturbation response prediction.

Predicting transcriptional responses to unseen compounds is limited by fragmented chemical coverage and heterogeneous experimental platforms and gene panels. To assess molecular generalization across these settings, we build on Chem-PerturBridge to benchmark eight datasets with 16,771 compounds, withholding test compounds from every training dataset. This comparison reveals that high overall response agreement can coexist with weak prediction of drug-specific differences, despite reproducible signals across repeated measurements. To exploit complementary chemical supervision while targeting these differences, we introduce Bison: a shared gene representation connects native panels, while two discrete diffusion models compose context-dependent responses with molecular deviations learned through matched drug-contrast supervision. A single Bison model jointly trained across all eight datasets achieves the highest mean overall-response and drug-contrast Pearson correlations on the full benchmark in comparison with 11 methods trained independently per dataset. Compared with dataset-specific training of the same architecture, joint training increases mean drug-contrast correlation by 27.4\%, with gains across all eight datasets and improvements in overall response prediction. These results demonstrate how matched drug contrasts turn complementary screens into shared molecular supervision for unseen-drug response prediction while preserving native gene measurements.

Instruction-tuned large language models produce helpful, structured responses, but how robust is this helpfulness under trivial constraints? We show that simple lexical constraints (banning a single punctuation character or common word) cause instruction-tuned LLMs to collapse their responses, losing 14--48\% of comprehensiveness across seven models spanning five families (7B--70B, open- and closed-weight). A blinded human evaluation with 10 STEM-trained evaluators confirms genuine content loss, with information criteria degrading 1.5--2.3times more than surface criteria, a finding corroborated by over 4,100 automated pairwise comparisons (77--100\% baseline preference) across three LLM judges from two model families. Diagnostic analysis identifies this as a planning failure: two-pass generation recovers 59--96\% of response length, and linear probes on prompt representations predict response length with R^2 = 0.51--0.94 before generation begins. The same probes yield negative R^2 on base models, confirming that instruction tuning introduces the representational structure underlying the collapse. Base models show no systematic degradation under identical constraints, demonstrating that instruction tuning couples task competence to narrow surface-form templates. The effect extends to realistic deployment constraints (preamble suppression, corporate tone guidelines, legal compliance hedging, accessibility requirements) causing comparable degradation (-22\% to -34\%), with suppressing the conversational opener alone (``Certainly!'') causing 40\% collapse on our most fragile model despite restricting only the opening tokens. We further show that standard independent LLM-as-judge evaluation detects only a 3.5\% quality drop where pairwise evaluation reveals 23\%, exposing a methodological blind spot in current evaluation practice.

Learning algorithms are often used in conjunction with expert decision makers in practical scenarios, however this fact is largely ignored when designing these algorithms. In this paper we explore how to learn predictors that can either predict or choose to defer the decision to a downstream expert. Given only samples of the expert's decisions, we give a procedure based on learning a classifier and a rejector and analyze it theoretically. Our approach is based on a novel reduction to cost sensitive learning where we give a consistent surrogate loss for cost sensitive learning that generalizes the cross entropy loss. We show the effectiveness of our approach on a variety of experimental tasks.

We propose a criterion for discrimination against a specified sensitive attribute in supervised learning, where the goal is to predict some target based on available features. Assuming data about the predictor, target, and membership in the protected group are available, we show how to optimally adjust any learned predictor so as to remove discrimination according to our definition. Our framework also improves incentives by shifting the cost of poor classification from disadvantaged groups to the decision maker, who can respond by improving the classification accuracy. In line with other studies, our notion is oblivious: it depends only on the joint statistics of the predictor, the target and the protected attribute, but not on interpretation of individualfeatures. We study the inherent limits of defining and identifying biases based on such oblivious measures, outlining what can and cannot be inferred from different oblivious tests. We illustrate our notion using a case study of FICO credit scores.

Every data selection method inherently has a target. In practice, these targets often emerge implicitly through benchmark-driven iteration: researchers develop selection strategies, train models, measure benchmark performance, then refine accordingly. This raises a natural question: what happens when we make this optimization explicit? To explore this, we propose benchmark-targeted ranking (BETR), a simple method that selects pretraining documents based on similarity to benchmark training examples. BETR embeds benchmark examples and a sample of pretraining documents in a shared space, scores this sample by similarity to benchmarks, then trains a lightweight classifier to predict these scores for the full corpus. We compare data selection methods by training over 500 models spanning 10^{19} to 10^{22} FLOPs and fitting scaling laws to them. From this, we find that simply aligning pretraining data to evaluation benchmarks using BETR achieves a 2.1x compute multiplier over DCLM-Baseline (4.7x over unfiltered data) and improves performance on 9 out of 10 tasks across all scales. BETR also generalizes well: when targeting a diverse set of benchmarks disjoint from our evaluation suite, it still matches or outperforms baselines. Our scaling analysis further reveals a clear trend: larger models require less aggressive filtering. Overall, our findings show that directly matching pretraining data to target tasks precisely shapes model capabilities and highlight that optimal selection strategies must adapt to model scale.

With the advent of LLMs, various tasks across the natural language processing domain have been transformed. However, their application in predictive tasks remains less researched. This study compares large language models, including GatorTron-Base (trained on clinical data), Llama 8B, and Mistral 7B, against models like BioBERT, DocBERT, BioClinicalBERT, Word2Vec, and Doc2Vec, setting benchmarks for predicting Shock in critically ill patients. Timely prediction of shock can enable early interventions, thus improving patient outcomes. Text data from 17,294 ICU stays of patients in the MIMIC III database were scored for length of stay > 24 hours and shock index (SI) > 0.7 to yield 355 and 87 patients with normal and abnormal SI-index, respectively. Both focal and cross-entropy losses were used during finetuning to address class imbalances. Our findings indicate that while GatorTron Base achieved the highest weighted recall of 80.5%, the overall performance metrics were comparable between SLMs and LLMs. This suggests that LLMs are not inherently superior to SLMs in predicting future clinical events despite their strong performance on text-based tasks. To achieve meaningful clinical outcomes, future efforts in training LLMs should prioritize developing models capable of predicting clinical trajectories rather than focusing on simpler tasks such as named entity recognition or phenotyping.

Interpretability research often aims to predict how a model will respond to targeted interventions on specific mechanisms. However, it rarely predicts how a model will respond to unseen input data. This paper explores the promises and challenges of interpretability as a tool for predicting out-of-distribution (OOD) model behavior. Specifically, we investigate the correspondence between attention patterns and OOD generalization in hundreds of Transformer models independently trained on a synthetic classification task. These models exhibit several distinct systematic generalization rules OOD, forming a diverse population for correlational analysis. In this setting, we find that simple observational tools from interpretability can predict OOD performance. In particular, when in-distribution attention exhibits hierarchical patterns, the model is likely to generalize hierarchically on OOD data -- even when the rule's implementation does not rely on these hierarchical patterns, according to ablation tests. Our findings offer a proof-of-concept to motivate further interpretability work on predicting unseen model behavior.

When a steering intervention changes a language model's behavior, which part of the intervention deserves the credit? We test this question for a target-centered, scaled conceptor complement by removing its fitted covariance filter while preserving the same target-specific center and gain. At the original aperture α=.05 and gain β=2, all 21 fitted maps across three models and seven targets expand every direction at the generation intervention layers. The matrix correction is 0.093%--7.815% of the matched-control displacement on held-out extraction activations. In 480 paired comparisons within a 1,920-response study, retaining the matrix changes many individual texts but does not establish a consistent additional target-suppression benefit on the four-target panel. A geometric aperture sweep shows that the operating regime changes with the filter setting. Separately, an invertible soft filter preserves what an unrestricted affine readout can recover, whereas dedicated erasure methods reduce prediction by newly fitted probes. Together, the results show why a whole-intervention comparison cannot by itself attribute generated behavior to the fitted matrix: analyze the complete transformation, hold shared components fixed, and test its output consequences directly.

Previous works on Treatment Effect Estimation (TEE) are not in widespread use because they are predominantly theoretical, where strong parametric assumptions are made but untractable for practical application. Recent work uses multilayer perceptron (MLP) for modeling casual relationships, however, MLPs lag far behind recent advances in ML methodology, which limits their applicability and generalizability. To extend beyond the single domain formulation and towards more realistic learning scenarios, we explore model design spaces beyond MLPs, i.e., transformer backbones, which provide flexibility where attention layers govern interactions among treatments and covariates to exploit structural similarities of potential outcomes for confounding control. Through careful model design, Transformers as Treatment Effect Estimators (TransTEE) is proposed. We show empirically that TransTEE can: (1) serve as a general purpose treatment effect estimator that significantly outperforms competitive baselines in a variety of challenging TEE problems (e.g., discrete, continuous, structured, or dosage-associated treatments) and is applicable to both when covariates are tabular and when they consist of structural data (e.g., texts, graphs); (2) yield multiple advantages: compatibility with propensity score modeling, parameter efficiency, robustness to continuous treatment value distribution shifts, explainable in covariate adjustment, and real-world utility in auditing pre-trained language models

Time-series forecasters are ranked almost entirely by accuracy metrics, but a forecast's decision value, its effect on the downstream decision, need not track accuracy and is rarely measured. This problem compounds as large language model (LLM) agents increasingly consume forecasters as tools, mediating them through stochastic, opaque policies. We present Vendster, an evaluation arena measuring how a forecaster's bias and prediction-interval width change the outcome of a buyer--vendor discount negotiation between two LLM agents. In the reference instance Vendster-M5, sampling base demand patterns from the M5 dataset, we evaluate two frontier-closed LLM families (Claude Opus 4.6 and GPT-5.6 Sol) and two open ones (DeepSeek-V3.2 and Qwen3-235B-A22B). Model-generated forecasts raise sales target attainment by up to +17 percentage points (p<0.001), yet standard forecast evaluation metrics such as relWQL and MASE do not predict negotiation outcomes at a statistically significant level. To isolate the causal structure, we substitute in synthetic forecasts with controlled bias and interval width. Under-prediction bias significantly improves outcomes for agents that react more to the forecasts---dose-response slopes -0.387 and -0.416 (p<0.001). Interval width has no statistically significant effect at zero bias. These findings indicate that the direction of forecast bias and agent forecast-reactivity are more strongly associated with downstream outcomes than forecast accuracy. Vendster is fully customizable and released under CC BY-NC 4.0 at https://github.com/amazon-science/Vendster.

The premise of identifiable and causal representation learning is to improve the current representation learning paradigm in terms of generalizability or robustness. Despite recent progress in questions of identifiability, more theoretical results demonstrating concrete advantages of these methods for downstream tasks are needed. In this paper, we consider the task of intervention extrapolation: predicting how interventions affect an outcome, even when those interventions are not observed at training time, and show that identifiable representations can provide an effective solution to this task even if the interventions affect the outcome non-linearly. Our setup includes an outcome Y, observed features X, which are generated as a non-linear transformation of latent features Z, and exogenous action variables A, which influence Z. The objective of intervention extrapolation is to predict how interventions on A that lie outside the training support of A affect Y. Here, extrapolation becomes possible if the effect of A on Z is linear and the residual when regressing Z on A has full support. As Z is latent, we combine the task of intervention extrapolation with identifiable representation learning, which we call Rep4Ex: we aim to map the observed features X into a subspace that allows for non-linear extrapolation in A. We show that the hidden representation is identifiable up to an affine transformation in Z-space, which is sufficient for intervention extrapolation. The identifiability is characterized by a novel constraint describing the linearity assumption of A on Z. Based on this insight, we propose a method that enforces the linear invariance constraint and can be combined with any type of autoencoder. We validate our theoretical findings through synthetic experiments and show that our approach succeeds in predicting the effects of unseen interventions.

