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01.
arXiv (CS.CL) 2026-06-16

SAMark: A Self-Anchored Text Watermarking with Paragraph-Level Paraphrase Robustness

Semantic-level watermarking (SWM) improves robustness against text modifications by treating sentences as the basic unit. However, robustness to paragraph-level paraphrasing remains difficult because such attacks globally disrupt watermark signals by changing sentence order. In this work, we propose SAMark, a self-anchored watermarking framework that removes the dependency on sentence order by establishing a step-independent green region in semantic space. To improve detectability, we introduce a multi-channel hyperbolic scoring mechanism that amplifies watermark signals while suppressing noise from weakly aligned candidates. We further propose a diversity-aware filtering strategy that combines hard filtering with soft regularization, extending beyond simple n-gram repetition filters to address semantic redundancy. Experimental results show that SAMark achieves up to 90.2% TP@FP1% under typical paragraph-level paraphrasing attacks, outperforming the strongest prior baseline by more than 30% on average, while maintaining generation quality competitive with unwatermarked text and breaking the robustness-quality trade-off that limits prior methods.

02.
arXiv (CS.LG) 2026-06-16

Tangram: Unlocking Non-Uniform KV Cache Compression for Efficient Multi-turn LLM Serving

arXiv:2606.06302v2 Announce Type: replace Abstract: Multi-turn LLM serving accumulates dialogue history whose Key-Value (KV) cache grows with every turn and every user, quickly exceeding the model weights themselves and making memory – not compute – the binding constraint on throughput. Non-uniform KV compression, which allocates heterogeneous budgets across attention heads, preserves accuracy far better than uniform schemes, yet remains impractical: modern serving stacks assume identical KV lengths across heads, so heterogeneity traps freed memory as page fragmentation, spends up to 25% of prefill time reclaiming scattered pages, and skews GPU workloads that inflate decode latency by up to $1.7\times$ or burn 15–20% of each decode step on re-planning. We observe that this heterogeneity need not be discovered at runtime: head-wise retention follows a two-level structural regularity – an input-invariant head ranking with narrowly bounded per-head ratios – that can be calibrated offline from as few as 50 samples. Building on this insight, we present Tangram, a serving framework that statically resolves what prior systems handle dynamically: Budget Reservation fixes each head's post-compression footprint at scheduling time, eliminating page reclamation; Ragged Paging clusters similar-budget heads into independent page tables, turning fragmentation into reclaimable memory; and Ahead-of-Time Load Balancing precomputes balanced GPU partitions with zero runtime planning. Implemented on vLLM, Tangram serves as a drop-in substrate for existing non-uniform compression methods, matching their accuracy while improving end-to-end throughput by up to $2.6\times$ over the full-KV baseline. Our implementation is publicly available at https://github.com/aiha-lab/TANGRAM.

03.
arXiv (CS.CV) 2026-06-15

SAFformer:Improving Spiking Transformer via Active Predictive Filtering

Spiking Neural Networks (SNNs) offer notable advantages in biological plausibility and energy efficiency, making them promising candidates for building low-power Transformers. However, existing Spiking Transformers largely adhere to a passive reactive paradigm, which struggles to focus on task-relevant information and incurs substantial computational overhead when processing redundant visual data. To overcome this fundamental yet underexplored limitation, we propose SAFformer, a novel Spiking Transformer architecture based on an active predictive filtering paradigm. Inspired by the brain's predictive coding mechanism, SAFformer actively suppresses predictable signals and focuses on salient visual features. Extensive experiments show that SAFformer establishes new state-of-the-art performance on CIFAR-10/100 and CIFAR10-DVS. Remarkably, on ImageNet-1K, it achieves 80.44% Top-1 accuracy with only 26.58M parameters and an energy consumption of 5.88 mJ, demonstrating an exceptional balance between accuracy and efficiency.

