Counterfactual Learning
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8 papers in the last four weeks, up 100% on the four weeks before. 0.1% of all new papers.
Latest papers 58
A common assumption holds that enough observational and interventional data, given to a strong enough predictor, suffices. We report a failure mode that contradicts it. Across hundreds of structural causal models, on identified quantities a strong predictor and a Bayesian baseline both succeed, but on unidentified quantities (the couplings between counterfactual worlds) the predictor collapses to a point, on 28% of models to one no valid model can produce, while the truth is an admissible interval more data never narrows. The gap is structural: prediction cannot represent uncertainty over counterfactual couplings. We cast a world model as a single positive semidefinite coupling kernel K(T,T') over admissible worlds, whose diagonal is the ordinary posterior (what a predictor recovers) and whose off-diagonal is the cross-world coupling it cannot, which every counterfactual reads. The paper is the theory of that off-diagonal. It is real: two states with identical posteriors differ on a cross-world query, and the off-diagonal is the coupling that fixes counterfactuals. It can be bounded: positive semidefiniteness is partial-identifying information the marginals lack, and enforcing it bounds counterfactuals in polynomial time where the exact response-type program is intractable. Logical structure sharpens it: ontology axioms tighten the bound by up to a third, propagating to couplings they never touch. It can be acquired: targeted scars, constraints learned from encountered infeasibilities, close the gap several times faster than untargeted ones. Its full reconstruction is approximate counting of the admissible worlds, tractable below the Sly-Sun threshold and inapproximable above; we do not claim to beat the worst case.
Querying Counterfactuals on Tissue Graphs with Supervised Disentanglement
Tissue graph counterfactuals ask how a cell's expression would change under altered spatial neighbor contexts. Such queries are central to predicting cell behavior in tissues, but lack a unified definition, with existing methods targeting specific intervention types or treating cells as i.i.d. In this work, we first formalize tissue graph counterfactuals as a class of spatial interventions that either rewire connections between cells (edge perturbation) or modify the expression of their neighbors (node perturbation). We then introduce Cellina (https://cellina.readthedocs.io) - a framework that uses supervised disentanglement to decompose a cell's intrinsic state from its spatial context, using the latter as a conditioning input for counterfactual predictions. Across benchmarks spanning over 2.5 million spatially-resolved cells in colorectal cancer and mouse brain, Cellina outperforms spatially-informed and non-spatial competitors in in-silico graph perturbations, disentanglement, and scalability. Additionally, we show that Cellina reveals biologically distinct cancer subdomains in an unsupervised manner and enables targeted neighbor perturbation simulations.
Are Good Generators Good Decision-Makers? Policy Learning for General Interventions via Retargeted Counterfactual Generation
Generative models are increasingly used to support decision-making in complex systems, where interventions may be joint and high-dimensional, and outcomes are high-dimensional. However, using generators for these decision-making settings are challenged by three problems. First, they are often trained on noisy logs with limited intervention data. Second, generator learning can be noisy across different environments. Third, generators are not optimized for the decisions they support. We introduce policy learning via retargeted counterfactual generation, which trains a generator for the decisions it supports in three steps. We (1) learn a doubly-robust, invariant counterfactual generator for high-dimensional interventions and outcomes, (2) conduct policy-learning based on its rollouts, and (3) retarget the generator toward the learned policy's interventions and relearn the policy, so the generator is accurate where decisions are made. Theoretically, our generator's excess counterfactual risk has a doubly robust product remainder, and retargeting removes the worst-case density ratio between the logged and learned policies from the regret. We demonstrate the efficacy of our approach across synthetic data, Cell Painting images of SARS-CoV-2-infected cells, and physical video simulations.
Causal Longitudinal Prior-Fitted Networks for Counterfactual Outcome Prediction
Longitudinal treatment decisions from multivariate time-series data 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 address this problem by training a new model for each cohort or simulator. We introduce Causal Longitudinal Prior-Fitted Networks (CausalLongPFN), a prior-fitted network for time-series causal inference in longitudinal treatment-response data and zero-shot in-context counterfactual outcome 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 remains frozen and is used zero-shot: it conditions on support trajectories, a query history, and a planned 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 the model 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 frozen, amortized alternative for zero-shot longitudinal treatment-response prediction when repeated domain-specific training is costly or impractical.
