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01.
arXiv (quant-ph) 2026-06-16

Reconstruction of detector error model for quantum error correction

arXiv:2606.16288v1 Announce Type: new Abstract: Fault-tolerant quantum computing fundamentally relies on the accurate characterization of circuit-level noise to optimize decoding algorithms. However, extracting complex multi-body error correlations remains challenging. Contemporary greedy inference algorithms can suffer from statistical distortion, discarding true physical mechanisms while introducing many unphysical false positives. Here, we introduce the Correlation-Analysis-based Hypergraph Reconstruction (CAHR) algorithm, a globally consistent framework to invert experimental syndrome statistics directly into discrete physical hypergraphs. By coupling exact algebraic correlation equations with a top-down concurrent-pruning strategy, CAHR recovers the fault topology without false positives for both $d=5$ rotated surface codes and dense 8-body 2D color codes in our benchmark settings. Furthermore, we show that exact continuous parameter extraction in dense codes is limited by a variance cascade, where absolute statistical variance accumulates linearly from high- to low-degree mechanisms. This motivates a two-stage inference paradigm: utilizing CAHR to extract the fault topology, followed by continuous probability optimization. This provides a practical approach for characterizing and decoding highly correlated noise in realistic quantum hardware.

02.
Nature Biotechnology 2026-06-09

Hybrid solid−liquid optics enable scalable, high-resolution light-sheet microscopy across diverse immersion media

Authors:

Many data-driven approaches rely on scalable and affordable three-dimensional (3D) imaging across subcellular to organ scales. Although advances in tissue clearing, expansion microscopy and light-sheet microscopy (LSM) have enabled high-resolution imaging of intact specimens, scalability in sample size, throughput and accessibility remains fundamentally limited by detection optics. Here we introduce hybrid solid−liquid optics (HySIL), a flexible refractive design framework in which a solid optical element and a refractive index (RI)-matched liquid function as a continuous optical system for wavefront correction and numerical aperture enhancement. We implement this framework as SCOPE and Super-SCOPE, enabling submicron-resolution, aberration-corrected LSM using long-working-distance air objectives. We demonstrate high-resolution volumetric imaging across diverse biological contexts, including cleared and expanded mouse, salamander and cavefish brains, human induced pluripotent stem cell (iPSC)-derived brain organoids and large intact human tissues for 3D histopathology. By combining enhanced optical performance with low-cost, long-working-distance and multi-immersion compatibility, HySIL provides an accessible and scalable foundation for next-generation volumetric imaging and data-driven biological discovery. Hybrid solid–liquid optics improve light-sheet imaging of intact biological samples.

03.
arXiv (quant-ph) 2026-06-17

A matching decomposition algorithm for simulating quantum walk Hamiltonians

arXiv:2601.11418v3 Announce Type: replace Abstract: In this work, we present a new algorithm for generating quantum circuits that efficiently implement continuous time quantum walks on arbitrary simple sparse graphs. The algorithm, called matching decomposition, works by decomposing a continuous-time quantum walk Hamiltonian into a collection of exactly implementable Hamiltonians corresponding to matchings in the underlying graph followed by a novel graph compression algorithm that merges edges in the graph. We develop a greedy matching heuristic and a compression-aware matching heuristic, both of which can be used in the quantum circuit algorithm. Lastly, we convert the walks to a circuit and Trotterize over these components. The dynamics of the walker on each edge in the matching can be implemented in the circuit model as sequences of CX and CRx gates. We do not use Pauli decomposition when implementing walks along each matching. Furthermore, we compare greedy (compression-aware) matching decomposition to a standard Pauli-based simulation pipeline and find that greedy (compression-aware) matching decomposition consistently yields substantial resource reductions, requiring up to 43$\%$ (70\%) fewer controlled gates and up to 54$\%$ (75\%) shallower circuits than Pauli decomposition across multiple graph families. Finally, we also present examples and theoretical results for when matching decomposition can exactly simulate a continuous-time quantum walk on a graph.

