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#machine learning Preprint Open access Sep 2026

Final Checkpoints Are Not Enough: Analyzing Latent Reasoning Faithfulness Along Training Trajectories

Latent reasoning performs multi-step inference in continuous hidden states, promising more compact and efficient reasoning. However, these opaque states raise a question of faithfulness: whether the latent reasoning steps drive the final answer. Prior work studies this question at selected checkpoints and reports several unfaithful behaviors. This endpoint view leaves how evidence of faithfulness evolves during training unexamined. We track behavioral and activation-based evidence across training using verified counterfactual edits and interventions on the latent reasoning states. We find that high task accuracy can coexist with low counterfactual responsiveness: as accuracy improves, responsiveness can decline, and different latent reasoning approaches follow distinct trajectories. On ProsQA, output sensitivity to norm-noise replacement declines alongside counterfactual responsiveness, although the result depends on the replacement. Across separately trained binary-choice and open-ended GSM settings, intervention sensitivity follows opposite trajectories. These results show that evaluating only a final checkpoint can obscure both when counterfactual responsiveness changes and what the latent states contribute.

Hengyu Jin, Shu Yang, Di Wang · 0 citations
#machine learning Preprint Open access Sep 2026

Beyond AHI: An Interpretable Causal-Discovery-Guided Framework for Sleep Recovery in Connected Health

Objective sleep assessment relies on polysomnography (PSG), yet clinical impact is often better reflected in patient-reported outcomes (PROs) such as sleepiness and fatigue. Existing summary indices, including the Apnea-Hypopnea Index (AHI), provide limited insight into the multidomain physiology underlying functional recovery. We propose an interpretable, causal-discovery-guided framework for deriving a hierarchical Sleep Recovery Score (SRS) from multimodal PSG. Using two large population cohorts (MESA: \(n=1{,}540\); MrOS: \(n=825\)), we apply directed acyclic graph (DAG) learning to identify candidate physiological drivers spanning respiratory burden, hypoxic burden, sleep fragmentation, sleep architecture, and autonomic regulation. Although derived from clinical PSG, these domains map naturally to sensing streams increasingly available in connected health technologies, including wearable ECG, oximetry, and sleep-stage estimation devices. To preserve mechanistic plausibility, we introduce a two-stage screening process that combines physiology-based constraints with constrained LLM-assisted auditing to identify and remove structural confounders and construct-overlapping variables. Across cohorts, these five domains emerge as recurrent physiological domains associated with recovery, and the resulting SRS shows up to \(3.4\times\) stronger alignment with perceived recovery than AHI. By linking multimodal sleep physiology to patient-centered outcomes through an interpretable, bias-aware, and domain-structured framework, this work provides a practical foundation for recovery modeling across both clinical sleep studies and emerging smart and connected health settings.

Saba A. Farahani, Elahe Khatibi, Manoj Vishwanath et al. · 0 citations
#machine learning Preprint Open access Sep 2026

Learning to Refine Hidden States for Reliable LLM Reasoning

Large language models show strong reasoning ability, but their internal reasoning process can remain unstable in complex multi-step settings, where early hidden-state errors may propagate to incorrect predictions. We propose ReLAR, a reinforcement-guided latent refinement framework that iteratively updates hidden representations before decoding. ReLAR maintains a compact latent reasoning state and uses learned depth and action controllers to adaptively determine both the number and direction of refinement steps. The controllers are trained with a policy gradient objective based on step-wise likelihood improvement, enabling efficient input-dependent reasoning without explicit chain-of-thought generation. Experiments on medical, mathematical, multi-hop reasoning, and open-ended generation benchmarks show that ReLAR improves accuracy, generation quality, and reasoning stability with substantially lower inference overhead than explicit reasoning baselines.

Chia-Hsuan Hsu, Jui-Ming Yao · 0 citations
#machine learning Preprint Open access Sep 2026

RECAP: Regression Evaluation for Continual Adaptation of Prompts

Production agentic systems routinely face evolving constraints and must comply from the very next interaction. Scenarios like a tool-call notification changing a compliance threshold or a policy update adding disclosure requirements fit this criteria, having close to no room for errors in production. This proactive adaptation setting is common in deployment, but absent from current benchmarks, which assume either static constraint sets or reactive protocols with evaluation feedback. We introduce RECAP, a benchmark that measures continual-learning phenomena (forgetting, regression, forward transfer) at the constraint level under a strictly proactive adapt-then-test protocol: prompt optimization methods receive only the constraint specification and must generalize before seeing any test data. Evaluating six methods across five LLMs and three schedules with evolving constraints, we find that these methods show no significant improvement in performance, even after incurring a higher latency. These methods, designed for offline or reactive settings, are inadequate for the proactive paradigm. Our work emphasizes the growing need for designing proactive prompt adaptation methods, where the models must remain robust to evolving needs in deployment.