We introduce RareTrap, a framework for estimating the probability of severe behaviors in black box large language models (LLMs). A key challenge for probability estimation is defining a tractable distribution over the input space. To accomplish that, RareTrap uses a surrogate LLM and constructs a geometry-aware mapping from a lower-dimensional latent reference space into its token-embedding space to induce an explicit and reproducible distribution over input prompts. A response-level performance function is utilized on the response to quantify behavior severity. This enables sequential rare event simulation that concentrates evaluations on progressively more severe behaviors while preserving probability under the induced prompt distribution, which would otherwise be prohibitive to measure. Across 10 open-weight and two frontier models (GPT-5.4 and Claude Sonnet 4.6), we find that RareTrap successfully induces severe resource consumption behaviors and computes their probability with as few as 200 evaluations. RareTrap provides model developers a principled approach for evaluating language models under a common distribution, and prioritizing alignment effort to improve safety and mitigate risks.

Instruction tuning has been widely adopted to ensure large language models (LLMs) follow user instructions effectively. The resulting instruction-following capabilities of LLMs heavily rely on the instruction datasets used for tuning. Recently, synthetic instruction datasets have emerged as an economically viable solution to provide LLMs diverse and high-quality instructions. However, existing approaches typically assume that larger or stronger models are stronger teachers for instruction tuning, and hence simply adopt these models as response generators to the synthetic instructions. In this paper, we challenge this commonly-adopted assumption. Our extensive experiments across five base models and twenty response generators reveal that larger and stronger models are not necessarily stronger teachers of smaller models. We refer to this phenomenon as the Larger Models' Paradox. We observe that existing metrics cannot precisely predict the effectiveness of response generators since they ignore the compatibility between teachers and base models being fine-tuned. We thus develop a novel metric, named as Compatibility-Adjusted Reward (CAR) to measure the effectiveness of response generators. Our experiments across five base models demonstrate that CAR outperforms almost all baselines.

Counterfactual prompting (i.e., perturbing a single factor and measuring output change) is widely used to evaluate things like LLM bias and CoT faithfulness. But in this work we argue that observed effects cannot be attributed to the targeted factor without accounting for baseline ``meaning-preserving'' modifications to text that establish general model sensitivity. This is because every counterfactual edit is a compound treatment that bundles the variable of interest with incidental surface-form variation; this violates treatment variation irrelevance. We observe prediction flip rates on MedQA of 14.9% when we surgically change patient gender. However, this is statistically indistinguishable from the flip rates induced by simply paraphrasing inputs (14.1%). In this case, it would therefore be unwarranted to conclude that the LLM is especially sensitive to patient gender. To account for this and robustly measure the effects of targeted interventions, we propose a framework in which we compare (via statistical testing) differences observed under target interventions to those induced by paraphrasing inputs. We then use this framework to revisit a analysis done on the MedPerturb dataset, which reported evidence of model sensitivity to patient demographics and stylistic cues. We find that these effects largely dissipate when we account for general model sensitivity, with only 5 of 120 tests reaching statistical significance. Applying the same framework to occupational biography classification, we detect clearly significant directional gender bias, showing that the framework identifies real directional effects even when they are small. We evaluate a range of metrics -- aggregate, per-sample distributional, and regression -- and find that per-sample metrics are dramatically more powerful than aggregate metrics and regression powerfully and uniquely characterizes effect direction and magnitude.

Automated scoring engines are increasingly being used to score the free-form text responses that students give to questions. Such engines are not designed to appropriately deal with responses that a human reader would find alarming such as those that indicate an intention to self-harm or harm others, responses that allude to drug abuse or sexual abuse or any response that would elicit concern for the student writing the response. Our neural network models have been designed to help identify these anomalous responses from a large collection of typical responses that students give. The responses identified by the neural network can be assessed for urgency, severity, and validity more quickly by a team of reviewers than otherwise possible. Given the anomalous nature of these types of responses, our goal is to maximize the chance of flagging these responses for review given the constraint that only a fixed percentage of responses can viably be assessed by a team of reviewers.

Recent time series foundation models (TSFMs) can consume covariates in-context, extending zero-shot forecasting to problems driven by external factors. This enables scenario analysis: forecasting how a target responds to events that set covariates to chosen future values. Whether they can do this reliably is an open question. We introduce WhatIf-Bench, a benchmark measuring how well forecasters use covariates to forecast a target's response to future events. WhatIf-Bench is semi-synthetic: time series come from mechanistic simulators of data centers, power grids, road traffic, and water networks, with controlled covariate-target relationships grounded in each system. Each task presents a history of events intervening on covariates, then asks to forecast a future event that either replays seen values (Replay) or sets them to unseen ones (Novel). Varying the number of covariates, historical events, and event length yields 37,665 tasks. Evaluating TSFMs, frontier LLMs, and simple regression baselines, we find the LLMs reach the highest skill (improvement over a naive baseline), ahead of the best TSFMs. Every model forecasts well on Replay futures (48 to 85% skill) but drops to -7 to 50% on Novel futures, with the regression baselines falling the most. Skill on Novel futures also falls as events set more covariates jointly. More historical events raise skill on Novel futures across the board, but large differences remain. WhatIf-Bench reveals generalization to Novel futures as the core challenge, and offers a testbed toward arbitrary scenario analysis.

Predicting the answer to interventional ``what if'' questions --- the outcome of an action never taken --- requires a mechanistic, causal model, not a curve fit; and learning such a model requires experiments, because passive data leaves its mechanisms unidentified. Experiments are expensive, so the central problem is data efficiency. We present the Model Discovery Agent (MDA), which couples a large language model (LLM), used as a proposer of candidate structures, with standard Bayesian machinery --- sequential Monte Carlo (SMC) for parameter and structure posteriors, simulation-based inference (SBI) for intractable likelihoods, and value-of-information (VoI) for experiment design --- to discover latent mechanistic world models from few interventions. MDA operates in the M-open setting: when the truth lies outside the current hypothesis class, a predictive check flags the inadequacy and the proposer expands the hypothesis space with a new model whose parameters are then identified by designed experiments. We show that discovery and design reinforce: the design step identifies the mechanism the discovery step proposes, and the identified mechanism improves predictions, enabling further discoveries from the remaining unexplained residuals. On three different benchmarks --- covering physics (\DPbench, wiemann2026discoverphysics), chemistry (\CHEMbench, kabra2026autoscilab) and biology (\HHbench, a new partially observed single-neuron electrophysiology benchmark we create) --- we show that MDA sets a new SOTA in terms of data-efficient model learning and reliable interventional prediction ability.

Early identification of sensitive cancer cell lines is essential for accelerating biomarker discovery and elucidating drug mechanism of action. Given the efficiency and low cost of small-scale drug screens relative to extensive omics profiling, we compared drug-response panel (DRP) descriptors against omics features for predictive capacity using gradient boosting tree models across the GDSC and CCLE drug response datasets. DRP descriptors consistently outperformed omics data across key performance metrics, with variable performance across different drugs. Using complementary explainability approaches, we confirmed known MAPK-inhibitor sensitivity signatures, and identified novel potential biomarker candidates for MEK1/2 and BTK/MNK inhibitors. Lastly, to demonstrate the utility of this approach in distinguishing phenotypes, we applied our models to the breast cancer line MCF7 versus the non-tumorigenic MCF10A, and successfully identified compounds that selectively inhibit MCF7 while sparing the non-tumorigenic MCF10A. This methodology, developed using focused drug and cell line panels, supports early-stage drug development by facilitating rational cell line selection and compound prioritisation, enabling more efficient biomarker identification and candidate assessment.

Instruction tuning-supervised fine-tuning using instruction-response pairs-is a foundational step in transitioning pre-trained Large Language Models (LLMs) into helpful and safe chat assistants. Our hypothesis is that establishing an adequate output space can enable such a transition given the capabilities inherent in pre-trained LLMs. To verify this, we propose Response Tuning (RT), which eliminates the instruction-conditioning step in instruction tuning and solely focuses on response space supervision. Our experiments demonstrate that RT models, trained only using responses, can effectively respond to a wide range of instructions and exhibit helpfulness comparable to that of their instruction-tuned counterparts. Furthermore, we observe that controlling the training response distribution can significantly improve their user preference or elicit target behaviors such as refusing assistance for unsafe queries. Our findings illuminate the role of establishing an adequate output space in alignment, highlighting the potential of the extensive inherent capabilities of pre-trained LLMs.

Causal inference, estimating causal effects from observational data, is a fundamental tool in many disciplines. Of particular importance across a variety of domains is the continuous treatment setting, where the variable of intervention has a continuous range. This setting is far less explored and represents a substantial shift from the binary treatment setting, with models needing to represent effects across a continuum of treatment values. In this paper, we present the first causal foundation model for the continuous treatment setting. Our model meta-learns the ability to predict causal effects across a wide variety of unseen tasks without additional training or fine-tuning. First, we design a novel prior over data-generating processes with continuous treatment variables in order to generate a rich causal training corpus. We then train a transformer to reconstruct individual treatment-response curves given only observational data, leveraging in-context learning to amortize expensive Bayesian posterior inference. Our model achieves state-of-the-art performance on individual treatment-response curve reconstruction tasks compared to causal models which are trained specifically for those tasks.

AI virtual cells aim to predict cellular responses to specified interventions, yet held-out predictive performance alone does not establish use of the supplied perturbation information. This prediction-claim gap matters in agentic model discovery, where language-model agents generate and revise predictors using score-based feedback. We introduce CELLAUDIT, which audits input-use claims by asking whether an input can enter the cited computation, whether fitted predictions depend on it, and whether that dependence improves prediction of observed response. On a paired morphology-transcriptomics perturbation benchmark (BBBC047), an agent-selected predictor attains a mean held-out Global Pearson correlation coefficient (PCC) of 0.3153 but remains invariant to compound replacement; a control-profile-only predictor reaches 0.3142. Source inspection identifies a compound-query pathway blocked by singleton key-value attention, and the invariance persists after refitting with disjoint control wells. In a stratified audit of 48 candidates across two linked tasks, 47 change predictions under compound replacement on both held-out folds, but only 20 show target-loss gains with intervals above zero on both folds. On BBBC047, falsification-guided revisions recover positive mean compound contributions while retaining gains over the control-profile-only baseline. In matched sci-Plex searches, audit-enriched feedback yields higher held-out performance and larger mean compound and dose contributions across five trajectories, although paired intervals span zero. Refitting fixed designs on an independently acquired cohort shows predictive generalization need not imply generalization of input-use claims: dose contribution persists, whereas support for compound identity does not. CELLAUDIT adds a falsification layer to agentic model discovery, moving from generate-score-revise toward discover-falsify-revise.