04.
arXiv (CS.CV) 2026-06-18

Low-Cost Neuromorphic Fall Detection Using Synthetic Event Data and Hybrid SNNs

This work presents the development of hybrid models that integrate spiking neural networks (SNNs) with components of convolutional neural networks (CNNs) to learn from simulated event-based camera data (Dynamic Vision Sensor, DVS) generated from conventional smartphone videos. Aimed primarily at human fall detection, the approach leverages the energy efficiency and spatio-temporal processing capabilities of SNNs by converting video frames into event-based data. The proposed models are evaluated through simulations on multiple datasets, comparing their performance to that of traditional machine learning models. Results demonstrate significant gains in efficiency without sacrificing accuracy, underscoring the potential of combining SNNs and DVS technology for complex tasks in real-world environments.

05.
arXiv (CS.CL) 2026-06-19

Improving Alignment Between Human and Machine Codes: An Empirical Assessment of Prompt Engineering for Construct Identification in Psychology

Due to their architecture and vast pre-training data, large language models (LLMs) demonstrate strong text classification performance. However, LLM output - here, the category assigned to a text - depends heavily on the wording of the prompt. While literature on prompt engineering is expanding, few studies focus on classification tasks, and even fewer address domains like psychology, where constructs have precise, theory-driven definitions that may not be well represented in pre-training data. We present an empirical framework for optimizing LLM performance for identifying constructs in texts via prompt engineering. We experimentally evaluate five prompting strategies – codebook-guided empirical prompt selection, automatic prompt engineering, persona prompting, chain-of-thought reasoning, and explanatory prompting - with zero-shot and few-shot classification. We find that persona, chain-of-thought, and explanations do not fully address performance loss accompanying a badly worded prompt. Instead, the most influential features of a prompt are the construct definition, task framing, and, to a lesser extent, the examples provided. Across three constructs and two models, the classifications most aligned with expert judgments resulted from a few-shot prompt combining codebook-guided empirical prompt selection with automatic prompt engineering. Based on our findings, we recommend that researchers generate and evaluate as many prompt variants as feasible, whether human-crafted, automatically generated, or ideally both, and select prompts and examples based on empirical performance in a training dataset, validating the final approach in a holdout set. This procedure offers a practical, systematic, and theory-driven method for optimizing LLM prompts in settings where alignment with expert judgment is critical.

06.
PLOS Computational Biology 2026-06-05

Heuristic multi-site optimization for protein sequence design using Masked Protein Language Models

Authors:

by Lijuan Wang, Yuze Wang, Chen Qiu, Liwei Xiao, Xianliang Liu, Junjie Chen Protein sequence design for tailored functional properties is a fundamental task in protein engineering, with critical applications in drug discovery and therapeutic development. Efficient navigation of the combinatorial vastness of protein sequence space to identify functional variants remains a formidable challenge. Conventional approaches, which predominantly rely on template-based local search or single-residue mutagenesis, are constrained by their susceptibility to local optima and their potential risk of destabilizing native structural stability. In this study, we introduce ProtHMSO, a heuristic multi-site optimization framework leveraging masked protein language models (ProtLMs) for context-aware sequence exploration. ProtHMSO mimics natural evolutionary mechanisms by employing ProtLM-derived substitution probabilities to guide heuristic searches for synergistic mutations, thereby constraining combinatorial search spaces through evolutionary and biophysical priors. ProtHMSO is further applied to replace the exploration strategies in genetic algorithms (GAs) and Monte Carlo tree search (MCTS) for improving their convergence efficiency. Benchmark experiments demonstrate that protein sequences generated by ProtHMSO exhibit superior functional performance and closer alignment with natural sequence distribution, compared with state-of-the-art methods. These advancements highlight that ProtHMSO has strong potential and compatibility to accelerate functional protein discovery, offering a robust framework for efficient and context-aware exploration of protein sequence space.

