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01.
arXiv (CS.LG) 2026-06-17

Constrained Diffusion Models with Primal-Dual Inference

arXiv:2606.17192v1 Announce Type: new Abstract: This paper develops constrained diffusion models with primal-dual inference (PDI) to sample from optimal distributions of entropy-regularized optimization problems with average constraints. We formalize constrained sampling in the Lagrangian dual domain, where the optimal distribution takes the form of a Gibbs distribution indexed by the optimal dual variable. Rather than estimating this dual multiplier before sampling and freezing it throughout generation, PDI jointly infers the optimal primal distribution and its parametrizing dual variable. Each reverse diffusion step denoises using the score field associated with the current multiplier and then updates the multiplier through dual ascent using the estimated constraint violation of the denoised samples. To enable this conditional score field, we train a single dual-conditioned score network over the family of Gibbs distributions induced by the dual variables encountered during inference. We prove that the time average of the dual variables generated along the inference trajectory converges to a neighborhood of the dual optimum and bound the effect of residual dual mismatch on the terminal distribution through schedule-dependent stability factors. We evaluate PDI on constrained sampling from a mixture of Gaussians, wireless resource allocation, and portfolio management.

02.
arXiv (CS.CL) 2026-06-15

ClaimFlow: Tracing the Evolution of Scientific Claims in NLP

Scientific papers advance $claims$ that later work supports, extends, or sometimes refutes. Yet existing methods for citation and claim analysis capture only fragments of this dialogue. In this work, we make these interactions explicit at the level of individual scientific claims. We introduce $\texttt{ClaimFlow}$, a claim-centric view of the NLP literature, built from $1{,}617$ ACL Anthology papers $(1979 - 2025)$ that are manually annotated with $5{,}689$ claims and $4{,}871$ cross-paper claim relations, indicating whether a citing paper $\texttt{supports}$, $\texttt{extends}$, $\texttt{qualifies}$, $\texttt{refutes}$, or references a cited claim as $\texttt{background}$. Building on $\texttt{ClaimFlow}$, we define a new task – $Claim Relation Classification$ – which requires models to infer the scientific stance toward a cited claim from the text and citation context. Evaluating neural models and large language models on this task, we report baseline performance of $0.81$ macro-F1, suggesting that the task is tractable while leaving room for improvement. We then scale this framework to $\sim$$13k$ NLP papers to study claim evolution across decades of NLP research. We show that $63.5\%$ claims are never reused; only $11.1\%$ are ever challenged. Widely propagated claims are more often $reshaped$ through qualification and extension than supported or refuted. Overall, $\texttt{ClaimFlow}$ offers a lens for examining how ideas shift and mature within NLP.

03.
arXiv (CS.AI) 2026-06-12

Boosting Direct Preference Optimization with Penalization

作者:

arXiv:2606.12505v1 Announce Type: cross Abstract: Offline preference optimization has become a practical substitute for reinforcement learning from human feedback, but pairwise objectives such as Direct Preference Optimization (DPO) and its variants use only the chosen and rejected responses stored in a static dataset. This leaves a useful signal unused: the response that the reference model itself would generate for the same prompt. We propose Direct Preference Optimization with Penalization (DPOP), a simple extension of DPO that augments the base preference loss with a gated penalty on reference-greedy responses. DPOP activates this penalty only when the current policy still assigns a lower likelihood to the preferred response than to the rejected response. On AlpacaEval 2.0, DPOP improves length-controlled win rate over DPO, SimPO, and AlphaDPO on both Llama-3-8b-it and Gemma-2-9b-it, achieving relative gains of 5.3\% and 4.4\% over baselines on the two models, respectively. Ablations further show that a SimNPO-style length-normalized penalty is stronger than NPO and token-level unlikelihood in this setting.