Harsh Deshpande, Kushal Chawla, Sangwoo Cho et al. · 0 citations
#machine learning Preprint Open access Sep 2026

What Do Students Learn? A Feature-Level Analysis of Dark Knowledge

Knowledge Distillation (KD) is a powerful tool for model compression, yet the precise mechanisms by which student models acquire feature representations remain underexplored. In this work, we analyze student feature learning using the Interaction Tensor framework. Our analysis reveals that effective KD acts as a regularizer that prunes low-frequency, sample-specific features, encouraging the student to rely on a compact set of highly reusable features. Crucially, we observe that the dataset-level confusion matrix contains structural information analogous to the teacher's "Dark Knowledge." Leveraging this insight, we propose Confusion Distillation (CD), a teacher-free self-distillation method that utilizes the model's own evolving )confusion patterns as dynamic soft targets. CD achieves competitive performance on ResNet-34 and ResNet-50 for CIFAR-100, outperforming existing self-distillation methods like CS-KD and PS-KD by 1.2% while offering a computationally efficient alternative to standard KD.

Seungu Kang, Songkuk Kim · 0 citations
#machine learning Preprint Open access Sep 2026

PEARL: Training Socratic Tutors with Pedagogically Aligned Reinforcement Learning

Large Language Models (LLMs) show strong potential as educational tutors. Existing approaches typically train them to solve problems and provide correct answers, but this problem-solving-centered paradigm overlooks key requirements of effective tutoring: progressive guidance and the coordination of multiple pedagogical objectives across multi-turn interactions. Developing such tutors remains challenging because student behavior varies substantially with individual knowledge states, pedagogical effectiveness depends on multiple factors beyond final-answer correctness, and coordinating these objectives over tutor-student interactions is inherently difficult. To address these challenges, we propose PEARL, a PEdagogically Aligned Reinforcement Learning framework for training Socratic tutoring agents. First, we introduce a controllable student simulator that disentangles latent cognitive states from response generation, enabling simulation of diverse abilities and misconceptions. Second, we develop a pedagogically aligned reward model that jointly assesses pedagogical quality and objective correctness. Finally, we propose a stable multi-objective reinforcement learning approach that balances competing pedagogical objectives during tutor training. Experiments across multiple benchmarks show that PEARL performs competitively against tutoring-specific open-source systems and leading proprietary LLMs.

Qikai Chang, Zhenrong Zhang, Linbo Chen et al. · 0 citations
#machine learning Preprint Open access Sep 2026

Latent Recurrent Transformer: Architecture Exploration, Training Strategies, and Scaling Behavior

We study Latent Recurrent Transformer (LRT), a lightweight augmentation of autoregressive transformers that reuses a high-level source-layer hidden state from the previous token as recurrent memory for the next token. Because this state is already computed during ordinary decoding, LRT introduces a cross-token, cross-layer latent pathway while preserving the standard attention mechanism, KV-cache interface, and one model forward per generated token. To pretrain this recurrence without sequentially unrolling the full sequence, we introduce interleaved parallel training: one full-sequence initialization forward constructs a shared buffer, followed by sequential refinement of disjoint position subsets with parallel computation within each subset. This provides every token with recurrent-memory-aware supervision at approximately 2x ideal token compute. Across 1.3B- and 2.1B-parameter nanochat-style backbones and a wide range of training budgets, LRT improves both BPB and CORE under matched effective compute. Additionally, LRT outperforms two-forward PonderLM-2 and matches a three-loop Transformer in BPB, while retaining one-forward-per-token decoding with 9% latency overhead over the standard Transformer.

Zeyi Huang, Xuehai He, LiLiang Ren et al. · 0 citations
#machine learning Preprint Open access Sep 2026

LLM-driven design of physics-constrained constitutive models: two agents are better than one

Developing constitutive models that capture how materials deform under load traditionally requires years of specialized expertise in continuum mechanics, machine learning, and scientific programming. Large language models (LLMs) have recently been shown to lower this barrier by generating constitutive models on demand, but existing single-agent pipelines lack systematic checks that the resulting models respect fundamental physical laws. To close this gap, we introduce the first multi-agent LLM-driven approach for constitutive model generation: a Creator agent proposes a model tailored to the data, while an Inspector agent critically audits each proposal against nine physical constraints and returns it for refinement whenever a violation is detected. We demonstrate this concept with constitutive artificial neural networks (CANNs) and benchmark it on brain tissue and rubber as isotropic materials, and on porcine skin tissue as a transversely isotropic material with a preferred fiber direction, using two different LLM backbones (Claude Opus 4.7 and Kimi K2.5). Whether a generated model satisfies the physical constraints is assessed numerically, by probing each constraint across a broad sample of deformation states, rotations, and perturbation directions. Adding the Inspector raises the share of exported models that pass all these checks from 90\% to 95\% for Opus and from 47\% to 60\% for Kimi. In addition, the generated models are on par with or even surpass expert-designed models in accuracy, extrapolate reliably beyond the training data, and generalize remarkably well to unseen loading paths. Separating generation from inspection thus turns LLM-driven constitutive modeling into a substantially more trustworthy process. The paradigm is deliberately technique-agnostic...