Benchmarking Counterfactual Prediction in Epidemic Time Series with Time-Varying Interventions
Deep learning has enabled significant advances in time-series causal inference, yet progress remains constrained by the lack of realistic benchmarks with observable counterfactual outcomes. Existing datasets either rely on real-world observations without ground-truth counterfactuals or on simplified simulations that fail to capture complex causal dynamics. To address this gap, we develop a large-scale benchmark for counterfactual prediction in epidemic time series under dynamic interventions. Unlike existing benchmarks, it supports static and time-varying treatments, as well as both single-policy and multi-policy intervention settings, enabling evaluation of causal inference methods across a broad range of causal inference scenarios. Leveraging a calibrated agent-based model grounded in real-world demographic, mobility, epidemiological, and policy data, we generate realistic counterfactual trajectories across more than 150 U.S. counties. Using this benchmark, we evaluate widely used and state-of-the-art causal inference methods, revealing substantial performance differences and highlighting the challenges of realistic time-series causal reasoning.
Policy-Conditioned Counterfactual Credit for Verifiable Reinforcement Learning of Long-Horizon Language Agents
Reinforcement learning with verifiable rewards improves reasoning and tool use, yet long-horizon language agents still learn unsupported evidence chains, belief drift, and shortcut actions that satisfy terminal checks. Existing process rewards are mostly correlational: they reward retrieval-, reflection-, or verification-like steps without estimating whether the step contributes to final verified success under a specified intervention. We propose CVT-RL, a constrained policy-gradient algorithm with dense verifiable rewards, intervention-validity gating, and a policy-conditioned counterfactual contribution (PCCC) estimator. Deletion, semantic substitution, evidence substitution, and tool-output perturbation define separate controlled interventions; continuations are sampled from a frozen reference policy, and a selection-adjusted doubly robust estimator augments the advantage. Belief control uses only prefix-observable labels, while an augmented Lagrangian constrains unsupported claims, skipped verification, tool tampering, and unsafe calls. On long-context QA, ALFWorld, ScienceWorld, and web/tool tasks, CVT-RL improves average task success from 71.8% for compute-matched non-causal RL and 75.4% for an information-matched counterfactual-process baseline to 78.9%, improves evidence F1 from 78.9 to 82.8 over the information-matched baseline, and reduces measured hacking from 7.2% to 3.9%. Independent human audit estimates 4.6% hacking for CVT-RL versus 8.1% for the information-matched baseline, and adaptive detector-evasion attacks raise hacking only to 7.1%. Stratified bootstrap and mixed-effects tests give p<0.01 after Holm correction for all primary metrics. Carefully scoped counterfactual credit, paired with validity gating, diagnostics, and verifiable constraints, provides a reproducible route toward more reliable long-horizon RL for language agents.
CFCamo: A Counterfactual Detect-or-Abstain Framework for Camouflaged Object Detection
Vision-language reinforcement learning has recently shown strong target-present localization for camouflaged object detection (COD). Yet localization is only one side of the decision: when the agent faces an ordinary image with no camouflaged target, will it still claim that a camouflaged object exists? Standard COD training and evaluation data are positive-only, so agents optimized under this setting can acquire an over-detect bias, a task-specific form of object hallucination that standard COD evaluation leaves unmeasured. To quantify this target-absent behavior, we construct Counterfactual COD (CF-COD), a paired benchmark that removes the camouflaged target from each held-out COD evaluation image while preserving a plausible background. CF-COD evaluates whether a model detects the target on the original image and abstains on the target-absent counterfactual, summarized by Pair Accuracy (PA). We further introduce CFCamo, a paired counterfactual framework for COD with abstention. For training, CFCamo optimizes a Qwen3-VL-4B-Instruct agent with Counterfactual Sequence Policy Optimization (CSPO), which samples paired original-counterfactual rollouts and uses a Counterfactual Paired Reward (CPR) to couple original-image detection with counterfactual abstention. On CAMO-test, CFCamo improves S_alpha by +3.7 pp over the prior RL-based COD baseline; across CF-COD, it reaches 80.0-90.8% PA. Ablations show that removing counterfactual coupling reduces PA to 1.4-5.2% despite strong target-present COD scores, showing that target-present evaluation alone does not characterize detect-or-abstain behavior. Overall, these results indicate that CFCamo improves COD agents by coupling target-present detection with target-absent abstention, rather than merely strengthening target-present localization. Code and data are available at https://github.com/suhang2000/CFCamo.