04.
arXiv (CS.AI) 2026-06-12

scLLM-DSC: LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering for Single-Cell RNA Sequencing

arXiv:2606.13007v1 Announce Type: cross Abstract: Clustering is fundamental to scRNA-seq analysis, serving as a cornerstone for identifying cell populations and resolving tissue heterogeneity. However, existing methods focus on mining numerical statistical patterns, suffering from semantic agnosticism by neglecting the intrinsic biological functions encoded by genes. While Large Language Models (LLMs) offer promising semantic capabilities, their direct adaptation to cell clustering is hindered by the structural mismatch between generative pre-training objectives and discriminative downstream tasks. To bridge this gap, we propose scLLM-DSC, a novel LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering framework. Diverging from data-driven paradigms, scLLM-DSC establishes a semantically-grounded representation by synergizing two views: a Knowledge-Driven Semantic View derived from NCBI gene priors and contextualized Cell2Sentence embeddings, and a Structure-Aware Topological View extracted via a graph-guided encoder. Crucially, we introduce a cross-modal contrastive alignment mechanism to enforce consistency between biological semantics and transcriptomic features within a unified latent space. Extensive benchmarks demonstrate that scLLM-DSC significantly outperforms eleven state-of-the-art baselines in clustering accuracy.

05.
arXiv (CS.LG) 2026-06-15

SemPiper: Interactive Code Synthesis for Semantic Operators in Machine Learning Pipelines

arXiv:2606.14361v1 Announce Type: new Abstract: Machine learning (ML) pipelines require extensive data preparation, feature engineering, and integration across heterogeneous sources, making them tedious and error-prone to develop. While large language models (LLMs) have recently shown promise for assisting programming tasks, chat-based interfaces provide limited control over pipeline behavior and often produce code that is difficult to optimize or integrate into production systems. We demonstrate SemPipes, a novel programming model that extends ML pipelines with declarative, LLM-powered semantic data operators. SemPipes allows developers to specify high-level natural language instructions for data-centric operations, while seamlessly combining these operators with arbitrary Python code from standard data science libraries. For the semantic operators, it synthesizes specialized implementations at pipeline training time, conditioned on dataset characteristics and pipeline context, enabling the flexible yet controlled integration of LLM capabilities. We demonstrate SemPipes through SemPiper, an interactive interface that visualizes computational graphs of the pipelines, synthesized operator implementations, and optimization trajectories produced by an evolutionary search procedure. Attendees can explore three end-to-end scenarios, modify pipelines, inspect generated code, and observe how semantic operators are synthesized and iteratively optimized. The demonstration highlights how declarative semantic operators enable controllable, optimizable, and practical integration of LLMs into ML pipeline development.

06.
arXiv (CS.AI) 2026-06-18

SAE Interventions are Unreliable: Post-Intervention Recovery of Suppressed Behavior

arXiv:2606.18322v1 Announce Type: cross Abstract: Sparse Autoencoders (SAEs) decompose residual-stream activations into interpretable features. Recent latent-space defenses increasingly rely on these decompositions, assuming that identified "unsafe" SAE features serve as actionable handles for monitoring and intervention. In this paradigm, clamping a specific harmful feature is expected to reliably prevent model misbehavior. However, we show that this success may hide a recoverable failure mode: the clamp may block one visible route to a behavior without eliminating the behavior itself. We formulate this vulnerability as post-intervention recovery, a constrained residual-space optimization problem. Starting from the post-intervention residual state, we optimize residual perturbations to recover the pre-intervention behavior while preserving the post-intervention values of the targeted SAE features. Even under a strong threat model where the intervention remains active throughout optimization and generation, recovery remains possible. To rule out that recovery simply undoes the intervention, we use encoder-orthogonal updates for single-layer interventions and the corresponding feature-map Jacobian in the cross-layer setting. Across TPP, unlearning, IOI, and refusal steering experiments, this stress test reveals recoverable behavior despite successful feature-level intervention. Especially in the safety-critical refusal-steering setting, we achieve a 95.8% recovery rate on valid samples while keeping defended-feature relative drift to 0.131, substantially below suffix-based baselines. A recovery-path attribution analysis further localizes this recovery to the SAE reconstruction residual, the component left unexplained by the SAE. These results expose a gap between feature-level control and behavioral completeness: SAE features can support causal intervention, but controlling them does not guarantee control over the underlying behavior.