04.
arXiv (CS.CV) 2026-06-16

Pathway-Structured Privileged Distillation for Deployable Computational Pathology

Integrating transcriptomics and histopathology can improve cancer risk modelling, yet practical use is constrained by the limited availability of RNA profiling in routine settings. Here we introduce Mixture of Pathway Experts (MoPE), a knowledge-distillation framework that reframes multimodal learning as privileged distillation for histology-only inference. MoPE is motivated by the partial observability between RNA profiles and whole-slide images: histology can capture morphology-linked consequences of certain molecular programmes, but cannot be expected to reconstruct the full transcriptomic state. MoPE encodes RNA-derived pathways and transfers the molecular supervision to pathway-indexed pathology experts through memory-usage alignment. Across diverse public benchmarks and two independent breast cancer cohorts, MoPE consistently improved WSI-only inference performance relative to baseline methods. Pathway-usage analyses and human-audited visual inspection provide bounded inspection of model behaviour and candidate morphology-linked readouts. These results support pathway-structured privileged distillation as a promising route to using molecular information during training while preserving RNA-free inference.

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

HiLo-Token: Input-Adaptive High-Low Frequency Token Compression for Efficient Image Editing

Creative image editing tools, such as Photoshop's Remove or Generative Fill buttons, are central to everyday customer use and account for a major share of traffic in Photoshop and Lightroom. However, current generative AI models face significant latency challenges, which become even more pronounced when transitioning from convolution-based U-Nets to Diffusion Transformers (DiTs). In our evaluation on hundreds of representative image editing samples spanning a wide range of mask ratios, the DiT module alone accounts for an average of 73% of the total model latency, even after being distilled from 50 timesteps down to 8 timesteps. To tackle this challenge, we propose $HiLo-Token$, an input-adaptive token compression framework that allocates more token budget to high-frequency, rich-context regions while assigning fewer tokens to low-frequency areas. Specifically, for the editing region specified by the user mask, we retain all tokens within a dilated mask to preserve strong locality and contextual relevance. Outside the editing region, we introduce a simple yet effective high-frequency token selection strategy based on spatial frequency to capture important local details, while using tokens from a 16x downsampled image to represent low-frequency components and preserve the blurry but global structure. Extensive experiments on production-level evaluation data validate the effectiveness of the proposed method, achieving 3.13x, 2.59x, and 1.67x DiT speedups on A100-80GB for image editing tasks across small, medium, and large mask ratio categories with average ratios of 6.38%, 15.92%, and 35.36%, respectively, without any regression in generation quality.

06.
PLOS Computational Biology 2026-06-22

TCRBinder: Unified pre-trained language model with paired-chain synergy for predicting T-cell receptor binding specificity

Authors:

by Weihe Dong, Qiang Yang, Long Xu, Xiaokun Li, Kuanquan Wang, Suyu Dong, Gongning Luo, Xianyu Zhang, Tiansong Yang, Xin Gao, Guohua Wang Deciphering how human T cells recognise peptide-HLA (pHLA) complexes underpins next-generation vaccines and personalised immunotherapies, yet extreme sequence diversity and paired-chains interdependence still hamper reliable in silico prediction of T-cell receptor (TCR) specificity. To overcome these hurdles, we built TCRBinder, a paired-chain-aware deep model with a multi-branch encoder that routes each molecular component through dedicated transformer-based modules to capture contextual signals in both HLA pseudo-sequences and antigenic peptides while simultaneously processing the TCR α and β chains. This design captures the synergistic interaction between paired chains to emulate peptide-HLA-TCR (PHT) interactions and expose residue-level contact motifs. Across PHT and peptide-TCR (pTCR) benchmarks, the model delivered state-of-the-art performance (AUC-ROC = 0.911, AUPR = 0.791 for the PHT task) and remained superior on multiple independent datasets. We tracked the dynamics of clonal expansion and, in a large SARS-CoV-2 repertoire containing completely unseen peptides, improved the AUC-ROC by up to 16.3% over the leading alternatives. Moreover, TCRBinder provided mechanistic insights by pinpointing contact hotspots and quantifying residue contributions to binding probability. These capabilities position TCRBinder as a versatile tool for rational antigen discovery, immunotherapy stratification, and neoantigen vaccine design.