Models that can predict the occurrence of events ahead of time with low false-alarm rates are critical to the acceptance of decision support systems in the medical community. This challenging task is typically treated as a simple binary classification, ignoring temporal dependencies between samples, whereas we propose to exploit this structure. We first introduce a common theoretical framework unifying dynamic survival analysis and early event prediction. Following an analysis of objectives from both fields, we propose Temporal Label Smoothing (TLS), a simpler, yet best-performing method that preserves prediction monotonicity over time. By focusing the objective on areas with a stronger predictive signal, TLS improves performance over all baselines on two large-scale benchmark tasks. Gains are particularly notable along clinically relevant measures, such as event recall at low false-alarm rates. TLS reduces the number of missed events by up to a factor of two over previously used approaches in early event prediction.

When users can benefit from certain predictive outcomes, they may be prone to act to achieve those outcome, e.g., by strategically modifying their features. The goal in strategic classification is therefore to train predictive models that are robust to such behavior. However, the conventional framework assumes that changing features does not change actual outcomes, which depicts users as "gaming" the system. Here we remove this assumption, and study learning in a causal strategic setting where true outcomes do change. Focusing on accuracy as our primary objective, we show how strategic behavior and causal effects underlie two complementing forms of distribution shift. We characterize these shifts, and propose a learning algorithm that balances between these two forces and over time, and permits end-to-end training. Experiments on synthetic and semi-synthetic data demonstrate the utility of our approach.

Within the field of causal inference, we consider the problem of estimating heterogeneous treatment effects from data. We propose and validate a novel approach for learning feature representations to aid the estimation of the conditional average treatment effect or CATE. Our method focuses on an intermediate layer in a neural network trained to predict the outcome from the features. In contrast to previous approaches that encourage the distribution of representations to be treatment-invariant, we leverage a genetic algorithm that optimizes over representations useful for predicting the outcome to select those less useful for predicting the treatment. This allows us to retain information within the features useful for predicting outcome even if that information may be related to treatment assignment. We validate our method on synthetic examples and illustrate its use on a real life dataset.

Many language tasks have no single answer that can be checked automatically. Rubrics provide criteria for judging responses to these tasks. For reinforcement learning, the resulting verdicts must be combined into a scalar reward. A common approach sums the points assigned to satisfied criteria. Distinct verdict patterns can thus receive the same reward, and the fixed points encode how much each criterion should count, not how strongly its verdict distinguishes the current rollouts. Beyond this aggregation problem, judging the full rubric needs more judge requests as the criterion count grows. To address these limitations, Rubric Response Theory (RRT) measures quality and selects criteria when rubric criteria are monotone indicators of a shared target. Rather than adding assigned points, RRT uses a two parameter item response model that treats the verdict pattern as evidence about scalar quality specific to the rubric. Under this model, its likelihood score maximizes the local signal-to-noise ratio for quality. Its Response Parameter Network (RPN) reads the prompt and criterion text to predict criterion difficulty and discrimination. As the policy distribution changes during training, RRT uses online expectation maximization to update the RPN from current rollout verdicts. With Qwen3.5-4B as the policy, RRT's macro criterion score across Medical, Science, Rubrics as Rewards Science, and RubricBench is 1.7 points above that of group relative policy optimization (GRPO). On hard and very hard criteria in Medical and Science, RRT gains 2.8 to 5.6 points over GRPO. At half the criterion budget, adaptive Fisher selection with a frozen RPN keeps the macro criterion score across four datasets within 0.1 points of GRPO with full judging. These results show RRT can reduce judge requests while remaining competitive with GRPO.

Pre-trained large language models (LLMs) can be tailored to adhere to human instructions through instruction tuning. However, due to shifts in the distribution of test-time data, they may not always execute instructions accurately, potentially generating factual errors or misaligned content when acting as chat assistants. To enhance the reliability of LLMs in following instructions, we propose the study of selective instruction following, whereby the system declines to execute instructions if the anticipated response quality is low. We train judge models that can predict numerical quality scores for model responses. To address data scarcity, we introduce Self-J, a novel self-training framework for developing judge models without needing human-annotated quality scores. Our method leverages the model's inherent self-evaluation capability to extract information about response quality from labeled instruction-tuning data. It incorporates a gold reference answer to facilitate self-evaluation and recalibrates by assessing the semantic similarity between the response sample and the gold reference. During the training phase, we implement self-distillation as a regularization technique to enhance the capability of reference-free estimation. To validate alignment evaluation on general instruction-following tasks, we collect large-scale high-quality instructions from Hugging Face for model training and evaluation. Extensive experiments on five open-source models show that our method correlates much more with GPT-4 than strong baselines, e.g., supervised models distilled from GPT-4 and GPT-3.5-turbo. Our analysis shows our model's strong generalization across domains. Additionally, our judge models serve as good reward models, e.g., boosting WizardLM-13B-V1.2 from 89.17 to 92.48 and from 12.03 to 15.90 in version v1 and v2 of AlpacaEval respectively using best-of-32 sampling with our judge models.

Randomized controlled trials often do not represent the populations where decisions are made, and covariate shift across studies can invalidate standard IPD meta-analysis and transport estimators. We propose a placebo-anchored transport framework that treats source-trial outcomes as abundant proxy signals and target-trial placebo outcomes as scarce, high-fidelity gold labels to calibrate baseline risk. A low-complexity (sparse) correction anchors proxy outcome models to the target population, and the anchored models are embedded in a cross-fitted doubly robust learner, yielding a Neyman-orthogonal, target-site doubly robust estimator for patient-level heterogeneous treatment effects when target treated outcomes are available. We distinguish two regimes: in connected targets (with a treated arm), the method yields target-identified effect estimates; in disconnected targets (placebo-only), it reduces to a principled screen--then--transport procedure under explicit working-model transport assumptions. Experiments on synthetic data and a semi-synthetic IHDP benchmark evaluate pointwise CATE accuracy, ATE error, ranking quality for targeting, decision-theoretic policy regret, and calibration. Across connected settings, the proposed method is best or near-best and improves substantially over proxy-only, target-only, and transport baselines at small target sample sizes; in disconnected settings, it retains strong ranking performance for targeting while pointwise accuracy depends on the strength of the working transport condition.

Motivation: Interpretability is not optional in biology: understanding gene regulation requires models whose learned structure can be directly interrogated, not merely accurate predictors whose internals resist mapping onto regulatory relationships. We ask whether an architecture mirroring the central dogma yields attention and gradient maps that recover known regulatory elements and networks in inspectable form. Results: Central Dogma Transformer II (CDT-II) mirrors the central dogma in its architecture -- DNA self-attention, RNA self-attention, and DNA-to-RNA cross-attention -- requiring only genomic embeddings and raw per-cell expression. On K562 CRISPR interference (CRISPRi) data with five genes held out entirely, CDT-II predicts perturbation effects (per-gene mean r = 0.84), recovers the GFI1B regulatory network (6.6-fold enrichment, P = 3.5 x 10^-17), and concentrates cross-attention on ENCODE regulatory elements including CTCF sites (mean 7.67x across 28 target genes, P < 0.001). Gradient attribution predicts consequences of perturbing therapeutic targets (mean r = 0.82). For TFRC, target of the anti-TfR1 antibody PPMX-T003, it identifies erythrocyte-structure, iron-dependent DNA-synthesis and oxidative-stress genes, matching anemia and ferroptosis reported clinically and preclinically -- without clinical data as input. CDT-II acts as an AI microscope, surfacing clinically relevant regulatory structure from perturbation experiments alone. Availability: Source code is available at https://github.com/nobusama/CDT2. Pre-computed embeddings, training data, and model weights are available at https://huggingface.co/datasets/nobusama17/CDT2-data.

Cancer survival prediction supports treatment planning, risk stratification, and follow-up management. Existing methods use structured clinical variables, whole-slide images, genomic profiles, or multimodal inputs, while patient reports remain underexplored. We study report-centric survival prediction using reports that organize pathological, clinical, and molecular evidence. Large language models (LLMs) can reason over such reports, but case-wise time regression introduces two mismatches. First, a formulation mismatch arises because survival evaluation depends on ordering comparable patients, whereas independent time predictions do not enforce ranking consistency. Second, a supervision mismatch arises because a censored patient's observed time indicates survival beyond that point and cannot serve as an exact regression target, although it still implies orderings relative to patients who died earlier. To address these mismatches, we propose CACSurv, a Concordance-Aligned Comparative framework for report-centric survival prediction. CACSurv reformulates survival modeling as mini-cohort comparative reasoning, where an LLM predicts relative prognostic orderings. We introduce concordance-aligned rewards derived from comparable relations under right censoring, enabling censored outcomes to provide ranking supervision without exact event-time targets. At inference, Monte Carlo Reference Aggregation compares each patient with sampled references and aggregates positions into a cohort-level ranking. We establish TCGA-SurvReport, a benchmark covering six TCGA cancer cohorts. CACSurv achieves the highest C-index on all six cohorts and an average C-index of 0.722, outperforming the strongest published survival model by 6.5 percentage points and the strongest LLM time-regression baseline by 4.2 percentage points. Our code, models, and dataset will be available at https://github.com/xmed-lab/CACSurv.

Adversarial attacks on vision-language models optimize an image toward a text target, then cite the attacked model's similarity score as evidence of success. We ask whether that score - victim-space target alignment (VTS) - predicts recovery of the target by an independent model. We first build a measurement instrument: supervised judges outside the attacked geometry, real-target blend controls, shuffled-target negatives, and a reference level derived from a 50% target-image blend. Two preregistered studies then compare six contrastive encoders under a matched attack at three perturbation budgets. Robustly trained encoders (FARE, TeCoA, PMG, TRADES) transfer substantially more independent evidence than vanilla CLIP or SigLIP; all eight contrasts reject at the bootstrap floor. However, no cell reaches the blend-derived reference level. The three best cells fall within its replication band, leaving practical recovery undecided. Within robust encoders, per-sample alignment gain correlates with evidence gain (ρ= 0.24-0.51); within vanilla CLIP the correlation is consistent with zero. Across encoders we find no monotone alignment-evidence relation. VTS is therefore informative only within a fixed robust encoder, and we provide a reporting protocol in its place.

Recent benchmarks reveal that models for single-cell perturbation response are often outperformed by simply predicting the dataset mean. We trace this anomaly to a metric artifact: control-referenced deltas and unweighted error metrics reward mode collapse whenever the control is biased or the biological signal is sparse. Large-scale in silico simulations and analysis of two real-world perturbation datasets confirm that shared reference shifts, not genuine biological change, drives high performance in these evaluations. We introduce differentially expressed gene (DEG)-aware metrics, weighted mean-squared error (WMSE) and weighted delta R^{2} (R^{2}_{w}(Δ)) with respect to all perturbations, that measure error in niche signals with high sensitivity. We further introduce negative and positive performance baselines to calibrate these metrics. With these improvements, the mean baseline sinks to null performance while genuine predictors are correctly rewarded. Finally, we show that using WMSE as a loss function reduces mode collapse and improves model performance.