07.
arXiv (CS.LG) 2026-06-12

Fed-FBD: Federated Functional Block Diversification for Isolation, Privacy, and Surgical Unlearning

arXiv:2606.12679v1 Announce Type: new Abstract: Federated learning (FL) enables collaborative model training without sharing raw patient data, but standard approaches such as FedAvg treat each client as a black box and provide no mechanism for isolating an adversarial contributor, auditing per-client influence, or honoring a departed participant's right to be forgotten. We present Fed-FBD (Federated Functional Block Diversification), a modular federated architecture that decomposes a ResNet backbone into six functional blocks (the stem, four residual groups, and the classification head) and maintains a warehouse of N color variants, each assembled from independently tracked and contributor-stamped blocks. Fed-FBD provides three capabilities absent in FedAvg: (i) architecturally guaranteed block-level isolation, so that an adversarial or mislabelled client cannot contaminate the clean colous; (ii) privacy-by-design, where membership inference advantage is already indistinguishable from chance before any privacy mechanism is applied; and (iii) surgical machine unlearning of a departed participant's contribution at sub-second cost and without retraining. Experiments on six MedMNIST-2D datasets, PathMNIST at 224x224, and CIFAR-10 show that Fed-FBD trades a modest 0.3%-3.1% IID accuracy gap on the adequately sized datasets for these guarantees, remains within 0.8%-4.0% of FedAvg at Dirichlet alpha=1.0 on three of four datasets, and confines all six adversarial attacks we study to the poisoned client's own blocks with at most +/-0.01 AUC drift on the clean colors.

08.
arXiv (CS.CV) 2026-06-12

ECA: Efficient Continual Alignment for Open-Ended Image-to-Text Generation

Incremental Learning (IL) for Open-ended Image-to-Text Generation (OpenITG) enables models to continuously generate accurate, contextually relevant text for new images while preserving previously acquired knowledge. Unlike prior studies, this paper addresses a more practical scenario in which the predominant category of visual data shifts over time as environments evolve. In this context, we introduce a new notion of continual alignment, which incrementally adapts the alignment module within pre-trained VLMs to preserve high-quality cross-modal representations. Based on this idea, we propose Efficient Continual Alignment (ECA), a novel exemplar-free IL approach for OpenITG. The key challenge is enabling the model to acquire new, task-specific features while minimizing interference with the established alignment without accessing raw data from previous tasks. To address this, ECA employs three core mechanisms: a Mixture of Query (MoQ) module that adapts task-specific query tokens, a Fisher Dynamic Expansion (FeDEx) that dynamically expands model structure based on a Fisher Information Matrix (FIM)-based metric, and an embedding dictionary with Dictionary Replay (DR) to retain past knowledge. To evaluate ECA's performance, we construct four new IL OpenITG benchmarks that better reflect real-world scenarios. Experimental results demonstrate that ECA significantly mitigates catastrophic forgetting and improves IL performance compared to baseline methods. Code and benchmarks are available at https://github.com/Snowball0823/ECA.

09.
arXiv (CS.LG) 2026-06-15

Recovery thresholds for hidden weighted sparse graphs

arXiv:2606.14335v1 Announce Type: cross Abstract: Recovering structural information from noisy high-dimensional data is a fundamental task in statistical inference. We investigate the recovery thresholds for a graph hidden in a randomly weighted complete graph. Specifically, an unknown graph $H^* \in H_n$ is chosen uniformly at random, and hidden in a complete graph of $n$ vertices as follows: the weight of an edge $e \in H$ is distributed independently according to $P_n$; otherwise the weight is distributed independently according to $Q_n$. The goal is to recover almost all of $H$ from these edge weights. Assuming a local Lipschitzness of the Rényi divergence between distributions $P_n$ and $Q_n$, and a mild density condition for the graphs $H_n$, we give a unified characterization of the information-theoretic limit for recovering almost all of $H$ (also known as almost exact recovery). Our characterization connects the KL divergence between $P_n$ and $Q_n$ to the logarithm of the first moment threshold of $H$ in the Erdős-Rényi random graph model $G(n,p)$. Our lower bound also extends to the task of partial recovery, in which only a constant $\lambda$-fraction of $H$ needs to be recovered. Last but not least, for certain Bernoulli and Exponential regimes, and for Gaussian distributions, we are able to show an All-or-Nothing (AoN) threshold phenomenon at the exponential scale.