08.
arXiv (CS.CL) 2026-06-18

Probing Semantic Alignment, Lexical Invariance, and Syntactic Influence in LLM Metaphor Processing

Large language models (LLMs) achieve strong performance on metaphor detection and interpretation tasks, yet it remains unclear what such behavioral success reveals about metaphor processing. We present a diagnostic analysis that examines the limits of behavioral evidence by probing three complementary dimensions: semantic attribute alignment, lexical invariance, and syntactic sensitivity. Using geometric probing, we assess whether model-generated interpretations align with reference semantic attributes; through context-varying substitution, we analyze the stability of lexical associations between metaphorical and literal expressions; and via controlled syntactic perturbations, we examine sensitivity in metaphor detection. Our analysis reveals that LLM-generated interpretations can exhibit semantic drift relative to reference attributes; stable lexical anchors persist across contextual conditions, potentially supporting conventional metaphors while biasing novel metaphors requiring contextual integration; and detection performance is sensitive to syntactic irregularities. These findings suggest that strong behavioral performance may reflect heterogeneous underlying signals, highlighting the need for caution when interpreting metaphor benchmarks as evidence of robust, integrated semantic understanding.

09.
arXiv (CS.AI) 2026-06-17

From Paper to Program: Knowledge Externalization for AI-Assisted Quantum Many-Body Code Generation

Authors:

arXiv:2604.04089v3 Announce Type: replace-cross Abstract: Large language models can write scientific code, but direct paper-to-program translation remains fragile when correctness depends on tacit conventions in the literature. We identify this bottleneck as knowledge externalization: converting implicit computational assumptions – index conventions, gauge choices, fermionic signs, contraction order, and memory constraints – into an explicit technical specification before implementation. We evaluate a multi-stage, human-in-the-loop workflow that inserts such a specification, with validation and stop gates, between theory extraction and code generation. The workflow is tested on two algorithmically distinct quantum many-body tasks: variational sweep-based Density-Matrix Renormalization Group (DMRG) from a pedagogical review and constructive Pfaffian conversion of Hartree–Fock–Bogoliubov states to matrix product states from the five-page Letter by Jin et al., Phys. Rev. B 105, L081101 (2022), for which no public code is available. For DMRG, all 16 specification-guided model pairings in a $4\times4$ grid satisfy physics-validation criteria, compared with 6/13 direct attempts. A prose-specification ablation indicates that externalized content, not \LaTeX{} formatting, is the essential ingredient. For Pfaffian-MPS, the workflow succeeds in 11/26 archived attempts, whereas direct prompting yields zero audited passes. Cross-specification transfer is asymmetric: non-GPT specifications implemented by GPT~5.5 pass 4/4, while GPT~5.5 specifications implemented by weaker models fail 4/4, indicating a residual implementation-model bottleneck. The resulting Paper-to-Program Many-Body skill provides an auditable protocol for AI-assisted implementation of many-body algorithms and for diagnosing where externalization succeeds or fails.

10.
arXiv (CS.CV) 2026-06-11

PIGEON: VLM-Driven Object Navigation via Points of Interest Selection

Object navigation in unseen indoor environments requires agents to perform semantic search under partial observability. Vision-language models (VLMs) provide strong semantic-spatial priors for this task, but how to interface them with robot navigation remains challenging: dense VLM inference is expensive, while abstracting environments into symbolic memories often separates high-level reasoning from the raw visual evidence that supports it. We propose we propose PIGEON (Point of Interest Guided Exploration for Object Navigation), a VLM-driven framework that formulates object navigation as raw-observation-grounded sparse decision problem. PIGEON introduces Points of Interest (PoIs) as sparse visual decision units that couple geometrically executable waypoints with raw egocentric observations. Rather than using VLMs as dense controllers or restricting them to frontier ranking, PIGEON enables VLMs to select among task-critical PoIs, including exploration frontiers, suspected target objects, traversable stairs, and floor-level summaries, while low-level planners execute continuous motion between them. This PoI interface further makes high-level navigation decisions verifiable, allowing us to develop an RLVR pipeline that improves local VLMs without manual Chain-of-Thought annotations. Extensive experiments on Habitat ObjectNav benchmarks show that PIGEON achieves state-of-the-art zero-shot performance, scales consistently with foundation model capacity, and transfers to Active Embodied Question Answering with only prompt modifications. Real-world deployments on physical robots further demonstrate its robustness and efficiency.