This paper studies the prediction of a target z from a pair of random variables (x,y), where the ground-truth predictor is additive E[z mid x,y] = f_star(x) +g_{star}(y). We study the performance of empirical risk minimization (ERM) over functions f+g, f in F and g in G, fit on a given training distribution, but evaluated on a test distribution which exhibits covariate shift. We show that, when the class F is "simpler" than G (measured, e.g., in terms of its metric entropy), our predictor is more resilient to heterogenous covariate shifts in which the shift in x is much greater than that in y. These results rely on a novel H\"older style inequality for the Dudley integral which may be of independent interest. Moreover, we corroborate our theoretical findings with experiments demonstrating improved resilience to shifts in "simpler" features across numerous domains.

LLMs are not generally able to adjust the length of their outputs based on strict length requirements, a capability that would improve their usefulness in applications that require adherence to diverse user and system requirements. We present an approach to train LLMs to acquire this capability by augmenting existing data and applying existing fine-tuning techniques, which we compare based on the trained models' adherence to the length requirement and overall response quality relative to the baseline model. Our results demonstrate that these techniques can be successfully applied to train LLMs to adhere to length requirements, with the trained models generating texts which better align to the length requirements. Our results indicate that our method may change the response quality when using training data that was not generated by the baseline model. This allows simultaneous alignment to another training objective in certain scenarios, but is undesirable otherwise. Training on a dataset containing the model's own responses eliminates this issue.

Many physical inverse problems are mediated by expensive stochastic simulators for which response gradients, adjoint sensitivities, or a differentiable simulator interface are unavailable. We introduce Multiple Target-based Confident Acquisition (MUTACO), an uncertainty-aware sequential-design method for response matching that requires only noisy forward evaluations and learns the multicomponent response together with its predictive uncertainty. We develop and evaluate MUTACO for a disordered network of stochastic phase oscillators. The inverse task is to infer statistical properties of the local potential and interactions from macroscopic rotation and synchronization curves under multiple driving conditions. Rather than requiring unique recovery of these statistical properties, MUTACO searches for parameter configurations whose predicted rotation and synchronization responses are compatible with the target response while accounting for predictive uncertainty. This response-centered formulation is appropriate when experimentally accessible observables characterize ensemble statistics rather than a particular microscopic realization. Under strictly limited simulation budgets, MUTACO achieves the lowest held-out response error among the tested adaptive-search, space-filling, and simulation-based inference methods, while also yielding lower parameter-recovery error than the compared methods. These results demonstrate that response-targeted sequential design is a simulator-efficient approach to inverse modeling from finite noisy forward evaluations and suggest broader applicability to stochastic physical systems with correlated multicomponent responses and weakly constrained parameter directions.

Evaluating software agents on a full benchmark is expensive. A small task subset can preserve agent rankings while yielding inaccurate scores. Historical responses provide useful structure, but tasks with identical source responses can have different outcomes for a new target agent. We introduce Hierarchical Score Posterior Recovery (HSPR), which combines source-fitted response factors with uncertain group success rates. Observed target outcomes update the posteriors over the target latent state and group rates; posterior-guided acquisition selects subsequent tasks. Its score-based criterion equals the expected one-step reduction in full-score posterior variance. Observed successes and posterior-predictive counts for unqueried tasks yield a full-score posterior. The final estimate uses its median with source-selected calibration. At a 10% task budget on four task banks from the SWE-bench family, HSPR achieves the lowest mean absolute error (MAE) on three banks and the lowest maximum absolute error (MaxErr) on all four among the methods compared. Removing group uncertainty or replacing adaptive queries increases macro MAE in the respective controls. Macro MAE decreases across 5-20% budgets.

We investigate the predictability of large language model (LLM) capabilities: given records of past experiments using different model families, numbers of parameters, tasks, and numbers of in-context examples, can we accurately predict LLM performance on new experiment configurations? Answering this question has practical implications for LLM users (e.g., deciding which models to try), developers (e.g., prioritizing evaluation on representative tasks), and the research community (e.g., identifying hard-to-predict capabilities that warrant further investigation). We study the performance prediction problem on experiment records from BIG-bench. On a random train-test split, an MLP-based predictor achieves an R^2 score greater than 95%, indicating the presence of learnable patterns within the experiment records. We then formulate the problem of searching for "small-bench," an informative subset of BIG-bench tasks from which the performance on the full set can be maximally recovered. We find a subset as informative as BIG-bench Hard for evaluating new model families, while being 3times smaller. Additionally, we find competitive subsets by clustering task representations learned by our MLP-based predictor and selecting tasks close to cluster centroids, highlighting the importance of task diversity in constructing "small-bench."

The paper shows that the application of the fixed-effect multiple linear regression model to an overparameterized dataset is equivalent to fitting the data with a hyper-curve parameterized by a single scalar parameter. This equivalence allows for a predictor-focused approach, where each predictor is described by a function of the chosen parameter. It is proven that a linear model will produce exact predictions even in the presence of nonlinear dependencies that violate the model assumptions. Parameterization in terms of the dependent variable and the monomial basis in the predictor function space are applied here to both synthetic and experimental data. The hyper-curve approach is especially suited for the regularization of problems with noise in predictor variables and can be used to remove noisy and "improper" predictors from the model.

Machine learning (ML) holds great potential for accurately forecasting treatment outcomes over time, which could ultimately enable the adoption of more individualized treatment strategies in many practical applications. However, a significant challenge that has been largely overlooked by the ML literature on this topic is the presence of informative sampling in observational data. When instances are observed irregularly over time, sampling times are typically not random, but rather informative -- depending on the instance's characteristics, past outcomes, and administered treatments. In this work, we formalize informative sampling as a covariate shift problem and show that it can prohibit accurate estimation of treatment outcomes if not properly accounted for. To overcome this challenge, we present a general framework for learning treatment outcomes in the presence of informative sampling using inverse intensity-weighting, and propose a novel method, TESAR-CDE, that instantiates this framework using Neural CDEs. Using a simulation environment based on a clinical use case, we demonstrate the effectiveness of our approach in learning under informative sampling.

We address the problem of learning the dynamics of an unknown non-parametric system linking a target and a feature time series. The feature time series is measured on a sparse and irregular grid, while we have access to only a few points of the target time series. Once learned, we can use these dynamics to predict values of the target from the previous values of the feature time series. We frame this task as learning the solution map of a controlled differential equation (CDE). By leveraging the rich theory of signatures, we are able to cast this non-linear problem as a high-dimensional linear regression. We provide an oracle bound on the prediction error which exhibits explicit dependencies on the individual-specific sampling schemes. Our theoretical results are illustrated by simulations which show that our method outperforms existing algorithms for recovering the full time series while being computationally cheap. We conclude by demonstrating its potential on real-world epidemiological data.

Candidate-scoring decision models return a probability distribution over a presented set of answers. Public documentation of one such system, Jev, and of an open counterpart, JevAny, describes three training ingredients that determine what these probabilities estimate: soft targets from larger models, a frozen pretrained backbone and temperature calibration. We analyze each ingredient in Gaussian surrogates where the finite-sample risk can be computed exactly. A student trained on teacher targets inherits the teacher's bias, which more student data does not remove and agreement with the teacher does not reveal. A fixed representation lowers the risk only below an explicit sample-size threshold. In a probit model the exact recalibration map is a temperature scaling, which removes all excess risk only when the teacher's coefficient has the correct direction and otherwise leaves a residual that calibration diagnostics do not detect. Under Luce's choice axiom, candidate scores are coherent across refinements of an event if and only if they aggregate by log-sum-exp. On 231,521 credit card complaints from the Consumer Financial Protection Bureau, where the decision is whether a complaint ends in monetary relief, a student trained on a logistic teacher's probabilities ends at the teacher's decision cost while a student trained on outcomes goes 8% below it, a 30B model read zero-shot remains worse than the teacher after recalibration, and that model departs from the coherence condition by 17.5 decibans. Pretrained representations reduce the labeled data required and calibration corrects the scale of the probabilities, but neither corrects a biased teacher, so the probabilities have to be checked against realized outcomes.

We present t_0, a family of open-weights foundation models for forecasting with multivariate context. We release its first two members: t0-alpha and t0-beta, respectively 102M and 256M parameters. Both condition their forecasts on target history, past covariates, and known-future covariates, without task-specific retraining. Their transformer layers alternate attention along time and across variates. They produce probabilistic forecasts through quantile predictions. Pretraining combines curated public data with synthetic generator families constructed to contain covariate-to-target dependencies. On GIFT-Eval, t0-alpha reaches an aggregate CRPS of 0.4941, and t0-beta a CRPS of 0.4738 and a MASE of 0.6865, third on both and within 4.0% of the best zero-shot TSFM. On fev-bench they score 42.2 and 46.7 in skill, the latter third again and 2.0 points behind the leader. We analyze t0-alpha in depth. Known-future covariates raise its skill by 6.3 percentage points across 30 tasks. The report also examines its calibration, its rollout strategy on long horizons, and its robustness to missing data. On the Victoria electricity-demand benchmark, t0-beta is among the most accurate models with a context of nearly a year. In an independent Macrocosm evaluation of hourly ERCOT prices over 29 months, both cut the MAE of the lagged-price baseline by 38%.

Rubric-based reinforcement learning enriches language model training by evaluating model outputs against explicit criteria. Yet in GRPO-style pipelines, these structured judgments are reduced to a scalar response-level reward and converted into a response-level advantage, which is broadcast uniformly to all generated tokens. This leaves no explicit mechanism for allocating credit within a response, even when different criteria are grounded in different spans, formatting decisions, or semantic choices. We propose CoRT, a token-level credit weighting method for rubric-conditioned GRPO. Instead of training an auxiliary token scoring model, CoRT uses counterfactual replay to rescore the same sampled response under the original rubric-conditioned prompt and a matched criteria-free prompt. The resulting tokenwise log-likelihood contrasts serve as a proxy for dependence on the rubric context. CoRT maps these contrasts to bounded, response-normalized weights and uses them to redistribute the signed GRPO advantage across tokens, without introducing an auxiliary scorer or changing the response-level reward. Experiments across instruction-tuned models and reward granularities show that CoRT improves over matched response-level GRPO in the vast majority of comparisons, with an average gain of 4.4 percentage points. The method remains competitive with learned token-level credit baselines while avoiding a separate relevance-learning stage. These results suggest that policy-internal counterfactual likelihood contrasts provide an effective training signal for within-response credit allocation while retaining the simplicity and stability of GRPO.

Drug discovery is a complex and resource-intensive process, making early prediction of approval outcomes critical for optimizing research investments. While classical machine learning and deep learning methods have shown promise in drug approval prediction, their limited interpretability constraints their impact. Here, we present DrugReasoner, a reasoning-based large language model (LLM) built on the LLaMA architecture and fine-tuned with group relative policy optimization (GRPO) to predict the likelihood of small-molecule approval. DrugReasoner integrates molecular descriptors with comparative reasoning against structurally similar approved and unapproved compounds, generating predictions alongside step-by-step rationales and confidence scores. DrugReasoner achieved robust performance with an AUC of 0.732 and an F1 score of 0.729 on the validation set and 0.725 and 0.718 on the test set, respectively. These results outperformed conventional baselines, including logistic regression, support vector machine, and k-nearest neighbors and had competitive performance relative to XGBoost. On an external independent dataset, DrugReasoner outperformed both baseline and the recently developed ChemAP model, achieving an AUC of 0.728 and an F1-score of 0.774, while maintaining high precision and balanced sensitivity, demonstrating robustness in real-world scenarios. These findings demonstrate that DrugReasoner not only delivers competitive predictive accuracy but also enhances transparency through its reasoning outputs, thereby addressing a key bottleneck in AI-assisted drug discovery. This study highlights the potential of reasoning-augmented LLMs as interpretable and effective tools for pharmaceutical decision-making.