On the Hidden Costs of Counterfactual Knowledge Training in LLM Unlearning
Counterfactual tuning (CFT) has emerged as a promising paradigm for Large Language Model (LLM) unlearning by training models to generate alternative fictitious knowledge in place of undesired content. However, in this work, we find that this paradigm still underperforms other paradigms in some aspects, and identify two previously overlooked pitfalls underlying this gap: (1) knowledge conflict, where mutual inconsistencies within counterfactual corpora induce conflicting gradients that disrupt parameter optimization, and (2) hallucination spillover, where fitting false targets instills a persistent fabrication bias, inflating hallucination rates on unrelated domains. To systematically diagnose these issues, we introduce RWKU+, an extended benchmark equipped with novel trade-off metrics and gradient-level diagnostic tools. Our work further discusses the limitations and overhead of the paradigm, aiming to provide insights and actionable guidance for more rigorous LLM unlearning research.
Geometry Adaptive Counterfactual Distribution Learning with Diffusion-Guided Smoothing
We study counterfactual distribution learning for high-dimensional outcomes whose counterfactual law may concentrate near lower-dimensional structure. Standard isotropic smoothing treats all ambient directions equally, leading to unfavorable scaling and unstable local inference. We propose two diffusion-guided estimators based on semiparametric debiasing: diffusion-informed smoothing for counterfactual densities and diffusion-informed score smoothing for counterfactual scores. The estimators combine causal nuisance adjustment with geometry-adaptive localization driven by diffusion score information, removing first-order nuisance bias while aligning smoothing with local outcome geometry. We establish asymptotic expansions, risk bounds, and inference procedures for smoothed density and score-based targets, with ambient density inference obtained under additional approximation conditions. Under structural geometry conditions, the leading stochastic error is governed by an effective dimension induced by the diffusion-guided kernel, rather than by the ambient dimension. Semi-synthetic experiments based on CelebA show steeper error decay for geometry-adaptive methods, supporting the proposed effective-dimension theory.
Learning Spatiotemporal Sensitivity in Video LLMs via Counterfactual Reinforcement Learning
Video large language models (Video LLMs) can achieve strong video-QA accuracy without reliably tracking spatiotemporal dynamics. A model may answer a motion question from static cues, for example, and give the same prediction even after the underlying motion is reversed. Correctness-based reinforcement learning does not directly address this problem because it rewards the final answer without requiring the policy to respond to task-relevant video dynamics. We propose Counterfactual Relational Policy Optimization (CRPO), which explicitly trains Video LLMs to respond to controlled changes in the visual input. For each training example, CRPO constructs a counterfactual video, such as a horizontally flipped or temporally reversed version of the original, and jointly optimizes rollouts from both videos under a shared policy. Factual supervision anchors what the model should answer, while counterfactual supervision constrains when that answer should change: predictions should change when an intervention alters task-relevant dynamics and remain stable when the queried property is preserved. This coupling provides a direct behavioral learning signal without requiring ground-truth labels for transformed videos or annotated spatiotemporal reasoning traces, while discouraging indiscriminate answer changes. To evaluate this property, we introduce DyBench, a paired counterfactual benchmark with 3{,}014 videos and a strict pair-accuracy metric. Across paired spatiotemporal evaluations and standard video benchmarks, CRPO improves sensitivity to motion and temporal changes while improving performance on general video understanding. The gains also extend to segment reordering, a transformation never used during training, suggesting that CRPO learns sensitivity to video dynamics beyond the training interventions. The project website can be found at https://ddz16.github.io/crpo.github.io/ .
COAL: Counterfactual and Observation-Enhanced Alignment Learning for Discriminative Referring Multi-Object Tracking
Referring Multi-Object Tracking (RMOT) faces a fundamental structural contradiction between the high-discriminability demand and the sparse semantic supervision. This mismatch is particularly acute in highly homogeneous scenarios that require fine-grained discrimination over complex compositional semantics. However, under sparse supervision, models overfit to salient yet insufficient cues, thereby encouraging shortcut learning and semantic collapse. To resolve this, we propose COAL (Counterfactual and Observation-enhanced Alignment Learning), a framework that advances RMOT beyond isolated structural optimization through knowledge regularization. First, we introduce Explicit Semantic Injection (ESI) via a VLM to densify the observation space and enhance instance discriminability. Second, leveraging LLM reasoning, we propose Counterfactual Learning (CFL) to augment supervision, enforcing strict attribute verification for robust compositional recognition. These strategies are unified within a Hierarchical Multi-Stream Integration (HMSI) architecture, which distills external knowledge into domain-specific discriminative representations. Experiments on Refer-KITTI and Refer-KITTI-V2 benchmarks validate COAL's efficacy. Notably, it surpasses the state-of-the-art by 7.28% HOTA on the highly challenging Refer-KITTI-V2. These results demonstrate the effectiveness of knowledge regularization for resolving the sparsity-discriminability paradox in RMOT.