11.
Nature Medicine 2026-06-12

Efficacy and target engagement of dopamine agonist pramipexole for anhedonic depression: a randomized placebo-controlled trial

Authors:

Anhedonia is a core and disabling symptom of mood disorders with limited treatment options. We evaluated the efficacy and safety of the dopamine agonist pramipexole in patients with mood disorders characterized by clinically significant anhedonia. In this single-center, randomized, double-blind, placebo-controlled trial, adults with major depressive disorder, dysthymia or bipolar depression and elevated Snaith−Hamilton Pleasure Scale (SHAPS) scores were assigned (1:1) to flexible dose, once-daily oral pramipexole as add-on treatment or placebo for 9 weeks. The primary outcome was change in SHAPS score from baseline to week 9. Analyses were conducted in the modified intention-to-treat population. Eighty-five participants were randomized, and 82 were included in the analysis. The primary outcome was met: pramipexole was associated with a greater reduction in SHAPS scores compared to placebo (mean difference: −4.04, 95% confidence interval: −6.89 to −1.18, P = 0.006, Hedges’ g = 0.62). Exploratory analyses indicated that pramipexole was associated with increased light physical activity and relative preservation of reward-related ventral striatal activation. Improvements in anhedonia were sustained during a 6-month open-label extension. Pramipexole was generally well tolerated compared to placebo. Pramipexole significantly improved anhedonia and showed a favorable safety profile, supporting its potential as an augmentation strategy in mood disorders. ClinicalTrials.gov identifiers: NCT05355337 and NCT05825235 . Pramipexole, in patients with major depressive disorder, dysthymia or bipolar depression, reduced Snaith−Hamilton Pleasure Scale scores significantly compared to placebo.

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

Plan, Don't Pose: Long Composite Motion Generation with Text-Aligned BFM

arXiv:2605.29906v2 Announce Type: replace Abstract: Text-to-motion (T2M) generation has broad applications in character animation, virtual avatars, and human-robot interaction. Existing methods typically generate pose trajectories or motion tokens directly from language, forcing a single model to handle semantic interpretation, long-horizon structure, and low-level physical realization. This coupling makes them costly and often unreliable for long, compositional, or semantically dense prompts. We propose Text2BFM, the first framework that aligns natural language with pretrained Behavioral Foundation Models (BFMs) for T2M generation without relying on heavy end-to-end motion generators. Text2BFM operates in the latent policy space of a frozen BFM, using it as an executable motion prior. A text-aligned variational behavioral bottleneck compresses BFM policy-latent sequences into compact motion representations that are compatible with language and preserve long-horizon behavioral structure. Generation is performed in this compact behavioral manifold with a lightweight conditional generator, and the resulting latent encoded behaviors are decoded into policy latents that drive the pretrained frozen BFM. By decoupling semantic planning from motion execution, Text2BFM achieves efficient, robust T2M generation and strong performance on long, compositional textual descriptions.

13.
arXiv (CS.CL) 2026-06-15

Sentinel: Decoding Context Utilization via Attention Probing for Efficient LLM Context Compression

Retrieval-augmented generation (RAG) often suffers from long and noisy retrieved contexts. Existing context compression methods typically rely on heuristic relevance estimation or supervised compression models rather than on how LLMs utilize retrieved context during inference. We propose Sentinel, a lightweight sentence-level compression framework that decodes inference-time contextual utilization behaviors from head-wise attention patterns of frozen LLMs. To ground supervision in retrieval-dependent answering behavior, Sentinel trains a lightweight probe using QA examples where the model succeeds only when retrieved context is available. Sentinel performs compression using only a single non-autoregressive forward pass without dedicated compression training or autoregressive scoring. Empirically, we find that effective contextual utilization signals remain accessible even in compact proxy models. On LongBench, Sentinel with a 0.5B proxy model achieves up to 5$\times$ compression while attaining question-answering performance competitive with compression methods built on 7B-scale models. Despite being trained only on English QA data, Sentinel also generalizes effectively to Chinese and out-of-domain settings.