Regression, the task of predicting a continuous scalar target y based on some features x is one of the most fundamental tasks in machine learning and statistics. It has been observed and theoretically analyzed that the classical approach, meansquared error minimization, can lead to suboptimal results when training neural networks. In this work, we propose a new method to improve the training of these models on regression tasks, with continuous scalar targets. Our method is based on casting this task in a different fashion, using a target encoder, and a prediction decoder, inspired by approaches in classification and clustering. We showcase the performance of our method on a wide range of real-world datasets.

Conditional generative models are increasingly used for scientific prediction beyond the direct training support. Yet scientific questions often concern whether one intervention changes the effect of another. Such interactions can be of primary interest while explaining little of the total variation, allowing models to appear accurate overall without recovering the relevant scientific effect. It remains unclear how these models learn interactions and when these successfully extrapolate to unseen conditions. We therefore study interaction recovery in flow-matching models using a physiological time-series simulator, drug dose-response data, combinatorial cell perturbations, and molecular conformer generations, where we separate recovery from hallucinated interaction structure. In the controlled setting, individual effects are learned much earlier than interactions and models hallucinate interactions where none exist. Across settings, we find qualitatively different generalization problems, with successful prediction depending on whether condition structure continues from observed to held-out targets. When it does, interactions are recoverable. If not, models can generate plausible responses while missing the interaction. We furthermore find that hallucinations increase as targets become less identifiable, and that successful interaction recovery in output space can fail under nonlinear readouts. Finally, we show that aggregate fidelity metrics can conceal whether models learn and extrapolate interactions.

There has been considerable recent interest in scoring properties on the basis of eviction risk. The success of methods for eviction prediction is typically evaluated using different measures of predictive accuracy. However, the underlying goal of such prediction is to direct appropriate assistance to households that may be at greater risk so they remain stably housed. Thus, we must ask the question of how useful such predictions are in targeting outreach efforts - informing action. In this paper, we investigate this question using a novel dataset that matches information on properties, evictions, and owners. We perform an eviction prediction task to produce risk scores and then use these risk scores to plan targeted outreach policies. We show that the risk scores are, in fact, useful, enabling a theoretical team of caseworkers to reach more eviction-prone properties in the same amount of time, compared to outreach policies that are either neighborhood-based or focus on buildings with a recent history of evictions. We also discuss the importance of neighborhood and ownership features in both risk prediction and targeted outreach.

Large Language Models (LLMs) are widely used as proxies for human labelers in both training (Reinforcement Learning from AI Feedback) and large-scale response evaluation (LLM-as-a-judge). Alignment and evaluation are critical components in the development of reliable LLMs, and the choice of feedback protocol plays a central role in both but remains understudied. In this work, we show that the choice of feedback protocol for evaluation (absolute scores versus relative preferences) can significantly affect evaluation reliability and induce systematic biases. In the context of LLM-as-a-judge evaluation, we show that pairwise protocols are more vulnerable to distracted evaluation. Generator models can exploit spurious attributes (or distractor features) favored by the LLM judge, resulting in inflated scores for lower-quality outputs. We find that absolute scoring is more robust to such manipulation, producing judgments that better reflect response quality and are less influenced by distractor features. Our results demonstrate that generator models can flip preferences by embedding distractor features, skewing LLM-as-a-judge comparisons and leading to inaccurate conclusions about model quality in benchmark evaluations. Pairwise preferences flip in about 35% of the cases, compared to only 9% for absolute scores. We offer recommendations for choosing feedback protocols based on dataset characteristics and evaluation objectives.

We propose a general method for measuring complex variables on a continuous, interval spectrum by combining supervised deep learning with the Constructing Measures approach to faceted Rasch item response theory (IRT). We decompose the target construct, hate speech in our case, into multiple constituent components that are labeled as ordinal survey items. Those survey responses are transformed via IRT into a debiased, continuous outcome measure. Our method estimates the survey interpretation bias of the human labelers and eliminates that influence on the generated continuous measure. We further estimate the response quality of each labeler using faceted IRT, allowing responses from low-quality labelers to be removed. Our faceted Rasch scaling procedure integrates naturally with a multitask deep learning architecture for automated prediction on new data. The ratings on the theorized components of the target outcome are used as supervised, ordinal variables for the neural networks' internal concept learning. We test the use of an activation function (ordinal softmax) and loss function (ordinal cross-entropy) designed to exploit the structure of ordinal outcome variables. Our multitask architecture leads to a new form of model interpretation because each continuous prediction can be directly explained by the constituent components in the penultimate layer. We demonstrate this new method on a dataset of 50,000 social media comments sourced from YouTube, Twitter, and Reddit and labeled by 11,000 U.S.-based Amazon Mechanical Turk workers to measure a continuous spectrum from hate speech to counterspeech. We evaluate Universal Sentence Encoders, BERT, and RoBERTa as language representation models for the comment text, and compare our predictive accuracy to Google Jigsaw's Perspective API models, showing significant improvement over this standard benchmark.

Longitudinal treatment decisions require predicting potential outcomes under future treatment sequences in the presence of time-varying confounding, heterogeneous patient dynamics, and limited domain-specific data. Existing longitudinal causal estimators typically train a new model for each cohort or simulator. We introduce Causal Longitudinal Prior-Fitted Networks (CausalLongPFN), a prior-fitted in-context predictor for longitudinal causal prediction. The model is pretrained entirely on synthetic episodes sampled from a broad prior over temporal structural causal models, exposing it to treatment-confounder feedback, latent heterogeneity, nonlinear state evolution, delayed effects, and cumulative treatment responses. At test time, CausalLongPFN is frozen: it conditions on support trajectories, a query history, and a proposed future treatment sequence, and returns a predictive distribution over future outcomes without gradient updates or propensity-model fitting. Multi-step predictions are obtained by recursively applying the one-step predictor under the specified treatment sequence. We evaluate on branchable cancer, HIV, and warfarin benchmarks with ground-truth counterfactual labels, and on factual-only rolling-origin prediction in MIMIC-III ICU trajectories. CausalLongPFN is competitive with domain-trained longitudinal baselines on counterfactual benchmarks and performs strongly on factual MIMIC-III prediction, suggesting that broad synthetic causal pretraining can provide a useful frozen alternative when repeated domain-specific training is costly or impractical.

Statistical prediction methods typically require some form of fine-tuning of tuning parameter(s), with K-fold cross-validation as the canonical procedure. For ridge regression there exist numerous procedures, but common for all, including cross-validation, is that one single parameter is chosen for all future predictions. We propose instead to calculate a unique tuning parameter for each individual for which we wish to predict an outcome. This generates an individualized prediction by focusing on the vector of covariates of a specific individual. The focused ridge -- fridge -- procedure is introduced with a two-part contribution: 1) first we define an oracle tuning parameter minimizing the mean squared prediction error of a specific covariate vector, 2) then we propose to estimate this tuning parameter by using plug-in estimates of the regression coefficients and error variance parameter. The procedure is extended to logistic ridge regression by utilizing parametric bootstrap. For high-dimensional data, we propose to use ridge regression with cross-validation as the plug-in estimate, and simulations show that fridge gives smaller average prediction error than ridge with cross-validation for both simulated and real data. We illustrate the new concept for both linear and logistic regression models in two applications of personalized medicine: predicting individual risk and treatment response based on gene expression data. The method is implemented in the R package "fridge".

User targeting, the process of selecting targeted users from a pool of candidates for non-expert marketers, has garnered substantial attention with the advancements in digital marketing. However, existing user targeting methods encounter two significant challenges: (i) Poor cross-domain and cross-scenario transferability and generalization, and (ii) Insufficient forecastability in real-world applications. These limitations hinder their applicability across diverse industrial scenarios. In this work, we propose FOUND, an industrial-grade, transferable, and forecastable user targeting foundation model. To enhance cross-domain transferability, our framework integrates heterogeneous multi-scenario user data, aligning them with one-sentence targeting demand inputs through contrastive pre-training. For improved forecastability, the text description of each user is derived based on anticipated future behaviors, while user representations are constructed from historical information. Experimental results demonstrate that our approach significantly outperforms existing baselines in cross-domain, real-world user targeting scenarios, showcasing the superior capabilities of FOUND. Moreover, our method has been successfully deployed on the Alipay platform and is widely utilized across various scenarios.

The open-ended nature of language generation makes the evaluation of autoregressive large language models (LLMs) challenging. One common evaluation approach uses multiple-choice questions (MCQ) to limit the response space. The model is then evaluated by ranking the candidate answers by the log probability of the first token prediction. However, first-tokens may not consistently reflect the final response output, due to model's diverse response styles such as starting with "Sure" or refusing to answer. Consequently, MCQ evaluation is not indicative of model behaviour when interacting with users. But by how much? We evaluate how aligned first-token evaluation is with the text output along several dimensions, namely final option choice, refusal rate, choice distribution and robustness under prompt perturbation. Our results show that the two approaches are severely misaligned on all dimensions, reaching mismatch rates over 60%. Models heavily fine-tuned on conversational or safety data are especially impacted. Crucially, models remain misaligned even when we increasingly constrain prompts, i.e., force them to start with an option letter or example template. Our findings i) underscore the importance of inspecting the text output as well and ii) caution against relying solely on first-token evaluation.

Predicting transcriptome-wide responses to unseen genetic perturbations remains a major computational challenge because accurate prediction requires recovering both perturbation-specific transcriptional shifts and heterogeneous cellular responses. Existing methods often entangle deterministic response structure with stochastic population-level variation, causing dominant shared patterns to mask weaker perturbation-specific signals and impair distributional modeling. To address these challenges, we propose DeMixPert, an approach for Decomposed response Modeling with Gaussian Mixtures for Out-Of-Distribution (OOD) single-cell Perturbation prediction. DeMixPert decomposes perturbation-induced changes into a basal-state-dependent systematic response, a perturbation-specific response, and population-level variation. The systematic component is derived from the basal state encoded from control-cell expression, whereas the perturbation-specific component is inferred from pretrained target embeddings for unseen-target generalization. DeMixPert models population-level variation using a Gaussian prototype Invertible Network and adaptively combines reusable Gaussian prototypes according to the basal state and perturbation condition. The resulting mixture is mapped to a condition-specific variation distribution. Sampled variations are integrated with the systematic and perturbation-specific components, followed by joint decoding with the basal state to reconstruct perturbed-cell gene expression. Experimental results show that DeMixPert effectively captures heterogeneous single-cell perturbation responses and achieves superior performance across unseen-perturbation settings. The source code is made publicly available upon publication.