COLLATOR: Compositional Multi-Agent Orchestration with Counterfactual Reinforcement Learning
Large language models (LLMs) provide a flexible foundation for multi-agent systems, but their effectiveness and computational cost depend critically on orchestration design. Across different tasks, role design, capacity assignment, and dependency construction jointly affect both solution quality and execution efficiency. Existing approaches automate parts of this design process, yet they often optimize these decisions partially or sequentially, and rely on execution-level feedback that provides limited credit assignment for local orchestration decisions. We propose LEMON (Learning Executable Multi-Agent Orchestration via Counterfactual Reinforcement Learning), an LLM-based orchestrator that learns to design efficient multi-agent orchestration. Given a task, LEMON designs a unified orchestration specification that composes customized agent duties, capacity levels, and dependency relations. To train the orchestrator, we augment the orchestration-level Group Relative Policy Optimization (GRPO) objective with a localized counterfactual credit signal that edits role, capacity, or dependency fields and applies the resulting reward contrast only to the edited spans. Experiments on six reasoning and coding benchmarks, including MMLU, GSM8K, AQuA, MultiArith, SVAMP, and HumanEval, show that LEMON achieves the best average performance among evaluated multi-agent orchestration methods while improving the accuracy-token trade-off.
Learning More from Less: Exploiting Counterfactuals for Data-Efficient Chart Understanding
Vision-Language Models (VLMs) have demonstrated remarkable progress in chart understanding, largely driven by supervised fine-tuning (SFT) on increasingly large synthetic datasets. However, scaling SFT data alone is inefficient and overlooks a key property of charts: charts are programmatically generated visual artifacts, where small, code-controlled visual changes can induce drastic shifts in semantics and correct answers. Learning this counterfactual sensitivity requires VLMs to discriminate fine-grained visual differences, yet standard SFT treats training instances independently and provides limited supervision to enforce this behavior. To address this, we introduce ChartCF, a data-efficient training framework designed to enhance counterfactual sensitivity. ChartCF consists of: (1) a counterfactual data synthesis pipeline via code modification, (2) a chart similarity-based data selection strategy that filters overly difficult samples for improved training efficiency, and (3) multimodal preference optimization across both textual and visual modalities. Experiments on five benchmarks show that ChartCF achieves superior or comparable performance to strong chart-specific VLMs while using significantly less training data.
Debiased Counterfactual Generation via Flow Matching from Observations
Estimating counterfactual distributions under interventions is central to treatment risk assessment and counterfactual generation tasks. Existing approaches model the counterfactual distribution as a standalone generative target, without exploiting its relationship to the observational data. In this work, we show that under standard assumptions, observational and counterfactual outcome distributions are tightly linked: they have identical support and tail behavior, remain statistically close under weak confounding, and share any features of high-dimensional outcomes which are invariant to confounders. These properties motivate learning counterfactual distributions not from scratch, but via a deconfounding flow from the observational distribution. We formulate this problem via flow-matching and derive a semiparametrically efficient estimator based on a novel efficient influence function correction. We subsequently extend our estimator to target minimal-energy flows in high-dimensions, which we show can be especially simple targets between observational and counterfactual distributions. In experiments, deconfounding flows outperform existing debiased counterfactual distribution estimators, while also mitigating known failure modes of flow-based methods.
