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May 21

Case-Grounded Evidence Verification: A Framework for Constructing Evidence-Sensitive Supervision

Evidence-grounded reasoning requires more than attaching retrieved text to a prediction: a model should make decisions that depend on whether the provided evidence supports the target claim. In practice, this often fails because supervision is weak, evidence is only loosely tied to the claim, and evaluation does not test evidence dependence directly. We introduce case-grounded evidence verification, a general framework in which a model receives a local case context, external evidence, and a structured claim, and must decide whether the evidence supports the claim for that case. Our key contribution is a supervision construction procedure that generates explicit support examples together with semantically controlled non-support examples, including counterfactual wrong-state and topic-related negatives, without manual evidence annotation. We instantiate the framework in radiology and train a standard verifier on the resulting support task. The learned verifier substantially outperforms both case-only and evidence-only baselines, remains strong under correct evidence, and collapses when evidence is removed or swapped, indicating genuine evidence dependence. This behavior transfers across unseen evidence articles and an external case distribution, though performance degrades under evidence-source shift and remains sensitive to backbone choice. Overall, the results suggest that a major bottleneck in evidence grounding is not only model capacity, but the lack of supervision that encodes the causal role of evidence.

  • 5 authors
·
Apr 9

Think Locally, Explain Globally: Graph-Guided LLM Investigations via Local Reasoning and Belief Propagation

LLM agents excel when environments are mostly static and the needed information fits in a model's context window, but they often fail in open-ended investigations where explanations must be constructed by iteratively mining evidence from massive, heterogeneous operational data. These investigations exhibit hidden dependency structure: entities interact, signals co-vary, and the importance of a fact may only become clear after other evidence is discovered. Because the context window is bounded, agents must summarize intermediate findings before their significance is known, increasing the risk of discarding key evidence. ReAct-style agents are especially brittle in this regime. Their retrieve-summarize-reason loop makes conclusions sensitive to exploration order and introduces run-to-run non-determinism, producing a reliability gap where Pass-at-k may be high but Majority-at-k remains low. Simply sampling more rollouts or generating longer reasoning traces does not reliably stabilize results, since hypotheses cannot be autonomously checked as new evidence arrives and there is no explicit mechanism for belief bookkeeping and revision. In addition, ReAct entangles semantic reasoning with controller duties such as tool orchestration and state tracking, so execution errors and plan drift degrade reasoning while consuming scarce context. We address these issues by formulating investigation as abductive reasoning over a dependency graph and proposing EoG (Explanations over Graphs), a disaggregated framework in which an LLM performs bounded local evidence mining and labeling (cause vs symptom) while a deterministic controller manages traversal, state, and belief propagation to compute a minimal explanatory frontier. On a representative ITBench diagnostics task, EoG improves both accuracy and run-to-run consistency over ReAct baselines, including a 7x average gain in Majority-at-k entity F1.

  • 10 authors
·
Jan 28

Gated Attention for Large Language Models: Non-linearity, Sparsity, and Attention-Sink-Free

Gating mechanisms have been widely utilized, from early models like LSTMs and Highway Networks to recent state space models, linear attention, and also softmax attention. Yet, existing literature rarely examines the specific effects of gating. In this work, we conduct comprehensive experiments to systematically investigate gating-augmented softmax attention variants. Specifically, we perform a comprehensive comparison over 30 variants of 15B Mixture-of-Experts (MoE) models and 1.7B dense models trained on a 3.5 trillion token dataset. Our central finding is that a simple modification-applying a head-specific sigmoid gate after the Scaled Dot-Product Attention (SDPA)-consistently improves performance. This modification also enhances training stability, tolerates larger learning rates, and improves scaling properties. By comparing various gating positions and computational variants, we attribute this effectiveness to two key factors: (1) introducing non-linearity upon the low-rank mapping in the softmax attention, and (2) applying query-dependent sparse gating scores to modulate the SDPA output. Notably, we find this sparse gating mechanism mitigates 'attention sink' and enhances long-context extrapolation performance, and we also release related https://github.com/qiuzh20/gated_attention{codes} and https://huggingface.co/QwQZh/gated_attention{models} to facilitate future research.

  • 13 authors
·
May 10, 2025 1

FAIR-RAG: Faithful Adaptive Iterative Refinement for Retrieval-Augmented Generation

While Retrieval-Augmented Generation (RAG) mitigates hallucination and knowledge staleness in Large Language Models (LLMs), existing frameworks often falter on complex, multi-hop queries that require synthesizing information from disparate sources. Current advanced RAG methods, employing iterative or adaptive strategies, lack a robust mechanism to systematically identify and fill evidence gaps, often propagating noise or failing to gather a comprehensive context. We introduce FAIR-RAG, a novel agentic framework that transforms the standard RAG pipeline into a dynamic, evidence-driven reasoning process. At its core is an Iterative Refinement Cycle governed by a module we term Structured Evidence Assessment (SEA). The SEA acts as an analytical gating mechanism: it deconstructs the initial query into a checklist of required findings and audits the aggregated evidence to identify confirmed facts and, critically, explicit informational gaps. These gaps provide a precise signal to an Adaptive Query Refinement agent, which generates new, targeted sub-queries to retrieve missing information. This cycle repeats until the evidence is verified as sufficient, ensuring a comprehensive context for a final, strictly faithful generation. We conducted experiments on challenging multi-hop QA benchmarks, including HotpotQA, 2WikiMultiHopQA, and MusiQue. In a unified experimental setup, FAIR-RAG significantly outperforms strong baselines. On HotpotQA, it achieves an F1-score of 0.453 -- an absolute improvement of 8.3 points over the strongest iterative baseline -- establishing a new state-of-the-art for this class of methods on these benchmarks. Our work demonstrates that a structured, evidence-driven refinement process with explicit gap analysis is crucial for unlocking reliable and accurate reasoning in advanced RAG systems for complex, knowledge-intensive tasks.

  • 3 authors
·
Oct 25, 2025

PRISM: Festina Lente Proactivity -- Risk-Sensitive, Uncertainty-Aware Deliberation for Proactive Agents

Proactive agents must decide not only what to say but also whether and when to intervene. Many current systems rely on brittle heuristics or indiscriminate long reasoning, which offers little control over the benefit-burden tradeoff. We formulate the problem as cost-sensitive selective intervention and present PRISM, a novel framework that couples a decision-theoretic gate with a dual-process reasoning architecture. At inference time, the agent intervenes only when a calibrated probability of user acceptance exceeds a threshold derived from asymmetric costs of missed help and false alarms. Inspired by festina lente (Latin: "make haste slowly"), we gate by an acceptance-calibrated, cost-derived threshold and invoke a resource-intensive Slow mode with counterfactual checks only near the decision boundary, concentrating computation on ambiguous and high-stakes cases. Training uses gate-aligned, schema-locked distillation: a teacher running the full PRISM pipeline provides dense, executable supervision on unlabeled interaction traces, while the student learns a response policy that is explicitly decoupled from the intervention gate to enable tunable and auditable control. On ProactiveBench, PRISM reduces false alarms by 22.78% and improves F1 by 20.14% over strong baselines. These results show that principled decision-theoretic gating, paired with selective slow reasoning and aligned distillation, yields proactive agents that are precise, computationally efficient, and controllable. To facilitate reproducibility, we release our code, models, and resources at https://prism-festinalente.github.io/; all experiments use the open-source ProactiveBench benchmark.

  • 5 authors
·
Feb 1

Jointly-Learned Exit and Inference for a Dynamic Neural Network : JEI-DNN

Large pretrained models, coupled with fine-tuning, are slowly becoming established as the dominant architecture in machine learning. Even though these models offer impressive performance, their practical application is often limited by the prohibitive amount of resources required for every inference. Early-exiting dynamic neural networks (EDNN) circumvent this issue by allowing a model to make some of its predictions from intermediate layers (i.e., early-exit). Training an EDNN architecture is challenging as it consists of two intertwined components: the gating mechanism (GM) that controls early-exiting decisions and the intermediate inference modules (IMs) that perform inference from intermediate representations. As a result, most existing approaches rely on thresholding confidence metrics for the gating mechanism and strive to improve the underlying backbone network and the inference modules. Although successful, this approach has two fundamental shortcomings: 1) the GMs and the IMs are decoupled during training, leading to a train-test mismatch; and 2) the thresholding gating mechanism introduces a positive bias into the predictive probabilities, making it difficult to readily extract uncertainty information. We propose a novel architecture that connects these two modules. This leads to significant performance improvements on classification datasets and enables better uncertainty characterization capabilities.