Mechanistic interpretability is often motivated for alignment auditing, where a model's verbal explanations can be absent, incomplete, or misleading. Yet many evaluations do not control whether black-box prompting alone can recover the target behavior, so apparent gains from white-box tools may reflect elicitation rather than internal signal; we call this the elicitation confounder. We introduce Pando, a model-organism benchmark that breaks this confound via an explanation axis: models are trained to produce either faithful explanations of the true rule, no explanation, or confident but unfaithful explanations of a disjoint distractor rule. Across 720 finetuned models implementing hidden decision-tree rules, agents predict held-out model decisions from 10 labeled query-response pairs, optionally augmented with one interpretability tool output. When explanations are faithful, black-box elicitation matches or exceeds all white-box methods; when explanations are absent or misleading, gradient-based attribution improves accuracy by 3-5 percentage points, and relevance patching, RelP, gives the largest gains, while logit lens, sparse autoencoders, and circuit tracing provide no reliable benefit. Variance decomposition suggests gradients track decision computation, which fields causally drive the output, whereas other readouts are dominated by task representation, biases toward field identity and value. We release all models, code, and evaluation infrastructure.

Patient world models are increasingly proposed as simulators of clinical trials, and recent surveys rank their capabilities on a ladder from temporal prediction to counterfactual rollouts. Position on that ladder is currently assigned by reading papers rather than by measurement. We turn the counterfactual rung into a measured quantity. From 30,119 completed phase 2/3 trials with results posted to ClinicalTrials.gov we construct 9,996 audited within-trial contrasts from 7,207 trials, and we score a simulator on how much of its accuracy depends on knowing which intervention was tested. The instrument is an intervention-blind reference: the same model, trained on the same trials, with every intervention-identifying field withheld. Interventional skill is the error the full model removes relative to that reference. On a temporal split (878 test contrasts from 655 trials) a registry-trained gradient-boosting simulator removes a fifth of the error of a trivial baseline, but its interventional skill is -0.12 (95% CI -0.21 to -0.05): withholding the intervention makes it better, and no alternative featurisation, stratum, temporal cut or same-molecule retrieval yields an interval above zero. A frontier language model reading only the registered protocol has interventional skill 0.20 [0.08, 0.31]; smaller and open-weight models sit at the limit of detection. Perturbation tests show the large model uses the intervention as such: swapping the arms reverses the sign of its prediction in 86% of contrasts. The blind reference is itself not drug-blind (a language model recovers the withheld drug class 45% of the time from the blind prompt), so interventional skill is a conservative lower bound. A reliability layer shows that ranking by predicted error lowers it but that calibrated error control does not transfer under temporal shift. Benchmark, code, prompts and per-call model outputs are released.

Large language models are increasingly evaluated by other models, raising a natural question: can a model predict how a judge will score its own output? We find that the ability is largely present before any targeted training: prompted few-shot, a base model already predicts an external judge's multi-attribute quality scores on open-ended responses well above chance across three benchmarks. We introduce Self-Evaluation Elicitation (SEE), a method that surfaces this latent ability through a short cycle comprising a calibration-coupled reinforcement learning phase that improves the answer and predicts the judge, followed by a masked distillation phase that sharpens the prediction while leaving the answer untouched. From 160 unique examples, roughly 31x fewer than a reinforcement learning baseline, SEE improves held-out calibration across three benchmarks while preserving answer quality. The elicited self-evaluation is sharply localized within the model's own token distribution and stable across judges it was never trained against, indicating a transferable notion of quality rather than a single judge's preference. These results reframe judge-aligned self-evaluation as a problem of elicitation rather than acquisition.

We study whether language models can evaluate the validity of their own claims and predict which questions they will be able to answer correctly. We first show that larger models are well-calibrated on diverse multiple choice and true/false questions when they are provided in the right format. Thus we can approach self-evaluation on open-ended sampling tasks by asking models to first propose answers, and then to evaluate the probability "P(True)" that their answers are correct. We find encouraging performance, calibration, and scaling for P(True) on a diverse array of tasks. Performance at self-evaluation further improves when we allow models to consider many of their own samples before predicting the validity of one specific possibility. Next, we investigate whether models can be trained to predict "P(IK)", the probability that "I know" the answer to a question, without reference to any particular proposed answer. Models perform well at predicting P(IK) and partially generalize across tasks, though they struggle with calibration of P(IK) on new tasks. The predicted P(IK) probabilities also increase appropriately in the presence of relevant source materials in the context, and in the presence of hints towards the solution of mathematical word problems. We hope these observations lay the groundwork for training more honest models, and for investigating how honesty generalizes to cases where models are trained on objectives other than the imitation of human writing.

Diffusion-based Large Language Models (D-LLMs) represent a promising frontier in generative AI, offering fully parallel token generation that can lead to significant throughput advantages and superior GPU utilization over the traditional autoregressive paradigm. However, this parallelism is constrained by the requirement of a fixed-size response length prior to generation. This architectural limitation imposes a severe trade-off: oversized response length results in computational waste on semantically meaningless padding tokens, while undersized response length causes output truncation requiring costly re-computations that introduce unpredictable latency spikes. To tackle this issue, we propose Predict-then-Diffuse, a simple and model-agnostic framework that enables compute-budgeted inference per input query by first estimating the response length and then using it to run inference with D-LLM. At its core lies an Adaptive Response Length Predictor (AdaRLP), which estimates the optimal response length given an input query. As a measure against under-estimating the response length and re-running inference with a higher value, we introduce a data-driven safety mechanism based on a small increase of the predicted length. As a whole, our framework avoids wasting computation on padding tokens, at the same time preserving output quality. Experimental validation on multiple datasets demonstrates that Predict-then-Diffuse significantly reduces computational costs (FLOP) compared to the default D-LLM inference mechanism, while being robust to skewed data distributions.

Prompt design is a primary control interface for large language models (LLMs), yet standard evaluations largely reduce performance to answer correctness, obscuring why a prompt succeeds or fails and providing little actionable guidance. We propose PEEM (Prompt Engineering Evaluation Metrics), a unified framework for joint and interpretable evaluation of both prompts and responses. PEEM defines a structured rubric with 9 axes: 3 prompt criteria (clarity/structure, linguistic quality, fairness) and 6 response criteria (accuracy, coherence, relevance, objectivity, clarity, conciseness), and uses an LLM-based evaluator to output (i) scalar scores on a 1-5 Likert scale and (ii) criterion-specific natural-language rationales grounded in the rubric. Across 7 benchmarks and 5 task models, PEEM's accuracy axis strongly aligns with conventional accuracy while preserving model rankings (aggregate Spearman rho about 0.97, Pearson r about 0.94, p < 0.001). A multi-evaluator study with four models shows consistent relative judgments (pairwise rho = 0.68-0.85), supporting evaluator-agnostic deployment. Beyond alignment, PEEM captures complementary linguistic failure modes and remains informative under prompt perturbations: prompt-quality trends track downstream accuracy under iterative rewrites, semantic adversarial manipulations induce clear score degradation, and meaning-preserving paraphrases yield high stability (robustness rate about 76.7-80.6%). Finally, using only PEEM scores and rationales as feedback, a zero-shot prompt rewriting loop improves downstream accuracy by up to 11.7 points, outperforming supervised and RL-based prompt-optimization baselines. Overall, PEEM provides a reproducible, criterion-driven protocol that links prompt formulation to response behavior and enables systematic diagnosis and optimization of LLM interactions.

Large language models fine-tuned for forecasting can be accurate yet poorly calibrated, and their chain-of-thought (CoT) reasoning may not faithfully reflect the evidence behind a forecast. We ask whether internal representations offer a more direct window into both. Working with Eternis-Forecaster 8B on OpenForesight, we train representation-pooling probes on intermediate activations and find they achieve substantially better calibration; a result that also holds for GLM-4.7-Flash and GLM-4.5-Air. We then assess CoT faithfulness through evidence ablation and diversionary injection: removing an influential source in the prompt often changes the model's forecast while leaving the reasoning trace untouched. The same probes function as lie detectors: their activations track behavioral shifts far better than the reasoning trace does, and they also predict the direction of change in 84% of cases, including when the CoT conceals the perturbation's influence. Finally, forced answering reveals that forecasts are largely fixed before reasoning begins: a single pre-reasoning pass recovers the committed answer and confidence, and routing questions by the spread of this pre-set answer distribution saves 30-47% of generated tokens, with no loss of accuracy. Together, these results establish probing internal representations as a practical tool for calibrating, auditing, and triaging language model forecasters and reasoning models more broadly.

Longitudinal clinical notes contain rich evidence of how patients evolve over time, but converting this signal into training supervision for clinical prediction remains challenging. We extend Foresight Learning to clinical prediction by converting time-ordered MIMIC-III notes into examples consisting of past patient context, a natural-language question about a possible future event, and a label resolved from later documentation. This process yields 6,900 prediction examples from 702 admissions across medications, procedures, organ support, microbiology, and mortality. A small LoRA adapter trained on these examples improves over the prompted base model, reducing expected calibration error from 0.1269 to 0.0398 and Brier score from 0.199 to 0.145, while slightly outperforming GPT-5 point estimates on held-out questions. The approach enables reusable clinical prediction supervision from longitudinal notes without hand-engineered structured features or endpoint-specific classifiers.

This article studies the change in the prediction accuracy of a response variable when the number of predictors increases, and all variables follow a multivariate normal distribution. Assuming that the correlations between variables are independently drawn, I show that adding variables leads to globally increasing returns to scale when the mean of the correlation distribution is zero. The speed of learning depends positively on the variance of the correlation distribution. I use simulations to study the more complex case of correlation distributions with a non-zero mean and find a pattern of decreasing returns followed by increasing returns to scale - as long as the variance of correlations is not degenerate, in which case globally decreasing returns emerge. I train a collaborative filtering algorithm using the MovieLens 1M dataset to analyze returns from adding variables in a more realistic setting and find globally increasing returns to scale across 2,000 variables. The results suggest significant scale advantages from additional variables in prediction tasks.

Language models are pretrained as passive predictors with no incentive to model the consequences of their own outputs. Post-training changes this: a model producing its own responses can benefit from recognizing that it is on-policy. We present evidence that post-trained models recognize their on-policy generations, and this recognition is implicitly encoded in their output distributions. In particular, on-policy output distribution entropy is 3--4times lower than off-policy entropy, across model families and size classes. We trace part of this effect to an internal representation of input surprise, tracking the unlikeliness of the most recent input token according to the model's prior predictions, that causally modulates output entropy. One example of these phenomena can be observed in response to open-ended prompts; post-trained models (unlike pretrained models) collapse their uncertainty over the topic of their upcoming response before the first output token; violating this cached intention with a different-topic prefill results in higher output entropy. We also tested whether models can distinguish on-policy contexts from prefills via explicit verbal report. We find that they can, but that interestingly, this explicit recognition routes through a different mechanism than implicit recognition.