Three-in-One World Model: Energy-Based Consistency, Prediction, and Counterfactual Inference for Marketing Intervention
Marketing decisions reflect the interaction of latent consumer heterogeneity, time-varying internal states, and explicit interventions, a structure that current prediction- and language-oriented models do not capture in a unified manner. We propose a Three-in-One world-model architecture in which a Deep Boltzmann Machine (DBM) learns a frozen belief representation from demographics, time, and lagged actions and outcomes, with lightweight task-specific adapters attached on top. The same belief supports three tasks within a single framework: (i) energy-based consistency evaluation through the DBM's free energy, (ii) outcome prediction through adapters, and (iii) counterfactual inference by holding the belief fixed and varying only the action input given to the adapter. Using a controlled simulation in which the latent price sensitivity, promotion responsiveness, and base preference of each consumer are known, we show that the adapters match a strong MLP baseline on visit- and purchase-AUC while recovering heterogeneous treatment effects substantially better than S-, T-, X-, and DR-learner meta-learners and a Causal Forest baseline built on the same raw features, with the largest gap on a confounded price-promotion intervention. Complementing this, free-energy clamps systematically penalize counterfactual purchase trajectories that lack prior promotional exposure, and the penalty itself depends on the latent base preference in the expected direction. These results indicate that DBM beliefs disentangle latent traits in a form that survives counterfactual queries, providing an integrated world-model substrate for marketing intervention.
ScriptHOI: Learning Scripted State Transitions for Open-Vocabulary Human-Object Interaction Detection
Open-vocabulary human-object interaction (HOI) detection requires recognizing interaction phrases that may not appear as annotated categories during training. Recent vision-language HOI detectors improve semantic transfer by matching human-object features with text embeddings, but their predictions are often dominated by object affordance and phrase-level co-occurrence. As a result, a model may predict \textit{cut cake} from the presence of a knife and a cake without verifying whether the hand, tool, target, contact pattern, and object state jointly support the action. We propose \textbf{ScriptHOI}, a structured framework that represents each interaction phrase as a soft scripted state transition. Rather than treating a phrase as a single class token, ScriptHOI decomposes it into body-role, contact, geometry, affordance, motion, and object-state slots. A visual state tokenizer parses each detected human-object pair into corresponding state tokens, and a slot-wise matcher estimates both script coverage and script conflict. These two quantities calibrate HOI logits, expose missing visual evidence, and provide training constraints for incomplete annotations. To avoid suppressing valid but unannotated interactions, we further introduce interval partial-label learning, which constrains unannotated candidates with script-derived lower and upper probability bounds instead of assigning closed-world negatives. A counterfactual script contrast loss swaps individual script slots to discourage object-only shortcuts. Experiments on HICO-DET, V-COCO, and open-vocabulary HOI splits show that ScriptHOI improves rare and unseen interaction recognition while substantially reducing affordance-conflict false positives.
SpecPL: Disentangling Spectral Granularity for Prompt Learning
Existing prompt learning for VLMs exhibits a modality asymmetry, predominantly optimizing text tokens while still relying on frozen visual encoder as holistic extractor and neglecting the spectral granularity essential for fine-grained discrimination. To bridge this, we introduce Disentangling Spectral Granularity for Prompt Learning (SpecPL), which approaches prompt learning from a novel spectral perspective via Counterfactual Granule Supervision. Specifically, we leverage a frozen VAE to decompose visual signals into semantic low-frequency bands and granular high-frequency details. A frozen Visual Semantic Bank anchors text representations to universal low-frequency invariants, mitigating overfitting. Crucially, fine-grained discrimination is driven by counterfactual granule training: by permuting high-frequency signals, we compel the model to explicitly distinguish visual granularity from semantic invariance. Uniquely, SpecPL serves as a universal plug-and-play booster, revitalizing text-oriented baselines like CoOp and MaPLe via visual-side guidance. Experiments on 11 benchmarks demonstrate competitive state-of-the-art performance, achieving a new performance ceiling of 81.51% harmonic-mean accuracy. These results validate that spectral disentanglement with counterfactual supervision effectively bridges the gap in the stability-generalization trade-off. Code is released at https://github.com/Mlrac1e/SpecPL-Prompt-Learning.