07.
arXiv (quant-ph) 2026-06-11

Rolling Stock Planning Using the Quantum Approximate Optimization Algorithm

arXiv:2606.11383v1 Announce Type: new Abstract: Rolling stock planning is a complex optimization problem in railway management that involves assigning physical trains to scheduled trips while minimizing operational costs. In this work, we address a specific instance of this problem featuring 190 trips over two days, subject to constraints such as mandatory maintenance stops. We reformulate the problem as a Maximum-Weight Independent Set (MWIS) problem on a graph where nodes represent feasible train cycles. To handle the computational complexity of the large search space, we propose a hybrid divide-and-conquer algorithm. This approach iteratively selects subgraphs and solves the MWIS problem using various solvers, including exact classical methods and the Quantum Approximate Optimization Algorithm (QAOA). We evaluate the algorithm's performance by comparing these methods and analyzing the scaling with respect to subgraph size, with QAOA assessed through both classical simulation and execution on a quantum device (IQM Emerald). Our results indicate that increasing the subgraph size generally improves solution quality, demonstrating that the hybrid framework can effectively bridge the gap between polynomial-time approximate solvers and exponential-time exact methods.

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

GEASS: Gated Evidence-Adaptive Selective Caption Trust for Vision-Language Models

Vision-Language Models (VLMs) hallucinate objects that are not present, and a growing line of work tries to curb this by feeding the model its own generated caption as auxiliary evidence – assuming that a caption, once available, is something to consume. We show this fails: naively appending a caption can lower accuracy rather than raise it, dropping Qwen2.5-VL-3B$^\dagger$ on HallusionBench by nearly ten points. To understand why, we build GD-Probe, a diagnostic set that pairs a global and a detail question on the same image, so that any difference in caption effect is attributable to the question alone. Caption utility proves to be a per-query property: the same caption helps global questions and harms detail ones, through a single mechanism – an embedded caption competes with the image for attention and pulls the model's evidence onto its own text – whose sign is set by whether the caption covers the queried content. Crucially, this regime is readable from quantities the decoder already emits, with no attention access or grounding. We turn this into GEASS (Gated Evidence-Adaptive Selective Caption Trust), a training-free, logit-level module that decides per query how much of the caption to trust, gating it by the clean path's confidence, weighting it by the entropy reduction it induces, and raising the evidence bar when the two pathways disagree. Across four VLMs and two benchmarks (POPE and HallusionBench), GEASS improves over both vanilla inference and contrastive decoding under a single fixed setting, adding only two forward passes and no parameters.

09.
arXiv (CS.CL) 2026-06-19

How LLMs Fail and Generalize in RTL Coding for Hardware Design?

Translating sequential programming priors into the parallel temporal logic of hardware design remains a crucial bottleneck for large language models(LLM). To investigate this, we introduce a new error taxonomy grounded in problem solvability, inspired by cognitive theory. Our taxonomy categorizes failures into syntactic, semantic, solvable functional, and unsolvable functional types. Evaluations reveal a strict empirical ceiling on the VerilogEval benchmark, as frontier models plateau at a 90.8% initial pass rate. These plateaus are defined by unsolvable functional errors, exposing persistent knowledge gaps immune to test time compute scaling. Furthermore, we expose a striking surface convergence gap: optimization readily eliminates syntax errors but concurrently exacerbates deeper functional failures. Our findings demonstrate that alignment techniques merely teach models to compile. While repeated sampling strategies can patch solvable errors, register-transfer level(RTL) coding capacity remains strictly bounded by pretraining knowledge. Addressing challenges in the current LLM based hardware generation pipeline requires more studies in model reasoning rather than alignment interventions.