  • 3 authors
·
Oct 13, 2023

CUE-R: Beyond the Final Answer in Retrieval-Augmented Generation

As language models shift from single-shot answer generation toward multi-step reasoning that retrieves and consumes evidence mid-inference, evaluating the role of individual retrieved items becomes more important. Existing RAG evaluation typically targets final-answer quality, citation faithfulness, or answer-level attribution, but none of these directly targets the intervention-based, per-evidence-item utility view we study here. We introduce CUE-R, a lightweight intervention-based framework for measuring per-evidence-item operational utility in single-shot RAG using shallow observable retrieval-use traces. CUE-R perturbs individual evidence items via REMOVE, REPLACE, and DUPLICATE operators, then measures changes along three utility axes (correctness, proxy-based grounding faithfulness, and confidence error) plus a trace-divergence signal. We also outline an operational evidence-role taxonomy for interpreting intervention outcomes. Experiments on HotpotQA and 2WikiMultihopQA with Qwen-3 8B and GPT-5.2 reveal a consistent pattern: REMOVE and REPLACE substantially harm correctness and grounding while producing large trace shifts, whereas DUPLICATE is often answer-redundant yet not fully behaviorally neutral. A zero-retrieval control confirms that these effects arise from degradation of meaningful retrieval. A two-support ablation further shows that multi-hop evidence items can interact non-additively: removing both supports harms performance far more than either single removal. Our results suggest that answer-only evaluation misses important evidence effects and that intervention-based utility analysis is a practical complement for RAG evaluation.

intuit Intuit
·
Apr 6 2

ClinSeekAgent: Automating Multimodal Evidence Seeking for Agentic Clinical Reasoning

Large language models (LLMs) and agentic systems have shown promise for clinical decision support, but existing works largely assume that evidence has already been curated and handed to the model. Real-world clinical workflows instead require agents to actively seek, iteratively plan, and synthesize multimodal evidence from heterogeneous sources. In this paper, we introduce ClinSeekAgent, an automated agentic framework for dynamic multimodal evidence seeking that shifts the paradigm from passive evidence consumption to active evidence acquisition. Given only a clinical query and access to raw data sources, ClinSeekAgent gathers evidence by querying medical knowledge bases, navigating raw EHRs, and invoking medical imaging tools; refines its hypotheses as new information emerges; and integrates the collected evidence into grounded clinical decisions. ClinSeekAgent serves both as an inference-time agent for frontier LLMs and as a training-time pipeline for distilling high-quality agent trajectories into compact open-source models. To validate its inference-time effectiveness, we construct ClinSeek-Bench, which pairs Curated Input reasoning from fixed pre-selected evidence with Automated Evidence-Seeking over raw clinical data. On text-only EHR tasks, ClinSeekAgent improves Claude Opus 4.6 from 60.0 to 63.2 overall F1 and MiniMax M2.5 from 43.1 to 47.3, with positive risk-prediction gains in 7 out of 9 evaluated host models. On multimodal tasks, ClinSeekAgent improves Claude Opus 4.6 from 47.5 to 62.6 (+15.1); all evaluated models improve across the three CXR-related task groups. We further validate ClinSeekAgent as a training pipeline by distilling agentic evidence-seeking trajectories into ClinSeek-35B-A3B, which achieves 34.0 average F1 on existing AgentEHR-Bench, improving over its Qwen3.5-35B-A3B baseline by +11.9 points and approaching Claude Opus 4.6.

  • 8 authors
·
May 18 1

Is Temperature Sample Efficient for Softmax Gaussian Mixture of Experts?

Dense-to-sparse gating mixture of experts (MoE) has recently become an effective alternative to a well-known sparse MoE. Rather than fixing the number of activated experts as in the latter model, which could limit the investigation of potential experts, the former model utilizes the temperature to control the softmax weight distribution and the sparsity of the MoE during training in order to stabilize the expert specialization. Nevertheless, while there are previous attempts to theoretically comprehend the sparse MoE, a comprehensive analysis of the dense-to-sparse gating MoE has remained elusive. Therefore, we aim to explore the impacts of the dense-to-sparse gate on the maximum likelihood estimation under the Gaussian MoE in this paper. We demonstrate that due to interactions between the temperature and other model parameters via some partial differential equations, the convergence rates of parameter estimations are slower than any polynomial rates, and could be as slow as O(1/log(n)), where n denotes the sample size. To address this issue, we propose using a novel activation dense-to-sparse gate, which routes the output of a linear layer to an activation function before delivering them to the softmax function. By imposing linearly independence conditions on the activation function and its derivatives, we show that the parameter estimation rates are significantly improved to polynomial rates.

  • 3 authors
·
Jan 24, 2024

Refusal Falls off a Cliff: How Safety Alignment Fails in Reasoning?

Large reasoning models (LRMs) with multi-step reasoning capabilities have shown remarkable problem-solving abilities, yet they exhibit concerning safety vulnerabilities that remain poorly understood. In this work, we investigate why safety alignment fails in reasoning models through a mechanistic interpretability lens. Using a linear probing approach to trace refusal intentions across token positions, we discover a striking phenomenon termed as refusal cliff: many poorly-aligned reasoning models correctly identify harmful prompts and maintain strong refusal intentions during their thinking process, but experience a sharp drop in refusal scores at the final tokens before output generation. This suggests that these models are not inherently unsafe; rather, their refusal intentions are systematically suppressed. Through causal intervention analysis, we identify a sparse set of attention heads that negatively contribute to refusal behavior. Ablating just 3\% of these heads can reduce attack success rates below 10\%. Building on these mechanistic insights, we propose Cliff-as-a-Judge, a novel data selection method that identifies training examples exhibiting the largest refusal cliff to efficiently repair reasoning models' safety alignment. This approach achieves comparable safety improvements using only 1.7\% of the vanilla safety training data, demonstrating a less-is-more effect in safety alignment.

rednote-hilab rednote-hilab
·
Oct 7, 2025 2

BMGQ: A Bottom-up Method for Generating Complex Multi-hop Reasoning Questions from Semi-structured Data

Building training-ready multi-hop question answering (QA) datasets that truly stress a model's retrieval and reasoning abilities remains highly challenging recently. While there have been a few recent evaluation datasets that capture the characteristics of hard-to-search but easy-to-verify problems -- requiring the integration of ambiguous, indirect, and cross-domain cues -- these data resources remain scarce and are mostly designed for evaluation, making them unsuitable for supervised fine-tuning (SFT) or reinforcement learning (RL). Meanwhile, manually curating non-trivially retrievable questions -- where answers cannot be found through a single direct query but instead require multi-hop reasoning over oblique and loosely connected evidence -- incurs prohibitive human costs and fails to scale, creating a critical data bottleneck for training high-capability retrieval-and-reasoning agents. To address this, we present an automated framework for generating high-difficulty, training-ready multi-hop questions from semi-structured knowledge sources. The system (i) grows diverse, logically labeled evidence clusters through Natural Language Inference (NLI)-based relation typing and diversity-aware expansion; (ii) applies reverse question construction to compose oblique cues so that isolated signals are underinformative but their combination uniquely identifies the target entity; and (iii) enforces quality with a two-step evaluation pipeline that combines multi-model consensus filtering with structured constraint decomposition and evidence-based matching. The result is a scalable process that yields complex, retrieval-resistant yet verifiable questions suitable for SFT/RL training as well as challenging evaluation, substantially reducing human curation effort while preserving the difficulty profile of strong evaluation benchmarks.