CRAFT: Counterfactual-to-Interactive Reinforcement Fine-Tuning for Driving Policies
Open-loop imitation learning has advanced modern autonomous driving policy architectures, but closed-loop deployment remains vulnerable to policy-induced distribution shift. Existing post-training paradigms exhibit fundamental trade-offs: closed-loop RL fine-tuning provides grounded feedback from executed actions but is constrained by the sparsity of informative events, whereas counterfactual fine-tuning provides dense supervision over candidate futures but inherits bias from imperfect future estimates. We introduce Counterfactual-to-Interactive Reinforcement Fine-Tuning (CRAFT), an on-policy framework that formulates closed-loop post-training as proxy-residual optimization. CRAFT uses group-normalized counterfactual advantages as a dense proxy for real closed-loop advantages and aligns this proxy with the closed-loop world through grounded residual correction from interaction-critical events. To stabilize adaptation, CRAFT regularizes the online policy toward an EMA teacher via asymmetric KL self-distillation. Theoretically, CRAFT decomposes the real closed-loop policy gradient into proxy and residual terms under the same visited-state distribution, reducing residual variance with an aligned proxy while mitigating proxy bias through grounded residual approximation. Empirically, CRAFT achieves the strongest closed-loop gains on Bench2Drive across hierarchical planning, vision-language-action, and vocabulary-scoring architectures. Ablations, scaling behavior, stability analyses, and transfer results further validate the complementary roles of dense counterfactual proxy and grounded residual correction. Project page: https://currychen77.github.io/CRAFT.
Counterfactual identifiability beyond global monotonicity: non-monotone triangular structural causal models
Structural causal models provide a unified semantics for interventions and counterfactuals, but most identifiability results rely on restrictive assumptions like global monotonicity, which are often violated in embodied interaction, where the same exogenous perturbation can induce opposite responses under different contact contexts. We ask what structure still suffices once global monotonicity is dropped. We introduce non-monotone triangular structural causal models (NM-TM-SCM), which retain triangular recursion but replace global monotonicity with mechanism-wise invertibility and context-independent inverse transport. We prove that these conditions are equivalent to exogenous isomorphism and imply complete counterfactual identifiability, and we give a counterexample showing that local invertibility alone is insufficient. We instantiate the theory in CausalInverter, with triangular invertible layers, orientation gates, and transport-stability regularization. On synthetic non-monotonic mechanisms, the structural bias yields systematic counterfactual gains as non-monotonicity increases. On MuJoCo Door, our model achieves perfect event-level counterfactual recovery, lowers continuous angle error relative to a Transformer baseline, and delivers substantially more stable recovery than Transformer and conditional-flow predictors. On MuJoCo Push, where non-monotonicity is weaker, the same low-data predictors remain competitive or better, consistent with a bias-variance boundary. These results identify a broader identifiable regime between globally monotone triangular models and unconstrained black-box world models.
Machine learning models for estimating counterfactuals in a single-arm inflammatory bowel disease study
Single-arm trials accelerate study timelines by reducing the number of patients that must be recruited for a concurrent control group. However, these designs require an alternative comparator to estimate treatment effects. One approach is to construct a virtual control arm using a machine learning (ML) model trained on external control data to predict the counterfactual outcomes of the treatment arm. Our aim in this study was to leverage virtual controls by developing and evaluating ML-based counterfactual outcome models trained on IFX-treated patients to predict 1-year steroid-free clinical remission (SFCR ) and a composite of C-reactive protein remission plus steroid-free clinical remission (CRP-SFCR) for ADA-treated pediatric Crohn's disease patients, and to compare the resulting IFX-versus-ADA treatment effect estimates with those obtained using propensity score matching to external controls. Five ML models were used to train counterfactual models on the observed IFX cohort data. The resulting models were used to predict the counterfactual outcomes for the ADA arm patients. LGBM yields the best OR closest to the propensity score matched reference, and all 95% CI results align with the conclusion from the reference study that no statistical difference in the primary and secondary outcomes has been observed between the patients treated with ADA or IFX. Our study supports virtual controls as a viable and effective substitute for expensive, lengthy or unethical patient recruitment in an inflammatory bowel disease (IBD) trial. The developed gradient boosted prediction model can be used as a pretrained model to generate IFX counterfactual predictions in future studies, pending external validation and assessment of transportability.
DeepImagine: Learning Biomedical Reasoning via Successive Counterfactual Imagining
Predicting the outcomes of prospective clinical trials remains a major challenge for large language models. Prior work has shown that both traditional correlational predictors, such as random forests and logistic regression, and strong commercial LLMs achieve limited performance on this task. In this paper, we propose DeepImagine, a framework for teaching LLMs biomedical reasoning through successive counterfactual imagining. The central idea is to approximate hidden causal mechanisms of clinical trials by training models to infer how observed trial results would change under controlled perturbations of experimental conditions, such as dosage, outcome measures, study arms, geography, and other trial attributes. To support this objective, we construct both natural and approximate counterfactual pairs from real clinical trials with reported outcomes. For settings where strict counterfactual supervision is available, such as paired outcome measures or dose-ranging study arms within the same trial, we train models with supervised fine-tuning. For broader settings where only approximate counterfactual pairs can be retrieved, we optimize models with reinforcement learning using verifiable rewards based on downstream benchmark correctness. We further augment training with synthetic reasoning traces that provide causally plausible explanations for local counterfactual transitions. Using this pipeline, we train language models under 10B parameters, including Qwen3.5-9B, and evaluate them on clinical trial outcome prediction. We aim to show that DeepImagine consistently improves over untuned language models and traditional correlational baselines. Finally, we aim to show that the learned reasoning trajectories provide interpretable signals about how models represent trial-level mechanisms, suggesting a practical path toward more mechanistic and scientifically useful biomedical language models.