10.
bioRxiv (Bioinfo) 2026-06-11

DLDN-Bench: A Benchmark Framework for Deep Learning de Novo Peptide Sequencing in Proteomics

De novo peptide sequencing is an essential approach for analyzing mass spectrometry data because it enables the identification of novel peptides without relying on protein sequence databases. Recent advances in deep learning have substantially improved the performance of de novo sequencing methods, but the rapid emergence of new models has led to heterogeneous evaluation practices and limited comparability. To address this, we introduce DLDN-Bench, a benchmark framework including a set of benchmark datasets derived from human muscle biopsy mass spectrometry data retrieved from PRIDE and annotated through consensus across multiple widely used database search engines. Using these datasets, we systematically benchmark recent deep learning-based de novo sequencing tools alongside traditional approaches. Performance is assessed using established metrics, including precision and coverage relative to a pseudo-ground truth defined by cross-engine agreement. To demonstrate the utility of DLDN-Bench, we benchmark four recent deep learning models and make all results publicly available. This benchmark framework provides a standardized basis for comparing state-of-the-art methods and offers an extensible resource for evaluating future tools in de novo peptide sequencing.

11.
arXiv (CS.AI) 2026-06-16

Red-Teaming Agent Execution Contexts: Open-World Security Evaluation on OpenClaw

arXiv:2605.11047v2 Announce Type: replace-cross Abstract: Agentic language-model systems increasingly rely on mutable execution contexts, including files, memory, tools, skills, and auxiliary artifacts, creating security risks beyond explicit user prompts. This paper presents DeepTrap, an automated framework for discovering contextual vulnerabilities in OpenClaw. DeepTrap formulates adversarial context manipulation as a black-box trajectory-level optimization problem that balances risk realization, benign-task preservation, and stealth. It combines risk-conditioned evaluation, multi-objective trajectory scoring, reward-guided beam search, and reflection-based deep probing to identify high-value compromised contexts. We construct a 42-case benchmark spanning six vulnerability classes and seven operational scenarios, and evaluate nine target models using attack and utility grading scores. Results show that contextual compromise can induce substantial unsafe behavior while preserving user-facing task completion, demonstrating that final-response evaluation is insufficient. The findings highlight the need for execution-centric security evaluation of agentic AI systems. Our code is released at: https://github.com/ZJUICSR/DeepTrap

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

EurekAgent: Agent Environment Engineering is All You Need For Autonomous Scientific Discovery

LLM-based agents have shown increasing potential in automating scientific discovery. Given an optimizable metric and an execution environment, they can propose, validate, and iterate scientific solutions, and have produced results that outperform human-designed approaches. As model capabilities continue to improve, we argue that the bottleneck for autonomous scientific discovery is shifting from prescribing agent workflows to designing agent environments: the resources, constraints, and interfaces that shape agent behavior. We frame this as environment engineering: building environments that amplify productive behaviors, such as open-ended exploration, systematic artifact management, and inter-agent collaboration, while suppressing harmful behaviors, such as reward hacking and high-friction human oversight. We present EurekAgent, an environment-engineered agent system for metric-driven autonomous scientific discovery. EurekAgent engineers the environment along four dimensions: permissions engineering for bounded agent execution and isolated evaluation; artifact engineering for filesystem and Git-based collaboration; budget engineering for budget-aware exploration; and human-in-the-loop engineering for easy human supervision and intervention. EurekAgent sets new state-of-the-art results on multiple mathematics, kernel engineering, and machine learning tasks, including new state-of-the-art 26-circle packing results discovered with less than $11 in total API cost. We open-source our code and results, and call for environment engineering as a core research direction for developing reliable autonomous research agents.