  • 9 authors
·
Oct 28, 2025

Mixture of Tunable Experts -- Behavior Modification of DeepSeek-R1 at Inference Time

We present the Mixture-of-Tunable-Experts (MoTE), a method that extends the Mixture-of-Experts architecture of Large Language Models (LLMs). Without additional training, MoTE enables meaningful and focused behavior changes in LLMs on-the-fly during inference time. By analyzing the digital LLM brain of DeepSeek-R1 using a technique we dub 'functional Token Resonance Imaging' (fTRI) -- inspired by fMRI and using prompts designed to elicit specific behavior (e.g., 'What happened {time}{place}?') -- we empirically identify distinctive experts associated with behaviors like refusal responses. Using MoTE we are able to intervene and control such specific behavior. We switched off the top 10 most refusal-relevant experts (0.07% of R1's 14,848 routed experts), achieving a 52% refusal reduction on sensitive reference prompts without performance degradation on MT-Bench. Random expert deactivation resulted in smaller behavioral shifts with increased noise, whereas forced expert activation led to significantly higher refusal rates. Our approach shares similarities with sparse autoencoders (SAEs) in terms of explainability and steerability. Unlike SAEs, MoTE does not require large training efforts, as within MoEs with a vast number of experts, specialization already emerged naturally during pretraining. Our findings suggest that significant functional mechanisms in Mixture-of-Experts architectures can at least partially be localized in a small number of specific experts, rather than being distributed throughout the model's weights. Expert subgroups can be tuned to trigger significant behavior variations, providing insights into the inner workings of LLMs.

  • 6 authors
·
Feb 16, 2025 2

Theoretical Foundations of Latent Posterior Factors: Formal Guarantees for Multi-Evidence Reasoning

We present a complete theoretical characterization of Latent Posterior Factors (LPF), a principled framework for aggregating multiple heterogeneous evidence items in probabilistic prediction tasks. Multi-evidence reasoning arises pervasively in high-stakes domains including healthcare diagnosis, financial risk assessment, legal case analysis, and regulatory compliance, yet existing approaches either lack formal guarantees or fail to handle multi-evidence scenarios architecturally. LPF encodes each evidence item into a Gaussian latent posterior via a variational autoencoder, converting posteriors to soft factors through Monte Carlo marginalization, and aggregating factors via exact Sum-Product Network inference (LPF-SPN) or a learned neural aggregator (LPF-Learned). We prove seven formal guarantees spanning the key desiderata for trustworthy AI: Calibration Preservation (ECE <= epsilon + C/sqrt(K_eff)); Monte Carlo Error decaying as O(1/sqrt(M)); a non-vacuous PAC-Bayes bound with train-test gap of 0.0085 at N=4200; operation within 1.12x of the information-theoretic lower bound; graceful degradation as O(epsilon*delta*sqrt(K)) under corruption, maintaining 88% performance with half of evidence adversarially replaced; O(1/sqrt(K)) calibration decay with R^2=0.849; and exact epistemic-aleatoric uncertainty decomposition with error below 0.002%. All theorems are empirically validated on controlled datasets spanning up to 4,200 training examples. Our theoretical framework establishes LPF as a foundation for trustworthy multi-evidence AI in safety-critical applications.

  • 1 authors
·
Mar 13 2

Dopamine: Brain Modes, Not Brains

Parameter-efficient fine-tuning (PEFT) methods such as adapt large pretrained models by adding small weight-space updates. While effective, weight deltas are hard to interpret mechanistically, and they do not directly expose which internal computations are reused versus bypassed for a new task. We explore an alternative view inspired by neuromodulation: adaptation as a change in mode -- selecting and rescaling existing computations -- rather than rewriting the underlying weights. We propose , a simple activation-space PEFT technique that freezes base weights and learns per-neuron thresholds and gains. During training, a smooth gate decides whether a neuron's activation participates; at inference the gate can be hardened to yield explicit conditional computation and neuron-level attributions. As a proof of concept, we study ``mode specialization'' on MNIST (0^circ) versus rotated MNIST (45^circ). We pretrain a small MLP on a 50/50 mixture (foundation), freeze its weights, and then specialize to the rotated mode using . Across seeds, improves rotated accuracy over the frozen baseline while using only a few hundred trainable parameters per layer, and exhibits partial activation sparsity (a minority of units strongly active). Compared to , trades some accuracy for substantially fewer trainable parameters and a more interpretable ``which-neurons-fire'' mechanism. We discuss limitations, including reduced expressivity when the frozen base lacks features needed for the target mode.

  • 1 authors
·
Feb 12

MedMMV: A Controllable Multimodal Multi-Agent Framework for Reliable and Verifiable Clinical Reasoning

Recent progress in multimodal large language models (MLLMs) has demonstrated promising performance on medical benchmarks and in preliminary trials as clinical assistants. Yet, our pilot audit of diagnostic cases uncovers a critical failure mode: instability in early evidence interpretation precedes hallucination, creating branching reasoning trajectories that cascade into globally inconsistent conclusions. This highlights the need for clinical reasoning agents that constrain stochasticity and hallucination while producing auditable decision flows. We introduce MedMMV, a controllable multimodal multi-agent framework for reliable and verifiable clinical reasoning. MedMMV stabilizes reasoning through diversified short rollouts, grounds intermediate steps in a structured evidence graph under the supervision of a Hallucination Detector, and aggregates candidate paths with a Combined Uncertainty scorer. On six medical benchmarks, MedMMV improves accuracy by up to 12.7% and, more critically, demonstrates superior reliability. Blind physician evaluations confirm that MedMMV substantially increases reasoning truthfulness without sacrificing informational content. By controlling instability through a verifiable, multi-agent process, our framework provides a robust path toward deploying trustworthy AI systems in high-stakes domains like clinical decision support.

  • 7 authors
·
Sep 29, 2025

Evidence Sufficiency Under Delayed Ground Truth: Proxy Monitoring for Risk Decision Systems

Machine learning systems in fraud detection, credit scoring, and clinical risk assessment operate under delayed ground truth: outcome labels arrive days to months after the decision they evaluate. During this blind period, governance evidence degrades through mechanisms that neither drift detection methods nor governance frameworks adequately address. This paper formalizes an evidence sufficiency model with four dimensions (completeness, freshness, reliability, representativeness) and a decision-readiness gate that quantifies how label latency degrades evidence quality. The model maps three drift types to dimension-specific degradation trajectories. A complementary proxy indicator framework comprising seven measurement categories estimates sufficiency degradation without labels, with explicit coverage mapping and characterized blind spots per drift type. Evaluation on the IEEE-CIS Fraud Detection dataset (~590K transactions) with controlled drift injection shows that composite proxy monitoring detects covariate and mixed drift with 100% detection rate, while concept drift without feature change remains undetected -- consistent with the theoretical impossibility of unsupervised detection when P(X) is unchanged. Blind period simulation confirms monotone sufficiency degradation, with concept drift degrading fastest (S=0.242 at day 60 vs 0.418 for no-drift). The framework contributes a governance sufficiency monitoring instrument; its value lies in translating drift signals into auditable sufficiency assessments with characterized blind spots. Mapping sufficiency levels to governance actions requires deployment-specific calibration beyond this study's scope.

  • 1 authors
·
Apr 16

ActivationReasoning: Logical Reasoning in Latent Activation Spaces

Large language models (LLMs) excel at generating fluent text, but their internal reasoning remains opaque and difficult to control. Sparse autoencoders (SAEs) make hidden activations more interpretable by exposing latent features that often align with human concepts. Yet, these features are fragile and passive, offering no mechanism for systematic reasoning or model control. To address this, we introduce ActivationReasoning (AR), a framework that embeds explicit logical reasoning into the latent space of LLMs. It proceeds in three stages: (1) Finding latent representations, first latent concept representations are identified (e.g., via SAEs) and organized into a dictionary; (2) Activating propositions, at inference time AR detects activating concepts and maps them to logical propositions; and (3)Logical reasoning, applying logical rules over these propositions to infer higher-order structures, compose new concepts, and steer model behavior. We evaluate AR on multi-hop reasoning (PrOntoQA), abstraction and robustness to indirect concept cues (Rail2Country), reasoning over natural and diverse language (ProverQA), and context-sensitive safety (BeaverTails). Across all tasks, AR scales robustly with reasoning complexity, generalizes to abstract and context-sensitive tasks, and transfers across model backbones. These results demonstrate that grounding logical structure in latent activations not only improves transparency but also enables structured reasoning, reliable control, and alignment with desired behaviors, providing a path toward more reliable and auditable AI.