A Probabilistic Consensus-Driven Approach for Robust Counterfactual Explanations
Counterfactual explanations (CFEs) are essential for interpreting black-box models, yet they often become invalid when models are slightly changed. Existing methods for generating robust CFEs are often limited to specific types of models, require costly tuning, or inflexible robustness controls. We propose a novel approach that jointly models the data distribution and the space of plausible model decisions to ensure robustness to model changes. Using a probabilistic consensus over a model ensemble, we train a conditional normalizing flow that captures the data density under varying levels of classifier agreement. At inference time, a single interpretable parameter controls the robustness level; it specifies the minimum fraction of models that should agree on the target class without retraining the generative model. Our method effectively pushes CFEs toward regions that are both plausible and stable across model changes. Experimental results demonstrate that our approach achieves superior empirical robustness while also maintaining good performance across other evaluation measures.
AULLM++: Structured-Token-Conditioned Large Language Models for Micro-Expression Action Unit Detection
Micro-expression Action Unit (AU) detection identifies localized AUs from subtle facial muscle activations, providing a foundation for decoding affective cues. Previous methods face three key limitations: (1) heavy reliance on low-density visual information, rendering discriminative evidence vulnerable to background noise; (2) coarse-grained feature processing that misaligns with the demand for fine-grained representations; and (3) neglect of inter-AU correlations, restricting the parsing of complex expression patterns. We propose AULLM++, a reasoning-oriented framework leveraging Large Language Models (LLMs), which injects visual features into textual prompts as actionable semantic premises to guide inference. It formulates AU prediction into three stages: evidence construction, structure modeling, and deduction-based prediction. Specifically, a Multi-Granularity Evidence-Enhanced Fusion Projector (MGE-EFP) fuses mid-level texture cues with high-level semantics, distilling them into a compact Content Token (CT). Furthermore, inspired by micro- and macro-expression AU correspondence, we encode AU relationships as a sparse structural prior and learn interaction strengths via a Relation-Aware AU Graph Neural Network (R-AUGNN), producing an Instruction Token (IT). We then fuse CT and IT into a structured textual prompt and introduce Counterfactual Consistency Regularization (CCR) to construct counterfactual samples, enhancing the model's generalization. Extensive experiments demonstrate AULLM++ achieves state-of-the-art performance on standard benchmarks and exhibits superior cross-domain generalization.
Counterfactual Modeling with Fine-Tuned LLMs for Health Intervention Design and Sensor Data Augmentation
Counterfactual explanations (CFEs) provide human-centric interpretability by identifying the minimal, actionable changes required to alter a machine learning model's prediction. Therefore, CFs can be used as (i) interventions for abnormality prevention and (ii) augmented data for training robust models. We conduct a comprehensive evaluation of CF generation using large language models (LLMs), including GPT-4 (zero-shot and few-shot) and two open-source models-BioMistral-7B and LLaMA-3.1-8B, in both pretrained and fine-tuned configurations. Using the multimodal AI-READI clinical dataset, we assess CFs across three dimensions: intervention quality, feature diversity, and augmentation effectiveness. Fine-tuned LLMs, particularly LLaMA-3.1-8B, produce CFs with high plausibility (up to 99%), strong validity (up to 0.99), and realistic, behaviorally modifiable feature adjustments. When used for data augmentation under controlled label-scarcity settings, LLM-generated CFs substantially restore classifier performance, yielding an average 20% F1 recovery across three scarcity scenarios. Compared with optimization-based baselines such as DiCE, CFNOW, and NICE, LLMs offer a flexible, model-agnostic approach that generates more clinically actionable and semantically coherent counterfactuals. Overall, this work demonstrates the promise of LLM-driven counterfactuals for both interpretable intervention design and data-efficient model training in sensor-based digital health. Impact: SenseCF fine-tunes an LLM to generate valid, representative counterfactual explanations and supplement minority class in an imbalanced dataset for improving model training and boosting model robustness and predictive performance
Did Models Learn Sufficiently? Attribution-Guided Training via Subset-Selected Counterfactual Augmentation