13.
arXiv (CS.LG) 2026-06-16

Pre-Training for Simulation-Based Science: A Study on Jet Foundation Model Training Objectives

arXiv:2606.14870v1 Announce Type: cross Abstract: Foundation models (FMs) trained on large datasets and fine-tuned on downstream tasks have emerged as a powerful paradigm in AI for science. Industrial FMs are typically trained using self-supervision with masking due to the lack of labels. In many scientific domains, accurate simulations are plentiful and facilitate large, labeled datasets. This opens up new possibilities for pre-training. We present a systematic comparison of pre-training methods using the OmniLearned High Energy Physics FM framework. We test supervised classification, flow-matching generation, and self-supervised masked particle modeling. All models are pre-trained on the JetClass dataset and fine-tuned on two representative downstream tasks, top jet classification and JetNet conditional generation. Among other observations, for classification tasks, we find that pure classifier pre-training is optimal when downstream labels and model capacity are plentiful, but combining it with self-supervised masked particle modeling (MPM) is uniquely powerful in the low-finetuning label regime. Flow matching-based generative pre-training seems to provide little benefit for downstream classification, and interestingly, for downstream generation, we find that flow matching must be in the pre-training objective to see a significant finetuning advantage, hinting at the orthogonality of classification and generation tasks. That is, for a model to transfer to both generative and classification downstream tasks, it must be pre-trained on both. This study provides a template for controlled scaling analysis of pre-training objectives for foundation models in simulation-based sciences.

14.
arXiv (CS.CL) 2026-06-25

Cross-Modal Robustness Transfer (CMRT): Training Robust Speech Translation Models Using Adversarial Text

End-to-End Speech Translation (E2E-ST) has seen significant advancements, yet current models are primarily benchmarked on curated, "clean" datasets. This overlooks critical real-world challenges, such as morphological robustness to inflectional variations common in non-native or dialectal speech. In this work, we adapt a text-based adversarial attack targeting inflectional morphology to the speech domain and demonstrate that state-of-the-art E2E-ST models are highly vulnerable it. While adversarial training effectively mitigates such risks in text-based tasks, generating high-quality adversarial speech data remains computationally expensive and technically challenging. To address this, we propose Cross-Modal Robustness Transfer (CMRT), a framework that transfers adversarial robustness from the text modality to the speech modality. Our method eliminates the requirement for adversarial speech data during training. Extensive experiments across four language pairs demonstrate that CMRT improves adversarial robustness by an average of more than 3 BLEU points, establishing a new baseline for robust E2E-ST without the overhead of generating adversarial speech.

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

The Faithfulness Gap: Certifying Semantic Equivalence Between Natural-Language and Formal Mathematical Statements

arXiv:2606.16541v1 Announce Type: new Abstract: Autoformalization, translating natural-language mathematics into formal proof assistants, is bottlenecked not by translation fluency but by faithfulness: a formal statement can typecheck and be provable, yet still encode a different theorem than the source intended. We introduce Bidirectional Provability Fingerprinting (\bpf{}), a framework that certifies faithfulness by characterizing each candidate through its forward and backward consequence neighborhoods in the ambient theory and matching these against probes derived from the natural-language statement. We further introduce four novel components: (i) Counterfactual Probe Generation (\cpg{}), a contrastive procedure that synthesizes probes targeting specific drift directions; (ii) the Equivalence Spectrum, a continuous faithfulness score that replaces brittle binary verdicts; (iii) Adaptive Probe Budget Allocation (\apba{}), an information-theoretic budget router; and (iv) Faithfulness-Guided Decoding (\fgd{}), which uses \bpf{} signals as a reward during autoformalization. We prove a drift detection theorem and a PAC-faithfulness result establishing that the equivalence class of a natural language statement is learnable from $\mathcal{O}(\log(1/\delta)/\varepsilon)$ probes under mild assumptions. We release \driftbench{}, a benchmark of $2{,}183$ NL/Lean~4 pairs with controlled drift labels across six subfields of mathlib4. \bpf{}\,+\,\cpg{} detects $89.6\%$ of drifted formalizations at a $3.0\%$ false-positive rate-against $41.2\%$ for typecheck and $63.3\%$ for LLM-judge baselines, and \fgd{} reduces the rate at which a state-of-the-art autoformalizer emits drifted statements by $47\%$. https://pmlrbd.github.io/BPF/