10.
arXiv (CS.CV) 2026-06-17

Enhancing Pathological VLMs with Cross-scale Reasoning

Pathological images are inherently multi-scale, requiring pathologists to integrate evidence from global tissue architecture at low magnification to cellular morphology at higher magnification for accurate diagnosis. While existing pathological datasets for vision-language model (VLM) include various scales, they often lack an explicit cross-scale reasoning objective. This limitation prevents VLMs from capturing essential cross-scale representations and learning evidence-based reasoning. To bridge this gap, we introduce the first cross-scale training and evaluation paradigm that formulates pathology interpretation as multi-magnification reasoning. However, creating such a task reveals a critical challenge: multi-image visual question answering (VQA) is prone to text-only shortcuts, which allow models to guess answers using magnification-dependent artifacts rather than visual evidence. To address this, we propose a leakage-aware curation pipeline that combines adversarial text-only screening with constraint-guided question design. Using this pipeline, we construct Scale-VQA, a high-quality benchmark with 4,685 multiple-choice questions grounded in 2,537 pathology images across multiple magnification levels. Finally, we present ScaleReasoner-R1, a model trained via reinforcement learning to optimize performance on the cross-scale VQA task. ScaleReasoner-R1 achieves state-of-the-art performance on our cross-scale reasoning benchmark and generalizes to SOTA performance on established single-scale benchmarks. Findings suggest that even the limited cross-scale supervision can significantly improve pathological understanding. The code and demos will be open-sourced.

11.
arXiv (quant-ph) 2026-06-17

Demonstration of Exponential Quantum Speedup with Constant-Depth Compiled Circuits for Simon's Problem

arXiv:2604.27457v2 Announce Type: replace Abstract: We demonstrate exponential algorithmic quantum speedup for a restricted-Hamming-weight version of Simon's problem, in which the hidden string $b$ is promised to satisfy $HW(b)\le w$ for a Hamming-weight cutoff $w$, on present-day superconducting quantum processors. We introduce a hardware-aware compilation strategy that reduces the quantum part of each Simon query circuit to constant depth. The resulting compiled circuits have $O(1)$ depth, require only linear nearest-neighbor connectivity, map directly onto common device layouts, and avoid additional routing and SWAP overhead. Implemented on IBM's $156$-qubit Boston and $120$-qubit Miami processors, these circuits achieve sufficient fidelity to exhibit algorithmic quantum speedup without error suppression. Using the number-of-queries-to-solution (NTS) metric, we observe exponential speedup over the classical lower-bound benchmark for all restricted-Hamming-weight cutoffs $w\ge 4$ on Boston and across low-to-intermediate Hamming-weight cutoffs on Miami; at higher Hamming-weight cutoffs on Miami, we still observe polynomial speedup. The same construction also enables unrestricted instances of Simon's problem, corresponding to $w=n$ for problem size $n$, over the finite problem-size ranges for which our NTS computation is feasible; in this regime, the observed scaling advantage is not limited to the restricted-Hamming-weight setting. These results show that careful hardware-aware compilation can make quantum speedup experimentally accessible for a canonical hidden-subgroup problem in the NISQ regime.

12.
medRxiv (Medicine) 2026-06-18

Entrainment of cortical gamma oscillations predicts improved bradykinesia and dyskinesia in Parkinson's disease

Background: Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is hypothesized to improve motor symptoms in Parkinson's disease (PD) by suppressing pathologically elevated beta activity and promoting "prokinetic" gamma activity in the cortico-basal ganglia-thalamo-cortical loop. Advances in bidirectional DBS devices have revealed that stimulation can modify gamma oscillations via subharmonic entrainment, though entrainment's therapeutic role remains unclear. Objectives: To identify stimulation parameters that entrain motor cortical and STN gamma oscillations in PD at rest and during movement, and examine their association with motor function. Methods: Sensorimotor cortex and STN field potentials were collected using a bidirectional DBS system in four subjects with PD over a range of stimulation amplitudes and frequencies. Entrainment amplitude at half the stimulation frequency was quantified at rest and during a finger-tapping task in the ON-medication state. The presence or absence of entrainment was studied as a physiomarker of motor symptom severity. Results: The amplitude of stimulation-entrained gamma oscillations was non-linearly related to stimulation intensity and frequency and varied by stimulation contact choice. Entrainment amplitude was highest in precentral gyrus and increased with movement. In the ON-medication state, precentral gyrus gamma entrainment was associated with reduced bradykinesia, dyskinesia, and dystonia. Subthalamic gamma entrainment predicted improved dystonia but was a less significant marker for motor benefit than cortical entrainment. Conclusions: Stimulation-entrained gamma oscillations in the motor network are a physiomarker for optimal DBS response in PD, and could have a role in physiology-guided DBS programming, complementing existing strategies based on suppression of basal ganglia beta activity.