  • 9 authors
·
Oct 20, 2025

Transitive Expert Error and Routing Problems in Complex AI Systems

Domain expertise enhances judgment within boundaries but creates systematic vulnerabilities specifically at borders. We term this Transitive Expert Error (TEE), distinct from Dunning-Kruger effects, requiring calibrated expertise as precondition. Mechanisms enabling reliable within-domain judgment become liabilities when structural similarity masks causal divergence. Two core mechanisms operate: structural similarity bias causes experts to overweight surface features (shared vocabulary, patterns, formal structure) while missing causal architecture differences; authority persistence maintains confidence across competence boundaries through social reinforcement and metacognitive failures (experts experience no subjective uncertainty as pattern recognition operates smoothly on familiar-seeming inputs.) These mechanism intensify under three conditions: shared vocabulary masking divergent processes, social pressure for immediate judgment, and delayed feedback. These findings extend to AI routing architectures (MoE systems, multi-model orchestration, tool-using agents, RAG systems) exhibiting routing-induced failures (wrong specialist selected) and coverage-induced failures (no appropriate specialist exists). Both produce a hallucination phenotype: confident, coherent, structurally plausible but causally incorrect outputs at domain boundaries. In human systems where mechanisms are cognitive black boxes; AI architectures make them explicit and addressable. We propose interventions: multi-expert activation with disagreement detection (router level), boundary-aware calibration (specialist level), and coverage gap detection (training level). TEE has detectable signatures (routing patterns, confidence-accuracy dissociations, domain-inappropriate content) enabling monitoring and mitigation. What remains intractable in human cognition becomes addressable through architectural design.

  • 1 authors
·
Jan 6

REFLEX: Self-Refining Explainable Fact-Checking via Disentangling Truth into Style and Substance

The prevalence of misinformation on social media threatens public trust, demanding automated fact-checking systems that provide accurate verdicts with interpretable explanations. However, existing large language model-based (LLM-based) approaches often rely heavily on external knowledge sources, introducing substantial latency and even hallucinations that undermine reliability, interpretability, and responsiveness, which is crucial for real-time use. To address these challenges, we propose REason-guided Fact-checking with Latent EXplanations REFLEX paradigm, a plug-and-play, self-refining paradigm that leverages the internal knowledge in backbone model to improve both verdict accuracy and explanation quality. REFLEX reformulates fact-checking as a role-play dialogue and jointly trains verdict prediction and explanation generation. It adaptively extracts contrastive activation pairs between the backbone model and its fine-tuned variant to construct steering vectors that disentangle truth into style and substance naturally. These activation-level signals guide inference and suppress noisy explanations, enabling more faithful and efficient reasoning. Experiments on real-world datasets show that REFLEX outperforms previous methods that steer toward a single truth direction and underscores the challenge traditional approaches face when handling the subtle, human-unknown truth in fact-checking tasks. Remarkably, with only 465 self-refined training samples, RELFEX achieves state-of-the-art performance. Furthermore, models trained with explanatory objectives can effectively guide those without them, yielding up to a 7.57% improvement, highlighting that internal explanation signals play a dual role in both interpreting and enhancing factual reasoning.

  • 5 authors
·
Nov 25, 2025 2

Digital Metabolism: Decoupling Logic from Facts via Regenerative Unlearning -- Towards a Pure Neural Logic Core

Large language models (LLMs) currently suffer from parameter entanglement, where general reasoning capabilities (logic) and specific factual knowledge (facts) exist in a superposition state within shared weights. This coupling leads to the "memory wall," where computational capacity is squandered on simulating retrieval, often resulting in hallucinations. In this paper, we propose "digital metabolism," a thermodynamic hypothesis suggesting that targeted forgetting is necessary for distilling a pure neural logic core. To validate this hypothesis, we introduce the Regenerative Logic-Core Protocol (RLCP), a dual-stream training framework that renders specific factual dependencies linearly undecodable via deep-layer gradient reversal. Applying RLCP to Qwen2.5-0.5B, we observe a distinct phase transition: the model achieves near-zero retention of targeted factual associations (Accuracy < 7%) while exhibiting changes consistent with an emergent "structural crystallization" effect. Empirical analysis on GSM8K reveals that the "metabolized" model spontaneously adopts chain-of-thought (CoT) scaffolding, which we interpret as compensating for the loss of direct associative recall (shifting from O(1) recall to O(N) reasoning). While the causal mechanism underlying this behavioral shift requires further investigation, our findings provide a dynamic weight-level counterpart to architectural innovations like DeepSeek's Engram, paving the way for modular "Neural CPU + Symbolic RAM" architectures.

  • 3 authors
·
Jan 14

Towards Foundational Models for Dynamical System Reconstruction: Hierarchical Meta-Learning via Mixture of Experts

As foundational models reshape scientific discovery, a bottleneck persists in dynamical system reconstruction (DSR): the ability to learn across system hierarchies. Many meta-learning approaches have been applied successfully to single systems, but falter when confronted with sparse, loosely related datasets requiring multiple hierarchies to be learned. Mixture of Experts (MoE) offers a natural paradigm to address these challenges. Despite their potential, we demonstrate that naive MoEs are inadequate for the nuanced demands of hierarchical DSR, largely due to their gradient descent-based gating update mechanism which leads to slow updates and conflicted routing during training. To overcome this limitation, we introduce MixER: Mixture of Expert Reconstructors, a novel sparse top-1 MoE layer employing a custom gating update algorithm based on K-means and least squares. Extensive experiments validate MixER's capabilities, demonstrating efficient training and scalability to systems of up to ten parametric ordinary differential equations. However, our layer underperforms state-of-the-art meta-learners in high-data regimes, particularly when each expert is constrained to process only a fraction of a dataset composed of highly related data points. Further analysis with synthetic and neuroscientific time series suggests that the quality of the contextual representations generated by MixER is closely linked to the presence of hierarchical structure in the data.

  • 5 authors
·
Feb 7, 2025

MIRAGE: Assessing Hallucination in Multimodal Reasoning Chains of MLLM

Multimodal hallucination in multimodal large language models (MLLMs) restricts the correctness of MLLMs. However, multimodal hallucinations are multi-sourced and arise from diverse causes. Existing benchmarks fail to adequately distinguish between perception-induced hallucinations and reasoning-induced hallucinations. This failure constitutes a significant issue and hinders the diagnosis of multimodal reasoning failures within MLLMs. To address this, we propose the {\dataset} benchmark, which isolates reasoning hallucinations by constructing questions where input images are correctly perceived by MLLMs yet reasoning errors persist. {\dataset} introduces multi-granular evaluation metrics: accuracy, factuality, and LLMs hallucination score for hallucination quantification. Our analysis reveals that (1) the model scale, data scale, and training stages significantly affect the degree of logical, fabrication, and factual hallucinations; (2) current MLLMs show no effective improvement on spatial hallucinations caused by misinterpreted spatial relationships, indicating their limited visual reasoning capabilities; and (3) question types correlate with distinct hallucination patterns, highlighting targeted challenges and potential mitigation strategies. To address these challenges, we propose {\method}, a method that combines curriculum reinforcement fine-tuning to encourage models to generate logic-consistent reasoning chains by stepwise reducing learning difficulty, and collaborative hint inference to reduce reasoning complexity. {\method} establishes a baseline on {\dataset}, and reduces the logical hallucinations in original base models.

  • 6 authors
·
May 30, 2025

AI scientists produce results without reasoning scientifically

Large language model (LLM)-based systems are increasingly deployed to conduct scientific research autonomously, yet whether their reasoning adheres to the epistemic norms that make scientific inquiry self-correcting is poorly understood. Here, we evaluate LLM-based scientific agents across eight domains, spanning workflow execution to hypothesis-driven inquiry, through more than 25,000 agent runs and two complementary lenses: (i) a systematic performance analysis that decomposes the contributions of the base model and the agent scaffold, and (ii) a behavioral analysis of the epistemological structure of agent reasoning. We observe that the base model is the primary determinant of both performance and behavior, accounting for 41.4% of explained variance versus 1.5% for the scaffold. Across all configurations, evidence is ignored in 68% of traces, refutation-driven belief revision occurs in 26%, and convergent multi-test evidence is rare. The same reasoning pattern appears whether the agent executes a computational workflow or conducts hypothesis-driven inquiry. They persist even when agents receive near-complete successful reasoning trajectories as context, and the resulting unreliability compounds across repeated trials in epistemically demanding domains. Thus, current LLM-based agents execute scientific workflows but do not exhibit the epistemic patterns that characterize scientific reasoning. Outcome-based evaluation cannot detect these failures, and scaffold engineering alone cannot repair them. Until reasoning itself becomes a training target, the scientific knowledge produced by such agents cannot be justified by the process that generated it.