16.
arXiv (quant-ph) 2026-06-12

Continuum Neural Momentum Eigenstate for Variationally Solving Quasiparticles

arXiv:2606.12928v1 Announce Type: cross Abstract: We design the first neural quantum state for continuum particles that, for any chosen allowed momentum $\mathbf{k}$, is by construction an exact eigenstate of total momentum with eigenvalue $\mathbf{k}$. Our architecture, EVE, enables off-the-shelf VMC to solve for momentum-sector ground states. We test EVE on 2D bosons with mutual $1/r$ interactions, finding that a single unified ansatz is capable of describing four qualitatively different states: superfluid, roton, crystal, and phonon. At different densities, we extract the underlying phase of matter from the dispersion's shape. At $r_s = 20.0$, we see the roton minimum at finite $k$ expected of a superfluid. At $r_s = 100.0$, we see striking zone folding indicative of crystalline order, with periodically spaced minima representing floating crystals connected by phonon arcs in between. Using density-density correlation functions, we confirm the phase diagnoses and probe the excitations' correlation structures. Finally, we analyze the roton's phase texture and find unexpected multi-particle phase strings, formed when several vortex dipoles merge, leaving two vortices connected by a phase slip.

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

Ensembles of Large Language Models for Identifying EQ-5D Studies in PubMed Based on Their Abstracts

The rapid increase in scientific publications leads to the fact that manual study screening in systematic literature reviews (SLRs) is increasingly resource consuming, inefficient, and inconsistent. Classifying studies that clearly report health-related quality-of-life results, such as EQ-5D data, requires a high level of clinical interpretation and poses challenges for human reviewers. This study investigates the use of Google's Gemini and Gemma large language models (LLMs) in automating EQ-5D detection in the PubMed biomedical database based only on published abstracts. A multi-phase framework is proposed that integrates few-shot prompting, weight ensembling aggregation, and a soft stacking meta-classifier. Nine LLMs are evaluated on a dataset of PubMed studies manually labeled by two experts regarding EQ-5D reporting. The weighted ensemble of gemini-2.5-pro, gemma-3-12b, and gemma-3-27b obtained a 0.74 weighted F1-score and 0.74 accuracy, exceeding individually attained results. The ensembling of top-performing models improved the balance between precision and recall compared to individual models, while the soft stacking approach provided greater reliability and interpretability. Feature analysis shows that the probability results from the models are important in guiding the final predictions. The findings suggest that an ensemble-based LLM setup is a reliable and scalable approach for automating screening in biomedical research.

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

Articulat3D: Reconstructing Articulated Digital Twins From Monocular Videos with Geometric and Motion Constraints

Building high-fidelity digital twins of articulated objects from visual data remains a central challenge. Existing approaches depend on multi-view captures of the object in discrete, static states, which severely constrains their real-world scalability. In this paper, we introduce Articulat3D, a novel framework that constructs such digital twins from casually captured monocular videos by jointly enforcing explicit 3D geometric and motion constraints. We first propose Motion Prior-Driven Initialization, which leverages 3D point tracks to exploit the low-dimensional structure of articulated motion. By modeling scene dynamics with a compact set of motion bases, we facilitate soft decomposition of the scene into multiple rigidly moving groups. Building on this initialization, we introduce Geometric and Motion Constraints Refinement, which enforces physically plausible articulation through learnable kinematic primitives parameterized by a joint axis, a pivot point, and per-frame motion scalars, yielding reconstructions that are both geometrically accurate and temporally coherent. Extensive experiments demonstrate that Articulat3D achieves state-of-the-art performance on synthetic benchmarks and real-world casually captured monocular videos, significantly advancing the feasibility of digital twin creation under uncontrolled real-world conditions. Our project page is available at https://maxwell-zhao.github.io/Articulat3D/.