Marius Tacke, Matthias Busch, Kian Abdolazizi et al. · 0 citations
#machine learning Preprint Open access Sep 2026

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 cause of reasoning shrinkage 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 encounters 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. (Data and code for reproducing our experiments are available at https://github.com/psunlpgroup/reasoning_forks )

Ngoc-Hieu Nguyen, Parshin Shojaee, Phuc Minh Nguyen et al. · 0 citations
#machine learning Preprint Open access Sep 2026

Reparameterization through Coverings and Topological Weight Priors

We generalise the reparameterization trick (RT) applied in variational autoencoders (VAEs) letting these have latent spaces of non-trivial topology - i.e. that of base manifolds covered with other ones, on which some technique for RT is available. That is possible since covering maps are measurable - moreover, this allows to establish an inequality on KL-divergence between pushforward (PF) densities on the base latent manifold, bounding it with KL-divergence between pullbacks on the cover, in some cases making the KL-term of VAE's ELBO analytically tractable, despite the topological non-triviality of the supporting latent manifold. Our development follows a route close but somewhat alternative to reparameterization on Lie groups, the latest proposal for which is to reparameterize PFs of normal densities from the Lie algebra - "through" the exponential map, seen by us as a particular case of what we propose to call reparameterization via covering (RVC). We demonstrate the working of our approach by constructing a VAE with the latent space of Klein bottle (not a Lie group) topology, which we call KleinVAE, successfully learning an appropriate artificial dataset. We discuss potential applicability of such topology-informed generative models as weight priors in Bayesian learning, particularly for convolutional vision models, where said manifold was peculiarly shown to have some relevance.

Maxim Beketov, Pavel Snopov · 0 citations
#machine learning Preprint Open access Sep 2026

Process-Aware AI for Rainfall-Runoff Modeling: A Mass-Conserving Neural Framework with Hydrological Process Constraints

Machine learning models can achieve high predictive accuracy in hydrological applications but often lack physical interpretability. The Mass-Conserving Perceptron (MCP) provides a physics-aware artificial intelligence (AI) framework that enforces conservation principles while allowing hydrological process relationships to be learned from data. In this study, we investigate how progressively embedding physically meaningful representations of hydrological processes within a single MCP storage unit improves predictive skill and interpretability in rainfall-runoff modeling. Starting from a minimal MCP formulation, we sequentially introduce bounded soil storage, state-dependent conductivity, variable porosity, infiltration capacity, surface ponding, vertical drainage, and nonlinear water-table dynamics. The resulting hierarchy of process-aware MCP models is evaluated across 15 catchments spanning five hydroclimatic regions of the continental United States using daily streamflow prediction as the target. Results show that progressively augmenting the internal physical structure of the MCP unit generally improves predictive performance. The influence of these process representations is strongly hydroclimate dependent: vertical drainage substantially improves model skill in arid and snow-dominated basins but reduces performance in rainfall-dominated regions, while surface ponding has comparatively small effects. The best-performing MCP configurations approach the predictive skill of a Long Short-Term Memory benchmark while maintaining explicit physical interpretability. These results demonstrate that embedding hydrological process constraints within AI architectures provides a promising pathway toward interpretable and process-aware rainfall-runoff modeling.

Mohammad A. Farmani, Hoshin V. Gupta, Ali Behrangi et al. · 0 citations
#machine learning Preprint Open access Sep 2026

Rigorous Error Certification for Neural PDE Solvers: From Empirical Residuals to Solution Guarantees

Uncertainty quantification for partial differential equations is traditionally grounded in discretization theory, where solution error is controlled via mesh/grid refinement. Physics-informed neural networks fundamentally depart from this paradigm: they approximate solutions by minimizing residual losses at collocation points, introducing new sources of error arising from optimization, sampling, representation, and overfitting. As a result, the generalization error in the solution space remains an open problem. Our main theoretical contribution establishes generalization bounds that connect residual control to solution-space error. We prove that when neural approximations lie in a compact subset of the solution space, vanishing residual error guarantees convergence to the true solution. We derive deterministic and probabilistic convergence results and provide certified generalization bounds translating residual, boundary, and initial errors into explicit solution error guarantees.

Amartya Mukherjee, Maxwell Fitzsimmons, David C. Del Rey Fern\'andez et al. · 0 citations

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MIT News · Artificial Intelligence Aug 27, 2026

Looking beyond natural sequences

A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.

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