13.
arXiv (math.PR) 2026-06-16

Hua-Chen New Theory of Economic Optimization

arXiv:2504.19134v4 Announce Type: replace-cross Abstract: Between 1957-1985, Chinese mathematician Loo-Keng Hua pioneered economic optimization theory through three key contributions: establishing economic stability's fundamental theorem, proving the uniqueness of equilibrium solutions in economic systems, and developing a consumption-integrated model 50 days before his death. Since 1988, Mu-Fa Chen has been working on Hua's theory. He introduced stochastics, namely Markov chains, to economic optimization theory. He updated and developed Hua's model and came up with a new model (Chen's model) which has become the starting point of a new economic optimization theory. Chen's theory can be applied to economic stability test, bankruptcy prediction, product ranking and classification, economic prediction and adjustment, economic structure optimization. Chen's theory can also provide efficient algorithms that are programmable and intelligent. {Stochastics} is the cornerstone of Chen's theory. There is no overlap between Chen's theory, and the existing mathematical economy theory and the economics developments that were awarded Nobel Prizes in Economics between 1969 and 2024. The distinguished features of Chen's theory from the existing theories are quantitative, calculable, predictable, optimizable, programmable and can be intelligent. This survey provides a theoretical overview of the newly published monograph [5rw24]. Specifically, the invariant of the economic structure matrix, also known as the Chen's invariant, was first published in this survey.

14.
arXiv (CS.AI) 2026-06-11

Reinforcement Learning Disrupts Gradient-Based Adversarial Optimization

arXiv:2606.12251v1 Announce Type: cross Abstract: Gradient-based adversarial attacks remain a dominant threat to deep neural networks (DNNs), as they exploit gradient information to efficiently optimize adversarial perturbations. To address this, we investigate whether reinforcement learning (RL) training can disrupt the gradient structure used by attackers by training image classifiers with policy-gradient objectives and epsilon-greedy exploration. Through systematic experiments across CIFAR-10, CIFAR-100, and ImageNet-100 with multiple architectures, we find that RL-trained classifiers significantly disrupt gradient-based adversarial optimization. To explain this, we conduct a comprehensive mechanism analysis using loss landscape visualization, static and dynamic gradient indicators, and predictive entropy. Our analysis reveals that RL acts as an implicit regularizer, producing models with highly unstable gradient directions and smaller gradient magnitudes. This combination makes each PGD step both unreliable in direction and limited in magnitude, causing gradient-based attacks to fail within practical iteration budgets. We further show that combining RL with adversarial training (RL-adv) provides a dual-layer defense operating at two complementary levels: RL degrades gradient information available to attackers (gradient-level defense), while adversarial training strengthens decision boundaries (boundary-level defense). RL-adv achieves the highest robustness across all major attack types evaluated, including gradient-based (PGD, AutoAttack), transfer-based, and query-based attacks, outperforming SL-adv by a significant margin. These findings identify RL-induced gradient disruption as a complementary robustness mechanism and motivate future research on hybrid SL-RL training schedules that combine SL's efficiency with RL's gradient-regularization properties.

15.
arXiv (CS.AI) 2026-06-16

Let Them Steal: Trapping Large Language Model Extraction Attacks with Knowledge Honeypot

arXiv:2606.15810v1 Announce Type: cross Abstract: Large language models deployed as commercial APIs are vulnerable to model extraction attacks, while existing defenses either act too late or degrade utility for legitimate users. We propose Knowledge Trap, a defense that redirects extraction attacks toward low-transferability knowledge through a Honeypot Knowledge Graph (HKG) and breadcrumb-guided exploration. Instead of blocking queries or perturbing outputs, Knowledge Trap consumes the attacker's limited query budget on knowledge with negligible downstream utility while preserving benign-user performance. Experiments in medical and financial domains show that Knowledge Trap reduces surrogate Agreement by 6.2\% on average without degrading legitimate-user accuracy, outperforming existing defenses that impose measurable user impact. These results suggest that defending knowledge-space traversal is a practical direction for mitigating LLM extraction attacks.