Predicting single-cell responses to genetic and chemical perturbations is important for understanding regulatory mechanisms and prioritizing therapeutic interventions. Existing methods have made progress by modeling perturbation-conditioned expression shifts with neural networks, graph priors, foundation-model representations, or distributional generative models. However, combinatorial perturbation prediction remains challenging because much of the response can be explained by additive single-perturbation effects, while the biologically informative signal often lies in a smaller non-additive residual induced by perturbation interactions. Directly generating the full post-perturbation expression profile may therefore allocate substantial capacity to the dominant additive component and underemphasize synergy-specific structure. To address this issue, we propose SynGeneFlow, a synergy-aware flow matching framework that anchors the source distribution at an additive prior and learns a residual flow toward the true perturbed state. SynGeneFlow further incorporates perturbation-conditioned gene interaction modeling, where a static gene-gene mask provides biological structure and a perturbation-dependent deformation bias dynamically modulates gene-gene coupling. To preserve population-level response structure, we align both endpoint distributions and biological residual distributions with MMD-based regularization. We evaluate SynGeneFlow on genetic and drug perturbation benchmarks under observed-single, held-out, and cross-modality settings. The results demonstrate that residualizing flow matching around additive perturbation effects provides a biologically grounded and robust framework for single-cell perturbation response prediction.

The training data for fine-tuning large language models (LLMs) is typically structured as input-output pairs. However, for many tasks, there can be multiple equally valid output variations for the same input. Recent studies have observed that the choice of output variation used in training can affect the model's performance. This raises an important question: how can we generate the most effective output from the many possible response generation strategy options? Rather than relying on the traditional but resource-intensive train-and-evaluate approach, this paper proposes a scalable, approximate method for estimating the quality of a small subset of generated training data derived from the same input. We then evaluate how well this small subset of generated output fits the target model we are trying to train. We present a large-scale benchmark covering diverse reasoning-based datasets to support our study. The central idea is that a good output should closely resemble the output generated by the target LLM. We formalize this 'closeness' as the expected alignment score between a candidate output and the output sampled from the target LLM. We connect this measurement to the perplexity metric used in previous literature and demonstrate that leveraging an alignment-based metric can provide better predictions of model performance. Using this strategy, we can evaluate a small subset of the generated output from each response generation strategy option, then select the most effective strategy. We show that an LLM trained on data generated by the selected strategy could lead to a significant performance gain in many cases.

We propose a novel approach to conformal prediction for generative language models (LMs). Standard conformal prediction produces prediction sets -- in place of single predictions -- that have rigorous, statistical performance guarantees. LM responses are typically sampled from the model's predicted distribution over the large, combinatorial output space of natural language. Translating this process to conformal prediction, we calibrate a stopping rule for sampling different outputs from the LM that get added to a growing set of candidates until we are confident that the output set is sufficient. Since some samples may be low-quality, we also simultaneously calibrate and apply a rejection rule for removing candidates from the output set to reduce noise. Similar to conformal prediction, we prove that the sampled set returned by our procedure contains at least one acceptable answer with high probability, while still being empirically precise (i.e., small) on average. Furthermore, within this set of candidate responses, we show that we can also accurately identify subsets of individual components -- such as phrases or sentences -- that are each independently correct (e.g., that are not "hallucinations"), again with statistical guarantees. We demonstrate the promise of our approach on multiple tasks in open-domain question answering, text summarization, and radiology report generation using different LM variants.

Research agents explain planned experiments. We measure predictive credit with paired forecasts sharing an intervention, forecaster, and outcome while varying description, matched explanation, and donor context. Five checks track commitment, delivery, predictive gain, alignment, and known-signal uptake. Across 336 prospective states in controlled learning, 12 Tox21 endpoints, and 24 OpenML tasks, v5's frozen credit decision was inconclusive. Tox21's preregistered ROC AUC interval-score harm test was unmet (D-M=-.0026, 95 percent interval [-.0174, .0104]); OpenML's joint formation, point-equivalence, and repeatability rule was unmet. Matched point-accuracy gains over description remained unconfirmed, and Tox21/OpenML seed-donor intervals spanned zero. Under requested DeepSeek V4 Pro, matched and donor cards reduced secondary Tox21 drift by 64.5 and 59.1 percent. A DeepSeek V4 Flash replay raised matched point MAE from .01823 to .02020 and missed matched-donor interval-score equivalence. OpenML full-card assignment widened nominal 80 percent intervals by 21 percent, with 49.3 percent coverage versus 51.4 percent for description and content in 66/144 cards. Direct-text Flash delivered all 144 notes without detectable matched point-accuracy gain. A researcher-authored mechanism positive control lowered point MAE by 2.60 percentage points versus description. The protocol measures predictive credit for research-agent benchmarks and scientific forecasting; natural-explanation credit remained unconfirmed at the tested donor resolutions.

The approval success rate of drug candidates is very low with the majority of failure due to safety and efficacy. Increasingly available high dimensional information on targets, drug molecules and indications provides an opportunity for ML methods to integrate multiple data modalities and better predict clinically promising drug targets. Notably, drug targets with human genetics evidence are shown to have better odds to succeed. However, a recent tensor factorization-based approach found that additional information on targets and indications might not necessarily improve the predictive accuracy. Here we revisit this approach by integrating different types of human genetics evidence collated from publicly available sources to support each target-indication pair. We use Bayesian tensor factorization to show that models incorporating all available human genetics evidence (rare disease, gene burden, common disease) modestly improves the clinical outcome prediction over models using single line of genetics evidence. We provide additional insight into the relative predictive power of different types of human genetics evidence for predicting the success of clinical outcomes.

Model-internal features can be studied through both their ability to identify a specified concept and their causal effect when manipulated, e.g., through steering or weight editing. A prominent approach to feature learning is Sparse Autoencoders (SAEs), which learn broad feature dictionaries whose relation to particular concepts is typically identified post hoc. However, many interpretability questions are instead hypothesis-driven and concern a concept specified in advance. We study this setting as targeted feature learning, where a single feature is constructed for such a predefined concept. We present a controlled comparison across three model signals (activation values, activation gradients, and parameter gradients) and two estimators (contrastive mean and a learned one-dimensional encoder-decoder), yielding six targeted methods, with CAA and GRADIEND as existing instances and four new methods covering the remaining combinations. We compare these methods against pretrained SAEs across 15 tasks and three language models, evaluating both detection and causal intervention. Across models, the strongest detection performance is achieved by contrastive activation value methods, whereas the strongest intervention performance is achieved by gradient-based methods. Overall, our results show that targeted feature quality depends jointly on the model signal and estimator, with detection and intervention capturing complementary properties.

Accurately predicting immunotherapy response in Non-Small Cell Lung Cancer (NSCLC) remains a critical unmet need. Existing radiomics and deep learning-based predictive models rely primarily on pre-treatment imaging to predict categorical response outcomes, limiting their ability to capture the complex morphological and textural transformations induced by immunotherapy. This study introduces ImmunoDiff, an anatomy-aware diffusion model designed to synthesize post-treatment CT scans from baseline imaging while incorporating clinically relevant constraints. The proposed framework integrates anatomical priors, specifically lobar and vascular structures, to enhance fidelity in CT synthesis. Additionally, we introduce a novel cbi-Adapter, a conditioning module that ensures pairwise-consistent multimodal integration of imaging and clinical data embeddings, to refine the generative process. Additionally, a clinical variable conditioning mechanism is introduced, leveraging demographic data, blood-based biomarkers, and PD-L1 expression to refine the generative process. Evaluations on an in-house NSCLC cohort treated with immune checkpoint inhibitors demonstrate a 21.24% improvement in balanced accuracy for response prediction and a 0.03 increase in c-index for survival prediction. Code will be released soon.

In this paper, we describe our participation in the subtask 1 of CASE-2022, Event Causality Identification with Casual News Corpus. We address the Causal Relation Identification (CRI) task by exploiting a set of simple yet complementary techniques for fine-tuning language models (LMs) on a small number of annotated examples (i.e., a few-shot configuration). We follow a prompt-based prediction approach for fine-tuning LMs in which the CRI task is treated as a masked language modeling problem (MLM). This approach allows LMs natively pre-trained on MLM problems to directly generate textual responses to CRI-specific prompts. We compare the performance of this method against ensemble techniques trained on the entire dataset. Our best-performing submission was fine-tuned with only 256 instances per class, 15.7% of the all available data, and yet obtained the second-best precision (0.82), third-best accuracy (0.82), and an F1-score (0.85) very close to what was reported by the winner team (0.86).

Decision models return probabilities over supplied options, but a deployed agent may also need to reply in words. The present study introduces System X, a large language model (LLM) decision model that adds a text-reply option to the LLM-as-Jev readout. When this option wins, or confidence is low, the same model continues from the decision's key-value (KV) cache, avoiding a repeated prompt prefill. Qwen3-0.6B has been fine-tuned with LoRA on Reason-9k and Bitext reply rows. JevBench accuracy shows no statistically significant change (55.4% to 54.5%, p=0.87), while expected calibration error falls from 0.292 to 0.169. Held-out Bitext routing accuracy reaches 98.3%. Cache reuse saves 15-37% of latency on an Apple M4 Pro, with token-identical replies in the FP32 demonstration cases. Scoring options on copies of the prompt cache matches full-sequence scoring to within 1.4e-6 in probability. Adding dialogue, industry and complaint data (System X+) improves support-task results but lowers IFEval accuracy from 55.5% to 45.0%. System X v4 uses Qwen3-1.7B, rebalanced data and teacher-rewritten reply targets. Against its base LLM, JevBench accuracy rises from 55.0% to 61.0% (p=0.04), with no statistically significant IFEval change (p=0.71). A matched latency test on unadapted Qwen3-1.7B saves 17-39%. One LLM judge prefers v4 replies to an unadapted 1.7B second call (31 to 11 pairs, p=0.003); the other's preference is not significant. These reply comparisons also differ in prompts and generation limits. State conflicts and unsupported reply details remain failure modes. Further studies with several seeds, human raters and real support data are recommended.

Large Language Models (LLMs) have shown remarkable capabilities across tasks, yet they often require additional prompting techniques when facing complex problems. While approaches like self-correction and response selection have emerged as popular solutions, recent studies have shown these methods perform poorly when relying on the LLM itself to provide feedback or selection criteria. We argue this limitation stems from the fact that common LLM post-training procedures lack explicit supervision for discriminative judgment tasks. In this paper, we propose Generative Self-Aggregation (GSA), a novel prompting method that improves answer quality without requiring the model's discriminative capabilities. GSA first samples multiple diverse responses from the LLM, then aggregates them to obtain an improved solution. Unlike previous approaches, our method does not require the LLM to correct errors or compare response quality; instead, it leverages the model's generative abilities to synthesize a new response based on the context of multiple samples. While GSA shares similarities with the self-consistency (SC) approach for response aggregation, SC requires specific verifiable tokens to enable majority voting. In contrast, our approach is more general and can be applied to open-ended tasks. Empirical evaluation demonstrates that GSA effectively improves response quality across various tasks, including mathematical reasoning, knowledge-based problems, and open-ended generation tasks such as code synthesis and conversational responses.