Thought Branches: Interpreting LLM Reasoning Requires Resampling

Most work interpreting reasoning models studies only a single chain-of-thought (CoT), yet these models define distributions over many possible CoTs. We argue that studying a single sample is inadequate for understanding causal influence and the underlying computation. Though fully specifying this distribution is intractable, it can be understood by sampling. We present case studies using resampling to investigate model decisions. First, when a model states a reason for its action, does that reason actually cause the action? In "agentic misalignment" scenarios, we resample specific sentences to measure their downstream effects. Self-preservation sentences have small causal impact, suggesting they do not meaningfully drive blackmail. Second, are artificial edits to CoT sufficient for steering reasoning? These are common in literature, yet take the model off-policy. Resampling and selecting a completion with the desired property is a principled on-policy alternative. We find off-policy interventions yield small and unstable effects compared to resampling in decision-making tasks. Third, how do we understand the effect of removing a reasoning step when the model may repeat it post-edit? We introduce a resilience metric that repeatedly resamples to prevent similar content from reappearing downstream. Critical planning statements resist removal but have large effects when eliminated. Fourth, since CoT is sometimes "unfaithful", can our methods teach us anything in these settings? Adapting causal mediation analysis, we find that hints that have a causal effect on the output without being explicitly mentioned exert a subtle and cumulative influence on the CoT that persists even if the hint is removed. Overall, studying distributions via resampling enables reliable causal analysis, clearer narratives of model reasoning, and principled CoT interventions.

  • 4 authors
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Oct 31, 2025

Demystifying deep search: a holistic evaluation with hint-free multi-hop questions and factorised metrics

RAG (Retrieval-Augmented Generation) systems and web agents are increasingly evaluated on multi-hop deep search tasks, yet current practice suffers from two major limitations. First, most benchmarks leak the reasoning path in the question text, allowing models to follow surface cues rather than discover reasoning chains autonomously. Second, evaluation is typically reduced to a single pass rate, which collapses diverse behaviours into one score and obscures whether failures stem from inadequate search, poor knowledge use, or inappropriate refusal. To address these issues, we present WebDetective, a benchmark of hint-free multi-hop questions paired with a controlled Wikipedia sandbox that ensures full traceability of model actions, and a holistic evaluation framework that separates search sufficiency, knowledge utilisation, and refusal behaviour. Our evaluation of 25 state-of-the-art models reveals systematic weaknesses across all architectures: models struggle with knowledge utilisation despite having sufficient evidence and demonstrate near-absent appropriate refusal when evidence is lacking. These patterns expose a fundamental gap: today's systems excel at executing given reasoning paths but fail when required to discover them. We develop an agentic workflow, EvidenceLoop, that explicitly targets the challenges our benchmark identifies, incorporating verification loops and systematic evidence tracking that improve both search and synthesis capabilities. This baseline demonstrates that WebDetective's diagnostic framework can guide concrete architectural improvements, establishing our benchmark as a critical tool for developing genuinely autonomous reasoning systems rather than pattern-following agents.

Why think step by step? Reasoning emerges from the locality of experience

Humans have a powerful and mysterious capacity to reason. By working through a series of purely mental steps, we can make inferences we would not be capable of making directly -- despite the fact that we get no additional data from the world. Similarly, when large language models generate a series of intermediate steps (a chain of thought) before answering a question, they often produce better answers than they otherwise would. We investigate why and how chain-of-thought reasoning is useful in language models, testing the hypothesis that reasoning is effective when training data consists of local clusters of variables that influence each other strongly. These training conditions enable the chaining of accurate local inferences in order to estimate relationships between variables that were not seen together in training. We prove that there will exist a "reasoning gap", where reasoning through intermediate variables improves inference, for the simple case of an autoregressive density estimator trained on local samples from a chain-structured probabilistic model. We then test our hypothesis empirically in more complex models, training an autoregressive language model on samples from Bayes nets but only including a subset of variables in each sample. We test language models' ability to match conditional probabilities with and without intermediate reasoning steps, finding that intermediate steps are only helpful when the training data is locally structured with respect to dependencies between variables and that the combination of locally-structured observations and reasoning is much more data-efficient than training on all variables. Our results illustrate how the effectiveness of reasoning step by step is rooted in the local statistical structure of the training data.

  • 3 authors
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Apr 7, 2023

Compliance versus Sensibility: On the Reasoning Controllability in Large Language Models

Large Language Models (LLMs) are known to acquire reasoning capabilities through shared inference patterns in pre-training data, which are further elicited via Chain-of-Thought (CoT) practices. However, whether fundamental reasoning patterns, such as induction, deduction, and abduction, can be decoupled from specific problem instances remains a critical challenge for model controllability, and for shedding light on reasoning controllability. In this paper, we present the first systematic investigation of this problem through the lens of reasoning conflicts: an explicit tension between parametric and contextual information induced by mandating logical schemata that deviate from those expected for a target task. Our evaluation reveals that LLMs consistently prioritize sensibility over compliance, favoring task-appropriate reasoning patterns despite conflicting instructions. Notably, task accuracy is not strictly determined by sensibility, with models often maintaining high performance even when using conflicting patterns, suggesting a reliance on internalized parametric memory that increases with model size. We further demonstrate that reasoning conflicts are internally detectable, as confidence scores significantly drop during conflicting episodes. Probing experiments confirm that reasoning types are linearly encoded from middle-to-late layers, indicating the potential for activation-level controllability. Leveraging these insights, we steer models towards compliance, increasing instruction following by up to 29%. Overall, our findings establish that while LLM reasoning is anchored to concrete instances, active mechanistic interventions can effectively decouple logical schemata from data, offering a path toward improved controllability, faithfulness, and generalizability.

  • 6 authors
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Apr 28 2

PathReasoner-R1: Instilling Structured Reasoning into Pathology Vision-Language Model via Knowledge-Guided Policy Optimization

Vision-Language Models (VLMs) are advancing computational pathology with superior visual understanding capabilities. However, current systems often reduce diagnosis to directly output conclusions without verifiable evidence-linked reasoning, which severely limits clinical trust and hinders expert error rectification. To address these barriers, we construct PathReasoner, the first large-scale dataset of whole-slide image (WSI) reasoning. Unlike previous work reliant on unverified distillation, we develop a rigorous knowledge-guided generation pipeline. By leveraging medical knowledge graphs, we explicitly align structured pathological findings and clinical reasoning with diagnoses, generating over 20K high-quality instructional samples. Based on the database, we propose PathReasoner-R1, which synergizes trajectory-masked supervised fine-tuning with reasoning-oriented reinforcement learning to instill structured chain-of-thought capabilities. To ensure medical rigor, we engineer a knowledge-aware multi-granular reward function incorporating an Entity Reward mechanism strictly aligned with knowledge graphs. This effectively guides the model to optimize for logical consistency rather than mere outcome matching, thereby enhancing robustness. Extensive experiments demonstrate that PathReasoner-R1 achieves state-of-the-art performance on both PathReasoner and public benchmarks across various image scales, equipping pathology models with transparent, clinically grounded reasoning capabilities. Dataset and code are available at https://github.com/cyclexfy/PathReasoner-R1.

  • 5 authors
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Jan 29

Dynamics Within Latent Chain-of-Thought: An Empirical Study of Causal Structure

Latent or continuous chain-of-thought methods replace explicit textual rationales with a number of internal latent steps, but these intermediate computations are difficult to evaluate beyond correlation-based probes. In this paper, we view latent chain-of-thought as a manipulable causal process in representation space by modeling latent steps as variables in a structural causal model (SCM) and analyzing their effects through step-wise do-interventions. We study two representative paradigms (i.e., Coconut and CODI) on both mathematical and general reasoning tasks to investigate three key questions: (1) which steps are causally necessary for correctness and when answers become decidable early; (2) how does influence propagate across steps, and how does this structure compare to explicit CoT; and (3) do intermediate trajectories retain competing answer modes, and how does output-level commitment differ from representational commitment across steps. We find that latent-step budgets behave less like homogeneous extra depth and more like staged functionality with non-local routing, and we identify a persistent gap between early output bias and late representational commitment. These results motivate mode-conditional and stability-aware analyses -- and corresponding training/decoding objectives -- as more reliable tools for interpreting and improving latent reasoning systems. Code is available at https://github.com/J1mL1/causal-latent-cot.