16.
PLOS Computational Biology 2026-06-03

IsoPepTracker: An interactive web application for peptide-driven isoform analysis

作者:

by Araf Mahmud, Chen Huang Alternative splicing affects 95% of multi-exon genes, generating protein isoforms with distinct functions. While current alternative splicing analyses effectively identify splice events at the RNA level, they provide limited protein-level insight. To address this gap, we developed IsoPepTracker (https://www.isopeptracker.org), a user-friendly web application for analyzing and visualizing differential peptides across canonical and novel isoforms that are theoretically detectable by shotgun mass spectrometry-based proteomics. IsoPepTracker features four modules: Canonical Isoform Analysis, Novel Isoform Discovery, Peptide Sequence Search, and Alternative Splicing Analysis. Each module is tailored for distinct and complementary proteogenomics analyses. Users can input genes, novel cDNA sequences, peptides, or alternative splicing results to pinpoint peptides of interest and identify their associations with target genes or isoforms. We demonstrate the straightforward application of IsoPepTracker in proteogenomics through case studies. IsoPepTracker not only provides informative peptide signatures to understand the protein-level consequences of alternative splicing but also supplies peptide candidates for validation in shotgun proteomics.

17.
arXiv (CS.CL) 2026-06-19

Large Language Models Hack Rewards, and Society

Reinforcement learning (RL) has become a dominant post-training paradigm, enabling large language models (LLMs) to learn from rewards. We observe that societal regulations are structurally similar to reward functions. They define measurable outcomes, thresholds, and exceptions, while often leaving institutional intent only partially specified. We hypothesise that the RL training process may exploit these gaps and therefore ask whether models' well-known tendency to hack reward functions during RL can scale into a more consequential failure mode named societal hacking: discovering loopholes in the rules society runs on. To study this phenomenon, we introduce SocioHack, a sandbox of 72 societal environments, and find that within these environments, reward hacking naturally emerges and leads to regulatory loophole discovery. Models learn to hack the social rules and generate strategies that remain technically compliant while defeating regulatory intent, and current LLM safeguards provide only limited mitigation. Therefore, collecting in-the-wild feedback for model training requires greater caution, and we need a next-generation post-training paradigm for safely iterating LLMs in real society.=

18.
arXiv (CS.AI) 2026-06-16

From Agent Traces to Trust: A Survey of Evidence Tracing and Execution Provenance in LLM Agents

arXiv:2606.04990v2 Announce Type: replace-cross Abstract: Large language model (LLM)-based agents are evolving from passive text generators into autonomous systems capable of planning, tool use, retrieval, memory access, environmental interaction, and multi-agent collaboration. These capabilities expand agent autonomy, but also make agent behavior harder to verify, debug, and audit. Final-answer accuracy alone cannot explain how an output was produced, which evidence supported each claim, whether tool calls were justified, how memory influenced later decisions, or where failures originated. This survey examines evidence tracing and execution provenance as foundations for process-level accountability in trustworthy LLM agents. We define execution provenance as the typed graph of an agent execution and evidence tracing as its projection onto evidence-support relations. This perspective connects retrieval grounding, claim support, tool-use safety, memory lineage, observability, debugging, audit, and recovery within a unified framework. We introduce a taxonomy covering trace sources, evidence and execution units, provenance relations, tracing granularity and timing, representation forms, and trust functions. We then review key methodological directions, including provenance representation, evidence attribution, tool-use provenance, runtime guardrails, provenance-bearing memory, observability, and failure diagnosis. Finally, we discuss benchmarks, datasets, metrics, and open challenges for building provenance-aware, auditable, and recoverable agent systems.

19.
PLOS Computational Biology 2026-06-11

Robust discovery of mutational signatures using power posteriors

by Catherine Xue, Jeffrey W. Miller, Scott L. Carter, Jonathan H. Huggins Mutational processes, such as the molecular effects of carcinogenic agents or defective DNA repair mechanisms, produce different mutation types with characteristic frequency profiles, known as mutational signatures. Non-negative matrix factorization (NMF) has been successfully used to discover many mutational signatures, yielding novel insights into cancer etiology and informing targeted therapies. However, the NMF model is only a rough approximation to reality, and even small departures from this assumed model can have large negative effects on the accuracy and reliability of the results. We propose BayesPowerNMF, a Bayesian NMF method that provides nonparametric robustness to model misspecification, principled automated selection of the number of latent processes, and uncertainty quantification of model parameters. In extensive simulation studies, we find that our proposed approach recovers more true signatures with greater accuracy than current leading methods. On whole-genome sequencing data for six cancer types from the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, we find that our method is able to accurately recover more signatures than the current state-of-the-art.