14.
arXiv (CS.CL) 2026-06-16

EIBench: A Simulator-Based Benchmark and Turn-Credit RL for Emotion Management

Emotional intelligence (EI) in Large Language Models (LLMs) is often evaluated through static understanding tasks or single-response dialogue generation. However, emotion management is interactive: a good model should not only recognize a user's emotion, but also improve the user's emotional and relational state over several turns. We introduce EIBench, a simulator-based benchmark for interactive emotion management. EIBench contains 2,222 scenarios, with 2,009 for training and 213 for held-out testing. The scenarios are organized by a 2x2 taxonomy covering Support, Defense, Repair, and Charm, which together capture different forms of support, boundary maintenance, trust repair, and rapport building. In each scenario, an LLM simulator plays the user, updates an emotion-relation state after each turn, and maps the final state to an anchor-based score. This design makes EIBench both an evaluation benchmark and a training environment: the final state gives the outcome reward, while the per-turn state updates provide dense feedback for RL. We evaluate 15 open- and closed-source LLMs. Current models perform well on support and rapport-building scenes, but struggle with boundary maintenance under user pressure. To improve the EI ability of LLMs, we propose Centered Turn-Credit GRPO (CTC-GRPO), a GRPO extension that reuses the simulator's per-turn state updates as dense turn-level feedback while preserving the final outcome reward. CTC-GRPO improves Qwen3-8B from -22.4 to +22.4 on EIBench and also improves on out-of-distribution evaluations including SAGE (+12.4) and EQBench3 (+20.9%). Our results show that simulator-tracked user states can support both evaluation and training for multi-turn emotion management.

15.
medRxiv (Medicine) 2026-06-17

Cardio Heart Connect: Protocol for a Randomized Trial of a Commercially Available mHealth Fitness Intervention for Cardiac Rehabilitation After Transcatheter Aortic Valve Replacement

Background: Despite ample evidence of the benefits of cardiac rehabilitation (CR), few transcatheter aortic valve replacement (TAVR) patients participate. Commercially available mobile health offers an opportunity to deliver activity-promotion content to populations that are challenged to participate in CR. This study aims to test the efficacy of clinically controlled, commercially available fitness programming for improving physical activity and cardiovascular health outcomes designed to be initiated while patients are on waitlists for traditional CR. Methods: The Cardio Heart Connect study is a hybrid type I effectiveness-implementation trial aiming to enroll N=200 patients who have been placed on a cardiac rehab waitlist following a TAVR procedure from the University of Colorado Hospital Heart and Vascular Center. Participants will be randomized 1:1 to the Cardio Heart Connect intervention with commercially available fitness or attention control, designed to control for technology access. At baseline, post-intervention (8 weeks), and follow-up (12 months), we will assess the primary outcome of participants? daily steps as measured by smartwatch accelerometer and secondary outcomes of interest including functional capacity (Duke Activity Status Index; VO2max), quality of life (Kansas City Cardiomyopathy Questionnaire), and cardiovascular health status (Life Essential 8). In addition, we will use mixed methodologies to evaluate the implementation of intervention using the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) Framework. Conclusions: Commercially available fitness programs have the potential to provide more accessible opportunities for patients recovering from TAVR to engage in physical activity and may be preferred due to their customizability, convenience, and ease of scheduling. Overall, this study will provide insight into the use of commercial mHealth to promote activity following TAVR.