  • 7 authors
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Feb 9

Med-V1: Small Language Models for Zero-shot and Scalable Biomedical Evidence Attribution

Assessing whether an article supports an assertion is essential for hallucination detection and claim verification. While large language models (LLMs) have the potential to automate this task, achieving strong performance requires frontier models such as GPT-5 that are prohibitively expensive to deploy at scale. To efficiently perform biomedical evidence attribution, we present Med-V1, a family of small language models with only three billion parameters. Trained on high-quality synthetic data newly developed in this study, Med-V1 substantially outperforms (+27.0% to +71.3%) its base models on five biomedical benchmarks unified into a verification format. Despite its smaller size, Med-V1 performs comparably to frontier LLMs such as GPT-5, along with high-quality explanations for its predictions. We use Med-V1 to conduct a first-of-its-kind use case study that quantifies hallucinations in LLM-generated answers under different citation instructions. Results show that the format instruction strongly affects citation validity and hallucination, with GPT-5 generating more claims but exhibiting hallucination rates similar to GPT-4o. Additionally, we present a second use case showing that Med-V1 can automatically identify high-stakes evidence misattributions in clinical practice guidelines, revealing potentially negative public health impacts that are otherwise challenging to identify at scale. Overall, Med-V1 provides an efficient and accurate lightweight alternative to frontier LLMs for practical and real-world applications in biomedical evidence attribution and verification tasks. Med-V1 is available at https://github.com/ncbi-nlp/Med-V1.

  • 15 authors
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Mar 5

Multi-Step Knowledge Interaction Analysis via Rank-2 Subspace Disentanglement

Natural Language Explanations (NLEs) describe how Large Language Models (LLMs) make decisions, drawing on both external Context Knowledge (CK) and Parametric Knowledge (PK) stored in model weights. Understanding their interaction is key to assessing the grounding of NLEs, yet it remains underexplored. Prior work has largely examined only single-step generation, typically the final answer, and has modelled PK and CK interaction only as a binary choice in a rank-1 subspace. This overlooks richer forms of interaction, such as complementary or supportive knowledge. We propose a novel rank-2 projection subspace that disentangles PK and CK contributions more accurately and use it for the first multi-step analysis of knowledge interactions across longer NLE sequences. Experiments on four QA datasets and three open-weight instruction-tuned LLMs show that diverse knowledge interactions are poorly represented in a rank-1 subspace but are effectively captured in our rank-2 formulation. Our multi-step analysis reveals that hallucinated NLEs align strongly with the PK direction, context-faithful ones balance PK and CK, and Chain-of-Thought prompting for NLEs shifts generated NLEs toward CK by reducing PK reliance. This work provides the first framework for systematic studies of multi-step knowledge interactions in LLMs through a richer rank-2 subspace disentanglement. Code and data: https://github.com/copenlu/pk-ck-knowledge-disentanglement.

  • 3 authors
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Nov 3, 2025 1

Causal Inference by String Diagram Surgery

Extracting causal relationships from observed correlations is a growing area in probabilistic reasoning, originating with the seminal work of Pearl and others from the early 1990s. This paper develops a new, categorically oriented view based on a clear distinction between syntax (string diagrams) and semantics (stochastic matrices), connected via interpretations as structure-preserving functors. A key notion in the identification of causal effects is that of an intervention, whereby a variable is forcefully set to a particular value independent of any prior propensities. We represent the effect of such an intervention as an endofunctor which performs `string diagram surgery' within the syntactic category of string diagrams. This diagram surgery in turn yields a new, interventional distribution via the interpretation functor. While in general there is no way to compute interventional distributions purely from observed data, we show that this is possible in certain special cases using a calculational tool called comb disintegration. We demonstrate the use of this technique on a well-known toy example, where we predict the causal effect of smoking on cancer in the presence of a confounding common cause. After developing this specific example, we show this technique provides simple sufficient conditions for computing interventions which apply to a wide variety of situations considered in the causal inference literature.

  • 3 authors
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Nov 20, 2018

Learning to Route Among Specialized Experts for Zero-Shot Generalization

Recently, there has been a widespread proliferation of "expert" language models that are specialized to a specific task or domain through parameter-efficient fine-tuning. How can we recycle large collections of expert language models to improve zero-shot generalization to unseen tasks? In this work, we propose Post-Hoc Adaptive Tokenwise Gating Over an Ocean of Specialized Experts (PHATGOOSE), which learns to route among specialized modules that were produced through parameter-efficient fine-tuning. Unlike past methods that learn to route among specialized models, PHATGOOSE explores the possibility that zero-shot generalization will be improved if different experts can be adaptively chosen for each token and at each layer in the model. Crucially, our method is post-hoc - it does not require simultaneous access to the datasets used to create the specialized models and only requires a modest amount of additional compute after each expert model is trained. In experiments covering a range of specialized model collections and zero-shot generalization benchmarks, we find that PHATGOOSE outperforms past methods for post-hoc routing and, in some cases, outperforms explicit multitask training (which requires simultaneous data access). To better understand the routing strategy learned by PHATGOOSE, we perform qualitative experiments to validate that PHATGOOSE's performance stems from its ability to make adaptive per-token and per-module expert choices. We release all of our code to support future work on improving zero-shot generalization by recycling specialized experts.

  • 4 authors
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Feb 8, 2024 2

How Alignment Routes: Localizing, Scaling, and Controlling Policy Circuits in Language Models

This paper localizes the policy routing mechanism in alignment-trained language models. An intermediate-layer attention gate reads detected content and triggers deeper amplifier heads that boost the signal toward refusal. In smaller models the gate and amplifier are single heads; at larger scale they become bands of heads across adjacent layers. The gate contributes under 1% of output DLA, but interchange testing (p<0.001) and knockout cascade confirm it is causally necessary. Interchange screening at n>=120 detects the same motif in twelve models from six labs (2B to 72B), though specific heads differ by lab. Per-head ablation weakens up to 58x at 72B and misses gates that interchange identifies; interchange is the only reliable audit at scale. Modulating the detection-layer signal continuously controls policy from hard refusal through evasion to factual answering. On safety prompts the same intervention turns refusal into harmful guidance, showing the safety-trained capability is gated by routing rather than removed. Thresholds vary by topic and by input language, and the circuit relocates across generations within a family while behavioral benchmarks register no change. Routing is early-commitment: the gate commits at its own layer before deeper layers finish processing the input. Under an in-context substitution cipher, gate interchange necessity collapses 70 to 99% across three models and the model switches to puzzle-solving. Injecting the plaintext gate activation into the cipher forward pass restores 48% of refusals in Phi-4-mini, localizing the bypass to the routing interface. A second method, cipher contrast analysis, uses plain/cipher DLA differences to map the full cipher-sensitive routing circuit in O(3n) forward passes. Any encoding that defeats detection-layer pattern matching bypasses the policy regardless of whether deeper layers reconstruct the content.

  • 1 authors
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Apr 12 2

Distortion Instead of Hallucination: The Effect of Reasoning Under Strict Constraints

With the widespread adoption of large language models (LLMs), hallucinations, which are non-factual fabrications in model outputs, have become serious concerns. Reasoning capabilities have received attention as a self-verification process to improve output reliability. However, the effect of reasoning within a closed system where LLMs cannot rely on external tools or knowledge has yet to be clarified. We therefore conduct experiments under strict constraints (recommending peer-reviewed journal articles in computer science) to examine the effect of reasoning across multiple models (GPT-5.2 and Gemini 3 Flash). Our results reveal a problematic trade-off between constraint compliance and factual accuracy. Non-reasoning models exhibit high constraint violation rates (66-75%) but maintain factual accuracy, while reasoning models reduce violations (13-26%) but systematically distort known facts to satisfy constraints and increase complete fabrication. This trade-off pattern is consistent across both models despite different architectures, indicating a fundamental limitation of reasoning. Furthermore, reasoning does not uniformly improve output authenticity: effects diverge by model, reflecting different allocations of the compliance-truthfulness trade-off. These findings challenge the assumption that reasoning universally improves reliability: reasoning models trade honest constraint violations for detection-resistant distortions.