20.
arXiv (CS.CL) 2026-06-19

A Survey of On-Policy Distillation for Large Language Models

As Large Language Models continue to grow in both capability and cost, transferring frontier capabilities into smaller, deployable students has become an important engineering problem, and knowledge distillation remains a common technique for this transfer. The prevailing recipe in industrial pipelines, static imitation of teacher-generated text, carries a structural weakness that grows more severe as tasks become longer and more reasoning-intensive. Because the student is trained on flawless teacher prefixes but generates its own at inference, small errors tend to accumulate into trajectories it has rarely been trained to recover from, and the resulting exposure bias has been shown to scale roughly with the square of sequence length. On-Policy Distillation reorganizes the training loop around this observation by having the teacher provide feedback on what the student actually produces, with the goal of reducing the compounding term toward linear and reframing distillation as an iterative correction process rather than single-pass imitation. The resulting literature has expanded along divergence design, reward-guided optimization, and self-play, yet contributions remain scattered across the knowledge distillation, RLHF, and imitation learning communities without a unified treatment. This survey provides such a treatment. We formalize OPD as f-divergence minimization over student-sampled trajectories, organize the field along three design axes (what to optimize, where the signal comes from, and how to stabilize training in practice), and consolidate success conditions, recurring failure modes, and the connection between OPD and KL-constrained reinforcement learning. We close with open problems that emerge from this synthesis, including distillation scaling laws, uncertainty-aware feedback, agent-level distillation, and the growing overlap between knowledge distillation and RL.

21.
bioRxiv (Bioinfo) 2026-06-11

EditorForge: An Active-Site-Aware Framework for Inverse-Folding-Based Protein Redesign

Inverse-folding models can rapidly generate protein sequences compatible with a supplied backbone, but unconstrained redesign is poorly suited to enzyme and genome-editor-associated domains, where catalytic, substrate-proximal, and conserved structural regions must remain protected. In this paper, we present EditorForge, a modular constraint-and-audit suite for editor-domain protein redesign that wraps fixed-backbone inverse folding with explicit design masks, fixed-position enforcement, active-site-proximity auditing, active-site-shielded regeneration, and downstream structural quality control. Using full-length Moloney murine leukemia virus reverse transcriptase structure 4MH8 (MMLV RT 4MH8) as a demonstration target, EditorForge first restricted redesign to a bounded 25-position envelope while fixing 428 residues. An initial audit detected active-site-proximal failure modes despite fixed-position integrity. Later, the Active Site Shield module then removed five unsafe design positions, replaced them with lower-contact alternatives, and regenerated candidates under stricter constraints. Post Shield Audit evaluated 24 regenerated candidates, all of which satisfied the hard sequence/mask and active-site-shield constraints. For the eight candidates that were selected or returned for structure-prediction/refolding quality control. Enhanced RefoldQC found that all 8 evaluated predicted structures passed the computational structure-QC screen. That said, the selected 8 candidates passed the computational structure-QC screen, with global C RMSD values of 1.2061–1.5555~[A], active-site C RMSD values of 0.4098–1.8397~[A], mutation-neighborhood C RMSD values of 1.3155-1.6848~[A], and average pLDDT-like confidence values of 94.87-95.11. In short, EditorForge provides a reproducible triage layer that converts general inverse-folding output into constrained and editor-specific candidate sets for downstream structural and biological review on top of existing structural prediction tools.

22.
arXiv (CS.AI) 2026-06-19

CTS-MoE: Implicit Terrain Adaptation via Mixture-of-Experts for Perceptive Locomotion

arXiv:2606.19633v1 Announce Type: cross Abstract: Perceptive legged locomotion over discontinuous terrain (e.g., stairs, gaps, and obstacles) requires adaptive behavior, as a single conservative gait cannot produce the anticipatory maneuvers needed for abrupt topology changes. Cast as multi-task reinforcement learning, this problem introduces a tension between sharing and separation. Tasks use a common locomotion base but have conflicting rewards, so a policy must share behavior while avoiding value interference. Prior work addresses only one side, with monolithic policies sacrificing specialization and hierarchical sub-policies sacrificing generalization across transitions and unseen terrain. We propose CTS-MoE, which combines a dense mixture-of-experts actor with perception-based gating to compose shared behaviors and a multi-critic with task-specific value heads to prevent interference. The model is trained end-to-end in a single-stage concurrent teacher-student setup that handles partial observability and avoids sequential distillation, with task labels used only during training. At deployment, routing depends solely on perception, allowing terrain adaptation without a high-level selector or terrain classifier. Experiments on a Unitree Go1 in simulation and on hardware across seen and unseen terrains show task-aware specialization, with lower tracking error and higher success rates than monolithic baselines. Project Website: https://cts-moe.github.io/ .