19.
arXiv (CS.CL) 2026-06-16

AmchiBias: Measuring Stereotypical Bias in Goan Identity Groups with a Minimal Pair Dataset in English and Konkani

Socio-cultural stereotypical bias is an important consideration in the development and deployment of NLP systems. It is however often considered only at the national level, despite rich subnational socio-cultural structures. We present AmchiBias, the first benchmark for measuring socio-cultural stereotypical bias for the Indian state of Goa with its unique historically multicultural setting. It covers various Goan identity groups and comprises 313 minimal pairs across eight sociodemographic dimensions in both English and Devanagari Konkani. We then evaluate stereotypical bias in five multilingual encoder models on this benchmark. We find near-chance scores in Konkani, reflecting language incompetence for general multilingual models and a lack of Goan cultural competence for Indian language models. Queried in English, models with a stronger Indian language coverage show higher bias for pan-Indian groups than hyperlocal Goan groups. This suggests the English signal reflects pan-Indian pretraining associations rather than genuine Goan cultural knowledge. Our findings highlight a critical gap in low-resource multilingual NLP evaluation for hyperlocal community identities.

20.
arXiv (CS.CL) 2026-06-12

PiDA: Phonetically-Informed Data Augmentation for Robust Vietnamese Speech Translation

Cascaded speech translation (ST) systems suffer from error propagation when Automatic Speech Recognition (ASR) outputs incorrect transcripts. We present the first systematic categorization of ASR errors for Vietnamese ST, classifying substitution errors by phonetic cause and quantifying their impact on downstream Neural Machine Translation (NMT) performance using Linear Mixed-Effects Modelling. We confirm that most ASR substitution errors arise from phonetic confusions rather than random noise, and that these phonetic errors significantly degrade ST quality. Motivated by this finding, we propose Phonetically-Informed Data Augmentation (PiDA), which generates ASR-like corruptions by substituting words with phonetically similar alternatives using phonetic word embeddings. Fine-tuning on a PiDA-augmented version of FLEURS Vietnamese-English improves translation of erroneous ASR outputs (up to +2.04 BLEU over standard fine-tuning) while also slightly improving clean-text performance.

21.
arXiv (CS.CL) 2026-06-25

MedGuards: Multi-Agent System for Reliable Medical Error Detection and Correction

As Large Language Models (LLMs) are increasingly deployed in healthcare settings, accurate error detection and correction in generated or existing text becomes critical, as even minor mistakes can pose risks to patient safety. Existing methods for error detection and correction, including automated checks and heuristic-based approaches, do not generalize well across unseen datasets. In this paper, we propose MedGuards as a medical safety guardrail, which is a new framework that treats medical error detection and correction as a multi-agent in-context learning task. Specialized agents separately detect, localize, and correct errors, while a confidence-guided arbitration mechanism resolves disagreements using reasoning traces and confidence scores. This design enhances interpretability, robustness, and adaptability, without requiring additional training of the base LLMs. Additionally, we introduce the Keyword-Prioritized Correction Score (KPCS), a new evaluation metric that considers whether critical keywords within the reference text are generated correctly, providing a more comprehensive assessment than conventional metrics. Experiments across four multilingual medical datasets consisting of clinical notes demonstrate significant improvements by the proposed framework across several metrics and models. Our aim is to enable safer deployment of LLMs in real-world healthcare applications. For reproducibility, we make our code publicly available at https://github.com/congboma/MedErrBench.