16.
arXiv (CS.CL) 2026-06-12

AI SciBrief as a Gateway to Research: A Framework for Onboarding Students into New Research Areas

Students at all levels of higher education face a significant barrier in the form of information overload, which often paralyzes the initial stages of the research process and suppresses motivation. In response, this article introduces a pedagogical framework that leverages AI SciBrief, a platform powered by a Large Language Model (LLM) designed to automatically generate digests of scientific trends. We describe how this multidisciplinary tool - with initial coverage in finance, medicine, and education - can be integrated into the curriculum to overcome this "entry barrier." The framework provides concrete methodologies for utilizing these digests to facilitate topic selection for term papers, accelerate literature reviews for dissertations, and enable postgraduate students to continuously monitor emerging trends. We conclude that AI SciBrief functions as a "gateway to research" effectively reducing students' cognitive load and empowering them to transition more rapidly from information searching to knowledge creation.

17.
arXiv (CS.CV) 2026-06-16

Enabling Real-Time Point-of-Care Ultrasound Segmentation: A GPU-Free Deployment in Resource-Limited Settings

Authors:

Ultrasound imaging is the most widely adopted medical modality globally due to its low cost and portability, yet artificial intelligence (AI) deployment remains constrained by reliance on GPU-accelerated models, creating a structural paradox where the cost of "intelligence" exceeds that of the imaging device itself. Here, we present the systematic adaptation and extensive evaluation of UltraSeg, an ultra-lightweight architecture originally developed for colonoscopic polyp segmentation, now engineered for point-of-care ultrasound (POCUS) across ten public datasets spanning six anatomical sites (breast, thyroid, kidney, carotid, fetal, and small-animal tumor). We systematically validate both variants in ultrasound domains: UltraSeg-130K (0.13M parameters) achieves 89.7 FPS on single-core CPUs and 34.8 FPS on a refurbished mobile device, while UltraSeg-500K (0.5M parameters) delivers 44.6 FPS on CPU and 16.1 FPS on mobile device. UltraSeg-500K matches or exceeds the Dice performance of the 31M-parameter UNet and approaches 105M-parameter TransUNet in average performance, with superior zero-shot cross-dataset generalization on external validation sets (UDIAT, DDTI). By enabling clinical-grade segmentation without GPU dependency, this work brings AI costs in line with ultrasound accessibility, making advanced diagnostics available in resource-limited settings.

18.
arXiv (CS.CL) 2026-06-15

Beyond Perplexity: UTF-8 Validity in Byte-aware Language Models

Byte-level tokenization enables language models to handle any Unicode input, but models can generate invalid UTF-8 sequences when encountering rare or unseen characters. We investigate the relationship between training scale and UTF-8 generation reliability with a 355M parameter model trained on 80B tokens from a balanced multilingual corpus of English, Japanese, Korean, and Chinese. We introduce multiple evaluation protocols that isolate UTF-8 structural validity from language modeling. UTF-8 validity convergence lags perplexity by a roughly a factor of two: perplexity stabilizes after 2.1B tokens, but UTF-8 validity requires 4.2B tokens. In context-free generation, rare characters achieve higher structural validity than common characters, suggesting over-specialization of frequent character representations. Through experiments, we observed that reliable UTF-8 generation is a distinct capability requiring evaluation beyond perplexity.

19.
arXiv (CS.LG) 2026-06-18

Do Time Series Foundation Model Benchmarks Hide Regime-Dependent Failures? Evidence from Traffic Speed Forecasting