23.
arXiv (CS.CV) 2026-06-12

Camera and LiDAR BEV Fusion for Cooperative 3D Object Detection on TUMTraf V2X

We describe a Camera and LiDAR fusion detector developed for the TUMTraf V2X cooperative 3D object detection track of the DriveX 2026 challenge. The detector fuses three roadside cameras with a fused infrastructure-plus-vehicle point cloud in a shared bird's-eye-view space and predicts boxes through a CenterPoint-style head with a generalized IoU regression loss and an IoU quality re-ranking head. Trained on the provided train and validation splits, the model reaches a 3D mAP of 0.85 on the public Codabench test split. While iterating on the system, we observed that 44 of the 50 test frames are also present in the released train (40) and validation (4) splits with their labels. We therefore conducted two additional studies to quantify how this overlap affects the final score: (1) a finetuning run that oversamples the 44 overlapping frames, reaching 0.89 mAP, and (2) a post-processing run that replaces predictions on those frames with the released ground truth, reaching 0.99 mAP (uploaded to our Codabench account for testing but not published on the leaderboard). All three configurations and their per-class results are reported.

24.
arXiv (CS.AI) 2026-06-16

STRIDE: Strategic Trajectory Reasoning via Discriminative Estimation for Verifiable Reinforcement Learning

arXiv:2606.15866v1 Announce Type: new Abstract: Reinforcement Learning with Verifiable Rewards (RLVR) has become an effective post-training paradigm for improving the reasoning abilities of large language models. However, existing RLVR methods typically rely on final-answer correctness to assign trajectory-level rewards, providing sparse supervision and treating all tokens uniformly regardless of their actual contribution to reasoning. Although recent studies introduce intermediate signals such as process rewards, high-entropy tokens, and semantic uncertainty, these signals are often not inherently verifiable and may fail to distinguish beneficial strategic patterns from harmful ones. To address this limitation, we propose STRIDE (Strategic Trajectory Reasoning with Discriminative Estimation), a fine-grained RLVR framework that derives strategic reasoning supervision from verifiable outcomes. STRIDE contrasts successful and failed trajectories within each response group to estimate the outcome-discriminative preference of each $n$-gram strategic pattern, and further combines this signal with reasoning saliency entropy to identify decision-relevant strategic patterns. These patterns are assigned differentiated advantage values during RL optimization, enabling more precise credit assignment while preserving the verifiability of RLVR. Extensive experiments demonstrate that STRIDE consistently improves reasoning performance across diverse models, tasks, and extended settings, including VLMs and agent-based systems.

25.
arXiv (CS.CL) 2026-06-18

CEO-Bench: Can Agents Play the Long Game?

Language model agents are becoming proficient executors at isolated, short-horizon tasks such as software engineering and customer service. Yet real-world challenges require a combination of sophisticated skills that remain largely untested in agents: (1) navigating long horizons amid uncertainty; (2) acquiring information in noisy environments; (3) adapting to a changing world; (4) orchestrating multiple moving parts toward a coherent goal. We introduce CEO-Bench, which evaluates these capabilities together by simulating a representative real-world task: operating a startup for 500 days. An agent manages pricing, marketing, budgeting, and many other aspects of a fictional company through a programmable Python interface, operating in the same environment and facing the same challenges as a human CEO. Success demands analyzing noisy, interconnected business databases, translating signals into sound strategy, and coordinating many decisions with programming. The strongest agents write sophisticated code that simulates customer cohorts to forecast future cash and mines negotiation history to uncover hidden customer preferences. Even so, most state-of-the-art models struggle in this environment. Only Claude Opus 4.8 and GPT-5.5 finish above the $1M starting balance, and neither consistently turns a profit. CEO-Bench takes a first step toward measuring the intelligence required to drive sustained, adaptive progress over time.