22.
arXiv (CS.CL) 2026-06-16

Less is More: Improving LLM Reasoning with Minimal Test-Time Intervention

Recent progress in large language models (LLMs) has focused on test-time scaling to improve reasoning via increased inference computation, but often at the cost of efficiency. We revisit test-time behavior and uncover a simple yet underexplored phenomenon: reasoning uncertainty is highly localized-only a small subset of high-entropy tokens dominantly affects output correctness. Motivated by this, we propose Minimal Test-Time Intervention (MTI), a training-free framework that enhances reasoning accuracy and stability with minimal overhead. MTI includes: (i) Selective CFG intervention, applying classifier-free guidance only at uncertain positions; and (ii) Lightweight negative-prompt guidance, reusing the main model's KV cache to approximate unconditional decoding efficiently. MTI yields consistent gains across general, coding, and STEM tasks-e.g., +9.28% average improvement on six benchmarks for DeepSeek-R1-7B and +11.25% on AIME2024 using Ling-mini-2.0-while remaining highly efficient.

24.
arXiv (CS.AI) 2026-06-18

TxBench-PP: Analyzing AI Agent Performance on Small-Molecule Preclinical Pharmacology

arXiv:2606.19245v1 Announce Type: new Abstract: Artificial intelligence (AI) agents promise to accelerate drug discovery by compressing interpretation and decision-making loops, but practical deployment requires trusted evaluation on realistic program decisions. We introduce TherapeuticsBench Preclinical Pharmacology (TxBench-PP), a verifiable benchmark for small-molecule preclinical pharmacology and the first focused slice of a broader TherapeuticsBench effort across drug-discovery stages and therapeutic modalities. TxBench-PP tests whether agents can recover accurate conclusions from real-world assay data rather than memorized facts from literature. The benchmark contains 100 evaluations indexed by program stage, assay type, and task structure, spanning mechanism-of-action (MoA) and pharmacodynamic (PD) reasoning, compound-target engagement, causal target validation, developability and safety, and translational efficacy. Agents receive realistic workflow snapshots, inspect files in a coding environment, and return structured answers graded deterministically. Across 16 model-harness configurations, comprising 11 models and 4,800 trajectories, no system reliably recovered preclinical pharmacology decisions. The strongest configuration, Claude Opus 4.8 / Pi, passed 59.3\% of endpoint attempts (178/300; 95\% CI, 51.1-67.6), followed by GPT-5.5 / Pi at 55.3\% (166/300; 47.0-63.6).

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

Shrinkage priors for Bayesian Substitute Confounders

arXiv:2606.18535v1 Announce Type: cross Abstract: Multi-cause observational studies contain information about unmeasured confounding through the dependence structure among causes. However, literal imputation of the unobserved confounder is often more complex than learning a lower-dimensional substitute score that preserves the shared assignment variation needed for stable causal adjustment. The deconfounder (Wang and Blei, 2019) and related substitute confounder methods exploit this idea, but flexible assignment models can fit the joint distribution of the causes while producing scores that over-encode the treatment vector, collapse overlap, or capture single-cause variation. We develop a Bayesian factor assignment framework for learning sparse substitute confounders that retain coarse multi-cause dependence with shrinkage priors. The theory is stated at the level of posterior concentration, factor score contraction, and overlap-preserving assignment geometry and therefore does not rely on a particular shrinkage prior. Under these conditions, the proposed regression-adjusted estimators are consistent for mean potential outcomes when the corresponding latent variable identification assumptions hold. Shrinkage priors provide a natural tool for latent structural learning: they favour low-dimensional factors supported by multiple causes, discourage effectively single-cause factors, and induce an ordering of the latent factors through progressive shrinkage. Synthetic experiments illustrate the roles of signal strength, outcome validity, and geometry-aware regularization. In an Alzheimer's Disease Neuroimaging Initiative (ADNI) baseline analysis, sparse substitute scores recover much of the adjustment obtained by directly conditioning on invasive cerebrospinal-fluid biomarkers, while collapse diagnostics identify when fitted factors reduce to individual observed measurements.