Current visual models often make predictions based on a limited set of discriminative visual cues. As a result, they may become unreliable when the distribution shifts or when these cues are missing. Faithful attribution methods can reveal such problematic reliance through localized explanations, but they are typically used post hoc and are not fed back into the model. To address this limitation, we propose Subset-Selected Counterfactual Augmentation (SS-CA), a training strategy that masks decision-relevant regions to construct counterfactual samples and guide the model toward more robust decision boundaries. Specifically, we extend LIMA, a subset-selection-based faithful attribution method, to Counterfactual LIMA to identify regions whose removal shifts the model toward a competing class. SS-CA then selects near-boundary masks that reduce the logit gap while preserving the original semantics, and applies an adaptive counterfactual filling strategy to replace the masked regions without introducing external semantics. Feeding these counterfactual samples back into training encourages the model to exploit the remaining informative evidence and shifts the decision boundary toward a more robust one. Extensive experiments across five ImageNet variants show that SS-CA effectively improves ID accuracy, OOD generalization, and perturbation robustness, achieving gains of 5.70%/18.04% on ImageNet-1k/ImageNet-R with CLIP ViT/32b, 9.52%/11.33% on ImageNet-R/ImageNet-S on TinyImageNet-200 with ResNet-101, and about 4% under Gaussian Noise corruption. The code will be released soon.
Semiparametric Inference for Counterfactual Regression under Intervention-Driven Shift
We study counterfactual regression, which maps features to outcomes under hypothetical scenarios that differ from those observed in the data. This problem is central to decision-making under distribution shift, where treatment patterns may change at deployment. We develop a semiparametric framework for counterfactual regression along a prespecified incremental-intervention path. The target is a finite-dimensional constrained projection of counterfactual risk, estimated using cross-fitted influence-function representations of the program components. For smooth programs with fixed constraints and finite-dimensional programs with estimated linear constraints, we establish consistency and local stability of the optimizer under class-specific conditions, and derive pointwise and uniform first-order expansions. These results yield asymptotically valid inference, including simultaneous confidence bands for the counterfactual regression path. Simulations and an application to SMS reminders illustrate the finite-sample performance and practical applicability of the proposed approach.
SPARC: Scalable Path-Specific Counterfactual Fairness via Causal Conditional Independence
Deep learning models exhibit fairness concerns when predictions are inadvertently influenced by sensitive attributes. However, existing attempts to make Path-Specific Counterfactual Fairness optimizable rely on estimating marginal potential outcome probabilities-an approach that fundamentally requires high-dimensional conditional density estimation and breaks down in modalities such as medical images, where the curse of dimensionality renders reliable estimation infeasible. To address this limitation, we reduce the problem of enforcing Path-Specific Counterfactual Fairness to a causal conditional independence constraint and prove that satisfying this constraint is sufficient to eliminate the unfair causal effect. This reduction replaces intractable counterfactual estimation with a discriminative optimization objective that remains scalable in high-dimensional settings.
Hierarchical Deep Counterfactual Regret Minimization
Imperfect Information Games (IIGs) are used to model games under uncertainty or lack complete information. Counterfactual Regret Minimization (CFR) is one of the most successful families of algorithms for IIGs. The integration of skill-based strategy learning with CFR could potentially mirror more human-like decision-making and improve learning on complex IIGs. It enables the learning of a hierarchical strategy, wherein low-level components represent skills for solving subgames and the high-level component manages the transition between skills. In this paper, we introduce the first hierarchical version of Deep CFR (HDCFR), an innovative method that boosts learning efficiency in tasks involving extensively large state spaces and deep game trees. Notably, HDCFR enables learning with predefined (human) expertise and extracting skills transferable to similar tasks. We first present the algorithm and establish its theory in a tabular setting, including hierarchical CFR update rules and a variance-reduced Monte Carlo sampling extension for the model-free setting, where backtracking is infeasible. We then extend HDCFR to large-scale tasks via deep learning objectives that match the tabular targets under exact function fitting. Code: https://anonymous.4open.science/r/HDCFR_RUN-677B.