  • 1 authors
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Jan 4

Detecting and Mitigating Treatment Leakage in Text-Based Causal Inference: Distillation and Sensitivity Analysis

Text-based causal inference increasingly employs textual data as proxies for unobserved confounders, yet this approach introduces a previously undertheorized source of bias: treatment leakage. Treatment leakage occurs when text intended to capture confounding information also contains signals predictive of treatment status, thereby inducing post-treatment bias in causal estimates. Critically, this problem can arise even when documents precede treatment assignment, as authors may employ future-referencing language that anticipates subsequent interventions. Despite growing recognition of this issue, no systematic methods exist for identifying and mitigating treatment leakage in text-as-confounder applications. This paper addresses this gap through three contributions. First, we provide formal statistical and set-theoretic definitions of treatment leakage that clarify when and why bias occurs. Second, we propose four text distillation methods -- similarity-based passage removal, distant supervision classification, salient feature removal, and iterative nullspace projection -- designed to eliminate treatment-predictive content while preserving confounder information. Third, we validate these methods through simulations using synthetic text and an empirical application examining International Monetary Fund structural adjustment programs and child mortality. Our findings indicate that moderate distillation optimally balances bias reduction against confounder retention, whereas overly stringent approaches degrade estimate precision.

JerzakLabs Jerzak Labs
·
Dec 30, 2025

Sparks of Science: Hypothesis Generation Using Structured Paper Data

Generating novel and creative scientific hypotheses is a cornerstone in achieving Artificial General Intelligence. Large language and reasoning models have the potential to aid in the systematic creation, selection, and validation of scientifically informed hypotheses. However, current foundation models often struggle to produce scientific ideas that are both novel and feasible. One reason is the lack of a dedicated dataset that frames Scientific Hypothesis Generation (SHG) as a Natural Language Generation (NLG) task. In this paper, we introduce HypoGen, the first dataset of approximately 5500 structured problem-hypothesis pairs extracted from top-tier computer science conferences structured with a Bit-Flip-Spark schema, where the Bit is the conventional assumption, the Spark is the key insight or conceptual leap, and the Flip is the resulting counterproposal. HypoGen uniquely integrates an explicit Chain-of-Reasoning component that reflects the intellectual process from Bit to Flip. We demonstrate that framing hypothesis generation as conditional language modelling, with the model fine-tuned on Bit-Flip-Spark and the Chain-of-Reasoning (and where, at inference, we only provide the Bit), leads to improvements in the overall quality of the hypotheses. Our evaluation employs automated metrics and LLM judge rankings for overall quality assessment. We show that by fine-tuning on our HypoGen dataset we improve the novelty, feasibility, and overall quality of the generated hypotheses. The HypoGen dataset is publicly available at huggingface.co/datasets/UniverseTBD/hypogen-dr1.

  • 7 authors
·
Apr 17, 2025

Lying with Truths: Open-Channel Multi-Agent Collusion for Belief Manipulation via Generative Montage

As large language models (LLMs) transition to autonomous agents synthesizing real-time information, their reasoning capabilities introduce an unexpected attack surface. This paper introduces a novel threat where colluding agents steer victim beliefs using only truthful evidence fragments distributed through public channels, without relying on covert communications, backdoors, or falsified documents. By exploiting LLMs' overthinking tendency, we formalize the first cognitive collusion attack and propose Generative Montage: a Writer-Editor-Director framework that constructs deceptive narratives through adversarial debate and coordinated posting of evidence fragments, causing victims to internalize and propagate fabricated conclusions. To study this risk, we develop CoPHEME, a dataset derived from real-world rumor events, and simulate attacks across diverse LLM families. Our results show pervasive vulnerability across 14 LLM families: attack success rates reach 74.4% for proprietary models and 70.6% for open-weights models. Counterintuitively, stronger reasoning capabilities increase susceptibility, with reasoning-specialized models showing higher attack success than base models or prompts. Furthermore, these false beliefs then cascade to downstream judges, achieving over 60% deception rates, highlighting a socio-technical vulnerability in how LLM-based agents interact with dynamic information environments. Our implementation and data are available at: https://github.com/CharlesJW222/Lying_with_Truth/tree/main.

  • 5 authors
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Jan 4

Gated Linear Attention Transformers with Hardware-Efficient Training

Transformers with linear attention allow for efficient parallel training but can simultaneously be formulated as an RNN with 2D (matrix-valued) hidden states, thus enjoying linear (with respect to output length) inference complexity. Recent works such as RetNet (Sun et al., 2023) and TransNormerLLM (Qin et al., 2023a) observe that adding a global decay term to the additive RNN update rule greatly improves performance, sometimes outperforming standard Transformers with softmax attention when trained at scale. In this work we show that adding a data-dependent gating mechanism further improves performance. We derive a parallel form of this gated linear attention layer that enables efficient training. However, a straightforward, numerically stable implementation of this parallel form requires generalized matrix multiplications in log-space for numerical stability, and thus cannot take advantage of tensor cores on modern GPUs which are optimized for standard matrix multiplications. We develop a hardware-efficient version of the parallel form that can still make use of tensor cores through block-parallel computations over sequence chunks. Experiments on moderate-scale language modeling (340M-parameter models trained on 15B tokens, 1.3B-parameter models trained on 100B tokens) show that gated linear attention (GLA) Transformers perform competitively against a strong LLaMA-architecture Transformer baseline (Touvron et al., 2023) as well as Mamba (Gu & Dao, 2023), a recently introduced state-space model with a data-dependent state transition mechanism. For training speed, our Triton-based implementation performs comparably to CUDA-optimized FlashAttention-2 (Dao, 2023) under the regular 2048 training length setting, while outperforming FlashAttention-2 when training on longer sequences beyond 4096.

  • 5 authors
·
Dec 11, 2023 2

Towards Error Centric Intelligence I, Beyond Observational Learning

We argue that progress toward AGI is theory limited rather than data or scale limited. Building on the critical rationalism of Popper and Deutsch, we challenge the Platonic Representation Hypothesis. Observationally equivalent worlds can diverge under interventions, so observational adequacy alone cannot guarantee interventional competence. We begin by laying foundations, definitions of knowledge, learning, intelligence, counterfactual competence and AGI, and then analyze the limits of observational learning that motivate an error centric shift. We recast the problem as three questions about how explicit and implicit errors evolve under an agent's actions, which errors are unreachable within a fixed hypothesis space, and how conjecture and criticism expand that space. From these questions we propose Causal Mechanics, a mechanisms first program in which hypothesis space change is a first class operation and probabilistic structure is used when useful rather than presumed. We advance structural principles that make error discovery and correction tractable, including a differential Locality and Autonomy Principle for modular interventions, a gauge invariant form of Independent Causal Mechanisms for separability, and the Compositional Autonomy Principle for analogy preservation, together with actionable diagnostics. The aim is a scaffold for systems that can convert unreachable errors into reachable ones and correct them.

  • 1 authors
·
Oct 16, 2025

Induction Signatures Are Not Enough: A Matched-Compute Study of Load-Bearing Structure in In-Context Learning

Mechanism-targeted synthetic data is increasingly proposed as a way to steer pretraining toward desirable capabilities, but it remains unclear how such interventions should be evaluated. We study this question for in-context learning (ICL) under matched compute (iso-FLOPs) using Bi-Induct, a lightweight data rewrite that interleaves short directional copy snippets into a natural pretraining stream: forward-copy (induction), backward-copy (anti-induction, as a directional control), or a balanced mix. Across 0.13B-1B decoder-only models, we evaluate (i) few-shot performance on standard LM benchmarks and function-style ICL probes, (ii) head-level copy telemetry, and (iii) held-out perplexity as a guardrail. Bi-Induct reliably increases induction-head activity, but this does not translate into consistent improvements in few-shot generalization: on standard LM benchmarks, Bi-Induct is largely performance-neutral relative to natural-only training, while on function-style probes the 1B natural-only model performs best. Despite explicit backward-copy cues, anti-induction scores remain near zero across scales, revealing a strong forward/backward asymmetry. Targeted ablations show a sharper distinction: removing the top 2% induction heads per layer harms ICL more than matched random ablations, with the largest relative drop occurring in the natural-only models. This indicates that natural-only training produces more centralized, load-bearing induction circuitry, whereas Bi-Induct tends to create more distributed and redundant induction activity. Our main conclusion is that eliciting a mechanism is not the same as making it load-bearing. For data-centric foundation model design, this suggests that synthetic data interventions should be evaluated not only by signature amplification, but by whether they create causally necessary computation while preserving natural-data modeling quality.