arXiv:2606.18367v1 Announce Type: new Abstract: Standard benchmarks evaluate time series foundation models (TSFMs) using aggregate metrics, but these can mask severe failures in critical operating regimes. We introduce regime-stratified evaluation and apply it to three TSFMs on two standard traffic speed benchmarks. Traffic exhibits abrupt regime switching between free-flow and congested states, producing bimodal speed distributions during transitions. When we stratify by traffic regime, both accuracy and prediction-interval coverage degrade sharply during transitions: transition-regime MAE reaches 11 mph (versus 3 mph overall), and empirical coverage of 90% prediction intervals drops as low as 55%. These failures are invisible in aggregate metrics because free-flow observations dominate the sample. A simple historical conditional baseline (sampling from per-sensor training distributions) achieves better transition coverage than any TSFM, but has far worse overall accuracy. We propose bimodal mixture augmentation (BMA), a post-hoc method that combines TSFM forecasts with historical distributional knowledge, approaching the historical baseline's transition coverage while preserving the TSFM's accuracy. Our results suggest that TSFM benchmarks should incorporate regime-aware evaluation to surface failures that aggregate metrics hide.

21.
arXiv (CS.CL) 2026-06-19

When Lower Privileges Suffice: Investigating Over-Privileged Tool Selection in LLM Agents

As LLM agents increasingly select tools autonomously, their choices among tools with different privileges become safety-relevant. However, prior tool-selection studies focus on safety-agnostic metadata preferences, leaving privilege-sensitive choices underexplored. To address this gap, we study over-privileged tool selection, in which an agent selects or escalates to a higher-privilege tool despite a sufficient lower-privilege alternative. We introduce ToolPrivBench to evaluate whether agents choose higher-privilege tools despite sufficient lower-privilege alternatives, measuring both initial selection and escalation after transient tool failures. Across eight domains and five recurring risk patterns, we find that over-privileged tool selection is common among mainstream LLM agents and is further amplified by transient failures. We further find that general safety alignment does not reliably transfer to least-privilege tool choice, while prompt-level controls provide only limited mitigation under transient failures. We therefore introduce a privilege-aware post-training defense that teaches agents to prefer sufficient lower-privilege tools and escalate only when necessary. Our mitigation experiments show that this defense substantially reduces unnecessary high-privilege tool use while preserving general capabilities.

22.
arXiv (CS.LG) 2026-06-15

Scalable Deep Unfolding of Conic Optimizers

arXiv:2606.13825v1 Announce Type: cross Abstract: Deep unfolding (DU) accelerates iterative optimizers by introducing learnable components and training them through unrolled iterations, but extending DU to the large-scale semidefinite programs (SDPs) common in robotics has remained limited. Unrolling a full-update conic solver such as COSMO exposes two obstacles that prior work on learned conic solvers has not: backpropagating through the per-iteration linear-system solve incurs memory quadratic in the problem size once the coefficient matrix is formed explicitly, and backpropagating through the positive semidefinite (PSD) cone projection becomes numerically unstable when eigenvalues coincide. We address the first obstacle with a matrix-free implicit differentiation rule that operates entirely through matrix-vector products, reducing memory from $O(n^2)$ to $O(n)$ and enabling backpropagation at scales where direct factorization runs out of memory. We address the second with a backward rule based on the Dalečkii–Krein representation of the Fréchet derivative, which remains well-defined under repeated eigenvalues. Together these make it possible to learn lightweight hyperparameter policies and warm-starts for a full-update conic solver. We evaluate on nonlinear covariance steering problems solved via sequential convex programming (SCP), as well as standalone SDPs and second-order cone programs ranging from max-cut and Lovász $\vartheta$ SDPs to robust estimation and control problems. The learned policies outperform state-of-the-art solvers across all problems, and can provide up to a 50$\times$ speedup depending on the class. When used as a subroutine in SCP, the learned approach delivers over a 30$\times$ speedup compared to COSMO.