Anticipating financial outcomes requires synthesizing evolving evidence and reasoning under uncertainty, making deep research systems promising tools for forecasting. Yet evaluating forecasting ability is challenging because historical backtests may reward memorized outcomes or information retrieved after the forecast date. Live forecasting avoids direct access to realized outcomes, but feedback arrives only after events resolve. To obtain timely feedback and assess historical scores, we introduce FinForesight, a diagnostic backtesting benchmark for financial deep research systems. Across the Chinese, U.S., and Hong Kong markets, the benchmark evaluates four forecasting tasks: valuation, return ranking, event direction, and future financial fundamentals. Two capability diagnostic tasks assess counterfactual reasoning and financial calculation, scored separately from forecasting performance. Our harness-compatible framework restricts retrieved evidence to information available at the forecast date. We compare pretraining-era, resolved post-cutoff, and live evaluations to test whether controlled backtests approximate future performance. Pretraining-era scores exceed post-cutoff scores in most temporal comparisons, and stronger retrieval controls narrow the gap between post-cutoff backtests and live results. Forecasting attribution and robustness analyses reveal how scores respond to retrieval policy and how predictions respond to prompt rewrites and numerical perturbations. The code and benchmark data are publicly available.

Being able to provide explanations for a model's decision has become a central requirement for the development, deployment, and adoption of machine learning models. However, we are yet to understand what explanation methods can and cannot do. How do upstream factors such as data, model prediction, hyperparameters, and random initialization influence downstream explanations? While previous work raised concerns that explanations (E) may have little relationship with the prediction (Y), there is a lack of conclusive study to quantify this relationship. Our work borrows tools from causal inference to systematically assay this relationship. More specifically, we study the relationship between E and Y by measuring the treatment effect when intervening on their causal ancestors, i.e., on hyperparameters and inputs used to generate saliency-based Es or Ys. Our results suggest that the relationships between E and Y is far from ideal. In fact, the gap between 'ideal' case only increase in higher-performing models -- models that are likely to be deployed. Our work is a promising first step towards providing a quantitative measure of the relationship between E and Y, which could also inform the future development of methods for E with a quantitative metric.

Large Language Models (LLMs) have shown remarkable capabilities across various tasks, but their deployment in high-stake domains requires consistent performance across multiple interaction rounds. This paper introduces a comprehensive framework for evaluating and improving LLM response consistency, making three key contributions. First, we propose a novel Position-Weighted Consistency (PWC) score that captures both the importance of early-stage stability and recovery patterns in multi-turn interactions. Second, we present a carefully curated benchmark dataset spanning diverse domains and difficulty levels, specifically designed to evaluate LLM consistency under various challenging follow-up scenarios. Third, we introduce Confidence-Aware Response Generation (CARG), a framework that significantly improves response stability by incorporating model confidence signals into the generation process. Empirical results demonstrate that CARG significantly improves response stability without sacrificing accuracy, underscoring its potential for reliable LLM deployment in critical applications.

Deployed large reasoning models (LRMs) often behave unexpectedly. Test-time steering controls LRM outputs by intervening on their hidden representations, but it can degrade output quality. We argue that prior steering work implicitly relies on internal features that detect behavior in already generated text. We show that these detection features are poor predictors of future behavioral outcomes, and thus not the natural intervention target. Instead, we train activation probes to predict future behavior likelihoods from intermediate reasoning steps. These probes predict the most likely behavior with 64%-91% accuracy, revealing a separate type of internal prediction features. Building on these prediction features, we introduce a text-level steering method, Future Probe Controlled Generation. FPCG samples multiple candidate sentences and chooses the best one according to a probe predicting the future behavior likelihood. This enables steering with almost no output quality degradation. FPCG also enables steering in several evaluations where activation steering fails. These results show that distinguishing detection and prediction features enables a more nuanced approach to controlling LRM behaviors.

A persistent challenge in machine learning for scientific applications is jointly achieving prediction and understanding. Statistical models excel on structured data but operate as black boxes, while existing interpretability methods are largely inspective: they answer "which features matter?" but do not articulate how features interact or refine explanations iteratively alongside human understanding. Asking an LLM to predict the target directly forces it to search the entire output space; we instead anchor predictions with a base model and ask the LLM the narrower question of what that model is missing. We introduce Multi-Agent Residual In-Context Learning (MARICL), an agentic framework in which LLM agents analyze where a base-model fails, hypothesize missing structure from high-residual examples provided in context, and produce explicit correction terms refined through multi-turn textual gradient optimization. Across nine benchmarks spanning scientific, biomedical, socioeconomic, and synthetic settings, MARICL improves consistently over its base model on all datasets. To test whether these corrections reflect real structure or batch-specific noise, we freeze formulas learned on one experimental batch of the Cell-Free Protein dataset and apply them (with no retraining and no further LLM calls) to held-out batches. Within the same reagent protocol, the frozen formulas improve predictions in over 92% of cases; across a different protocol, they fail systematically. The success boundary aligns with the biochemistry, not the batch count; direct evidence of mechanistic generalization.

Instruction tuning commonly means finetuning a language model on instruction-response pairs. We discover two forms of adaptation (tuning) that are deficient compared to instruction tuning, yet still yield instruction following; we call this implicit instruction tuning. We first find that instruction-response pairs are not necessary: training solely on responses, without any corresponding instructions, yields instruction following. This suggests pretrained models have an instruction-response mapping which is revealed by teaching the model the desired distribution of responses. However, we then find it's not necessary to teach the desired distribution of responses: instruction-response training on narrow-domain data like poetry still leads to broad instruction-following behavior like recipe generation. In particular, when instructions are very different from those in the narrow finetuning domain, models' responses do not adhere to the style of the finetuning domain. To begin to explain implicit instruction tuning, we hypothesize that very simple changes to a language model's distribution yield instruction following. We support this by hand-writing a rule-based language model which yields instruction following in a product-of-experts with a pretrained model. The rules are to slowly increase the probability of ending the sequence, penalize repetition, and uniformly change 15 words' probabilities. In summary, adaptations made without being designed to yield instruction following can do so implicitly.

We identify Harmfulness Propagation Dynamics (HPD): for harmful prompts, the projection of the last-token hidden state onto a learned harm direction rises monotonically with transformer depth, whereas benign prompts remain flat or oscillatory. This cross-layer signature reflects harmful intent as a progressively resolved semantic property: surface form appears early, while pragmatic intent consolidates later, making the trajectory shape more informative than any single-layer snapshot. Moreover, LDA-based harm directions, learned per layer, remain stable across random splits (pairwise cosine similarity >0.97), supporting the projection sequence as a reproducible structured signal. Building on HPD, we introduce \herald{} (Harmful Encoding Recognition via Activation Layer Dynamics). This lightweight input moderator extracts a seven-dimensional feature record, slope, curvature, monotonicity, onset layer, and related statistics from the cross-layer projection sequence and classifies it with a 288-parameter MLP. stores one d-dimensional direction per layer (262\,KB for a 32-layer, d{=}4096 model), requires no gradient computation during training, and adds only 2.6{times}10^{-6} prefill FLOPs at inference. Across eight prompt-harmfulness benchmarks and four model families, achieves an average F1 of 89.3 on OLMo2-7B, surpassing all tested guard models on adversarial jailbreak detection (98.4 vs.\ 96.9 F1) and outperforming prior latent-based methods by 2.3-4.1 F1 points on every backbone. Per-instance trajectories provide machine-readable audit records that reveal when and how harmfulness emerges, offering an interpretability advantage over single-layer approaches.

LeWorldModel trains a latent world model with a prediction loss and a single anti-collapse regulariser, and reports approximately 87% of goals reached on TwoRoom, its simplest diagnostic environment. We reproduce that result by independent reimplementation on roughly $25 of rented compute, with all evaluation on one laptop CPU. We reach 94.0% at the repository's evaluation goal offset, against 84.0% for the authors' own released checkpoint measured under our protocol on identical episodes, and we reproduce the reported representation result directly (position probe Pearson r = 0.9988 against a reported 0.996). Reaching that point required four conventions that determine the outcome and appear in no released configuration file: dense action gathering across a frameskip block, a programmatically-set action-encoder width, ImageNet pixel normalisation, and action z-scoring. A reproducer following the released configurations alone obtains a model whose predictor cannot converge. The evaluation protocol is itself contested by the released material. The paper's appendix and the repository's configuration specify different goal offsets and step budgets; on the authors' own weights these yield 14.0% and 84.0%, and only the configuration's values reproduce the reported figure. On fifty identical episodes, changing nothing but how the goal is constructed moves that checkpoint from 84.0% to 8.0%. Two findings generalise. One-step prediction accuracy does not predict long-horizon planning success: across three checkpoints spanning a sevenfold range in prediction error, including the authors' own, it orders short-horizon success monotonically and fails to order long-horizon success at all. And a batch normalisation layer inflated our reported validation loss by up to a factor of 300, concealing a training loss that was flat throughout.

Accurately predicting conversion rate (CVR) is essential in various recommendation domains such as online advertising systems and e-commerce. These systems utilize user interaction logs, which consist of exposures, clicks, and conversions. CVR prediction models are typically trained solely based on clicked samples, as conversions can only be determined following clicks. However, the sparsity of clicked instances necessitates the collection of a substantial amount of logs for effective model training. Recent works address this issue by devising frameworks that leverage non-clicked samples. While these frameworks aim to reduce biases caused by the discrepancy between clicked and non-clicked samples, they often rely on heuristics. Against this background, we propose a method to counterfactually generate conversion labels for non-clicked samples by using causality as a guiding principle, attempting to answer the question, "Would the user have converted if he or she had clicked the recommended item?" Our approach is named the Entire Space Counterfactual Inference Multi-task Model (ESCIM). We initially train a structural causal model (SCM) of user sequential behaviors and conduct a hypothetical intervention (i.e., click) on non-clicked items to infer counterfactual CVRs. We then introduce several approaches to transform predicted counterfactual CVRs into binary counterfactual conversion labels for the non-clicked samples. Finally, the generated samples are incorporated into the training process. Extensive experiments on public datasets illustrate the superiority of the proposed algorithm. Online A/B testing further empirically validates the effectiveness of our proposed algorithm in real-world scenarios. In addition, we demonstrate the improved performance of the proposed method on latent conversion data, showcasing its robustness and superior generalization capabilities.

Machine learning models trained on Earth observation data, such as satellite imagery, have demonstrated significant promise in predicting household-level wealth indices, enabling the creation of high-resolution wealth maps that can be leveraged across multiple causal trials. However, because standard training objectives prioritize overall predictive accuracy, these predictions inherently suffer from shrinkage toward the mean, leading to attenuated estimates of causal treatment effects and limiting their utility in policy. Existing debiasing methods, such as Prediction-Powered Inference, can handle this attenuation bias but require additional fresh ground-truth data at the downstream stage of causal inference, which restricts their applicability in data-scarce environments. Here, we introduce and evaluate two correction methods -- linear calibration correction and Tweedie's correction -- that substantially reduce prediction bias without relying on newly collected labeled data. Linear calibration corrects bias through a straightforward linear transformation derived from held-out calibration data, whereas Tweedie's correction leverages empirical Bayes principles to directly address shrinkage-induced biases by exploiting score functions derived from the model's learning patterns. Through analytical exercises and experiments using Demographic and Health Survey data, we demonstrate that the proposed methods meet or outperform existing approaches that either require (a) adjustments to training pipelines or (b) additional labeled data. These approaches may represent a promising avenue for improving the reliability of causal inference when direct outcome measures are limited or unavailable, enabling a "one map, many trials" paradigm where a single upstream data creation team produces predictions usable by many downstream teams across diverse ML pipelines.