  • 2 authors
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Mar 13

Why Do Reasoning Models Lose Coverage? The Role of Data and Forks in the Road

Recent progress in large language models has led to the emergence of reasoning models, which have shown strong performance on complex tasks through specialized fine-tuning procedures. While these methods reliably improve pass@1 accuracy, prior works have observed that they show a coverage shrinkage behavior, where pass@k degrades relative to the base model. In this paper, we investigate the reasoning shrinkage arise under SFT-based post-training. We hypothesize that this behavior is driven by properties of the fine-tuning data, specifically related to decision points or "forks in the road" scenarios where model faces indecipherable patterns with multiple valid reasoning paths. To test this hypothesis, we design controlled case studies that simulate such decision-point settings, spanning indecipherable nodes in graph branching, and reasoning modes. By tracking post-training dynamics in these settings, we find that the shrinkage phenomenon is tightly correlated with the prevalence of decision-point scenarios in the training data. We also demonstrate that this shrinkage behavior can be partially mitigated through targeted data synthesis design of decision-points, and a more systematic diversity-encouraging decoding mechanism. Our findings identify data-centric factors as a key driver of shrinkage in reasoning models and highlight diversity-aware designs as an effective lever for controlling it.

  • 7 authors
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May 15 1

Stemming Hallucination in Language Models Using a Licensing Oracle

Language models exhibit remarkable natural language generation capabilities but remain prone to hallucinations, generating factually incorrect information despite producing syntactically coherent responses. This study introduces the Licensing Oracle, an architectural solution designed to stem hallucinations in LMs by enforcing truth constraints through formal validation against structured knowledge graphs. Unlike statistical approaches that rely on data scaling or fine-tuning, the Licensing Oracle embeds a deterministic validation step into the model's generative process, ensuring that only factually accurate claims are made. We evaluated the effectiveness of the Licensing Oracle through experiments comparing it with several state-of-the-art methods, including baseline language model generation, fine-tuning for factual recall, fine-tuning for abstention behavior, and retrieval-augmented generation (RAG). Our results demonstrate that although RAG and fine-tuning improve performance, they fail to eliminate hallucinations. In contrast, the Licensing Oracle achieved perfect abstention precision (AP = 1.0) and zero false answers (FAR-NE = 0.0), ensuring that only valid claims were generated with 89.1% accuracy in factual responses. This work shows that architectural innovations, such as the Licensing Oracle, offer a necessary and sufficient solution for hallucinations in domains with structured knowledge representations, offering guarantees that statistical methods cannot match. Although the Licensing Oracle is specifically designed to address hallucinations in fact-based domains, its framework lays the groundwork for truth-constrained generation in future AI systems, providing a new path toward reliable, epistemically grounded models.

  • 2 authors
·
Nov 8, 2025 2

Can AI Validate Science? Benchmarking LLMs for Accurate Scientific Claim rightarrow Evidence Reasoning

Large language models (LLMs) are increasingly being used for complex research tasks such as literature review, idea generation, and scientific paper analysis, yet their ability to truly understand and process the intricate relationships within complex research papers, such as the logical links between claims and supporting evidence remains largely unexplored. In this study, we present CLAIM-BENCH, a comprehensive benchmark for evaluating LLMs' capabilities in scientific claim-evidence extraction and validation, a task that reflects deeper comprehension of scientific argumentation. We systematically compare three approaches which are inspired by divide and conquer approaches, across six diverse LLMs, highlighting model-specific strengths and weaknesses in scientific comprehension. Through evaluation involving over 300 claim-evidence pairs across multiple research domains, we reveal significant limitations in LLMs' ability to process complex scientific content. Our results demonstrate that closed-source models like GPT-4 and Claude consistently outperform open-source counterparts in precision and recall across claim-evidence identification tasks. Furthermore, strategically designed three-pass and one-by-one prompting approaches significantly improve LLMs' abilities to accurately link dispersed evidence with claims, although this comes at increased computational cost. CLAIM-BENCH sets a new standard for evaluating scientific comprehension in LLMs, offering both a diagnostic tool and a path forward for building systems capable of deeper, more reliable reasoning across full-length papers.

  • 6 authors
·
Jun 9, 2025

One-hot Generalized Linear Model for Switching Brain State Discovery

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

  • 5 authors
·
Oct 23, 2023

KG-TRACES: Enhancing Large Language Models with Knowledge Graph-constrained Trajectory Reasoning and Attribution Supervision

Large language models (LLMs) have made remarkable strides in various natural language processing tasks, but their performance on complex reasoning problems remains hindered by a lack of explainability and trustworthiness. This issue, often manifesting as hallucinations or unattributable reasoning processes, limits their applicability in complex reasoning scenarios. To address this, we propose Knowledge Graph-constrained Trajectory Reasoning Attribution and Chain Explanation Supervision (KG-TRACES), a novel framework that enhances the reasoning ability of LLMs through explicit supervision over reasoning paths and processes. KG-TRACES jointly supervises the model to: (1) predict symbolic relation paths, (2) predict full triple-level reasoning paths, and (3) generate attribution-aware reasoning processes grounded in the reasoning paths. At inference phase, the model adapts to both KG-available and KG-unavailable scenarios, retrieving reasoning paths from a KG when possible or predicting plausible reasoning paths with only intrinsic knowledge when not. This design enables the model to reason in an explainable and source-attributable pattern. Through extensive experiments on complex reasoning tasks, we demonstrate that KG-TRACES significantly outperforms existing SOTA: it improves Hits@1 by 1.6% and F1 by 4.7% on WebQSP, and achieves improvements of 4.8% in Hits@1 and 2.1% in F1 on CWQ. Moreover, we show its transferability to specialized domains such as medicine. By visualizing the intermediate steps of reasoning processes, we further show that the explicit supervision introduced by KG-TRACES leads to more stable and goal-directed reasoning processes, aligning closely with correct answers. Code is available at https://github.com/Edaizi/KG-TRACES.

  • 8 authors
·
May 31, 2025

Transfer Learning for Meta-analysis Under Covariate Shift

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.

  • 3 authors
·
Apr 5

Unveiling and Bridging the Functional Perception Gap in MLLMs: Atomic Visual Alignment and Hierarchical Evaluation via PET-Bench

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable proficiency in tasks such as abnormality detection and report generation for anatomical modalities, their capability in functional imaging remains largely unexplored. In this work, we identify and quantify a fundamental functional perception gap: the inability of current vision encoders to decode functional tracer biodistribution independent of morphological priors. Identifying Positron Emission Tomography (PET) as the quintessential modality to investigate this disconnect, we introduce PET-Bench, the first large-scale functional imaging benchmark comprising 52,308 hierarchical QA pairs from 9,732 multi-site, multi-tracer PET studies. Extensive evaluation of 19 state-of-the-art MLLMs reveals a critical safety hazard termed the Chain-of-Thought (CoT) hallucination trap. We observe that standard CoT prompting, widely considered to enhance reasoning, paradoxically decouples linguistic generation from visual evidence in PET, producing clinically fluent but factually ungrounded diagnoses. To resolve this, we propose Atomic Visual Alignment (AVA), a simple fine-tuning strategy that enforces the mastery of low-level functional perception prior to high-level diagnostic reasoning. Our results demonstrate that AVA effectively bridges the perception gap, transforming CoT from a source of hallucination into a robust inference tool and improving diagnostic accuracy by up to 14.83%. Code and data are available at https://github.com/yezanting/PET-Bench.

  • 17 authors
·
Jan 6

On the Step Length Confounding in LLM Reasoning Data Selection

Large reasoning models have recently demonstrated strong performance on complex tasks that require long chain-of-thought reasoning, through supervised fine-tuning on large-scale and high-quality datasets. To construct such datasets, existing pipelines generate long reasoning data from more capable Large Language Models (LLMs) and apply manually heuristic or naturalness-based selection methods to filter high-quality samples. Despite the proven effectiveness of naturalness-based data selection, which ranks data by the average log probability assigned by LLMs, our analysis shows that, when applied to LLM reasoning datasets, it systematically prefers samples with longer reasoning steps (i.e., more tokens per step) rather than higher-quality ones, a phenomenon we term step length confounding. Through quantitative analysis, we attribute this phenomenon to low-probability first tokens in reasoning steps; longer steps dilute their influence, thereby inflating the average log probabilities. To address this issue, we propose two variant methods: ASLEC-DROP, which drops first-token probabilities when computing average log probability, and ASLEC-CASL, which applies a causal debiasing regression to remove the first tokens' confounding effect. Experiments across four LLMs and five evaluation benchmarks demonstrate the effectiveness of our approach in mitigating the step length confounding problem.