23.
bioRxiv (Bioinfo) 2026-06-11

Amylo-Pipe: an integrated web server for mechanistic and kinetic prediction of protein and peptide aggregation

Protein aggregation is central to amyloid-related disorders and remains a major developability challenge for protein therapeutics. Over the past two decades, significant advances have been made to predict aggregation-prone regions (APRs) and estimate aggregation propensity in proteins and peptides. In contrast, the prediction of aggregation kinetics has received relatively less attention due to the limited availability and heterogeneity of experimental data. Consequently, aggregation propensities from APR prediction algorithms were widely accepted as a means to predict relative changes in the aggregation kinetics of proteins and mutants. Previous studies have demonstrated, using large-scale datasets, that aggregation propensity shows a weak or inconsistent correlation with aggregation kinetics. In the present study, we have integrated complementary state-of-the-art mechanistic and kinetic prediction tools for protein aggregation into a unified, user-friendly web framework entitled "Amylo-Pipe". Amylo-Pipe also implements practical features that are especially useful for protein engineering, such as gatekeeper-residue mutational scanning to support the design of aggregation-resistant variants. By consolidating multiple prediction tasks in a single interface, Amylo-Pipe enables a more comprehensive assessment of aggregation behavior than APR-only workflows. The web server is freely accessible at: https://web.iitm.ac.in/bioinfo2/amylopipe/.

24.
arXiv (CS.LG) 2026-06-17

Learn from Your Mistakes: Self-Correcting Masked Diffusion Models

arXiv:2602.11590v3 Announce Type: replace Abstract: Masked diffusion models (MDMs) have emerged as a promising alternative to autoregressive models, enabling parallel token generation while achieving competitive performance. Despite these advantages, MDMs face a fundamental limitation: once tokens are unmasked, they remain fixed, leading to error accumulation and ultimately degrading sample quality. We address this by proposing a framework that trains a model to perform both unmasking and correction. By reusing outputs from the MDM denoising network as inputs for corrector training, we train a model to recover from potential mistakes. During generation we apply additional corrective refinement steps between unmasking ones in order to change decoded tokens and improve outputs. We name our training and sampling method Progressive Self-Correction (ProSeCo) for its unique ability to iteratively refine an entire sequence, including already generated tokens. We conduct extensive experimental validation across multiple conditional and unconditional tasks, demonstrating that \method~yields better quality-efficiency trade-offs (up to ~4x faster sampling) and enables inference-time compute scaling to further increase sample quality beyond standard MDMs (up to ~1.2x improvement on benchmarks).

25.
arXiv (CS.LG) 2026-06-19

HEPTv2: End-to-End Efficient Point Transformer for Charged Particle Reconstruction

arXiv:2606.20437v1 Announce Type: cross Abstract: Charged-particle tracking – reconstructing trajectories from sparse detector measurements – is a fundamental high-energy-physics inference problem and a canonical example of learning under extreme combinatorial ambiguity. At the High-Luminosity Large Hadron Collider (HL-LHC), tracking must remain accurate and efficient despite unprecedented collision densities. Graph neural networks perform strongly, but incur substantial costs from graph construction and processing, while transformer-based approaches rely on auxiliary stages that prevent end-to-end optimization. To address this, we present HEPTv2, an end-to-end point-transformer architecture that reconstructs tracks from detector hits in one trainable pipeline. HEPTv2 combines a locality-aware point encoder with a track decoder that predicts complete trajectories without graph-building, clustering, or filtering. The encoder uses locality-sensitive hashing in detector coordinate space to preserve tracking-relevant geometry while enabling efficient local attention. The decoder resolves ambiguities through sectorized decoding and direct hit-to-track prediction under joint encoder-decoder supervision, allowing the full pipeline to be optimized end-to-end. On TrackML, HEPTv2 achieves 98.6% double-majority tracking efficiency at a 0.8% fake rate, while requiring only $\sim$15~ms inference time and 0.4~GB peak memory per event on a NVIDIA A100 GPU. Latency and memory scale approximately linearly for events with up to $5\times10^5$ hits. HEPTv2 establishes a new state of the art in the accuracy-latency trade-off, improving efficiency by 4.5% over the strongest prior transformer and by 1.1–2.2% over optimized graph-based pipelines, while reducing latency by factors of 7 and 38–52, respectively. These results show end-to-end transformers can deliver the accuracy and efficiency required for real-time particle reconstruction at the HL-LHC.