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01.
arXiv (CS.AI) 2026-06-11

MPC-Patch-Bench: Security-Aware LLM Code Patch for Multi-Party Computation

arXiv:2606.11416v1 Announce Type: cross Abstract: Repository-level benchmarks for evaluating Large Language Model (LLM) code repair on Secure Multi-Party Computation (MPC) software do not yet exist, and directly transplanting general-purpose benchmarks such as SWE-bench fails on three structural fronts: (i) MPC repositories are dominated by generic Python infrastructure rather than cryptographic logic; (ii) high-value MPC fixes lack the standardized tests rigid extraction pipelines require; and (iii) standard fail-to-pass evaluation is insufficient for code that must also be cryptographically safe. MPC is increasingly deployed for privacy-preserving machine learning, biomedical collaboration, and secure analytics. Existing MPC-specific code-synthesis efforts cover only operator-level or single-framework tasks; evaluating LLM agents on real repository-level MPC repair instead demands MPC-aware data curation and a verifier matched to the security and numerical-fidelity guarantees MPC programs must obey neither of which existing benchmarks provide. We introduce MPC-Patch-Bench, a repository-level benchmark organised around two frameworks. (1)The Data Curation Framework combines a domain-specific curation agent that filters raw pull requests through three cryptographic layers with a human-AI completion engine that synthesizes missing problem statements and Fail-to-Pass/Pass-to-Pass tests, yielding 205 fully verified instances. (2)The MPC Verifier provides dedicated security and numerical-fidelity checks via dynamic differential testing against plaintext oracles and MPC-specific static analysis rules that flag unsafe reveals, insecure arithmetic, and illegal public/private casts. The strongest evaluated LLM functionally resolves only 22.9% of MPC-Patch-Bench tasks; the MPC Verifier further reduces verified resolution to 17.1%, with up to 40% of functionally-passing patches rejected for cryptographic or numerical-fidelity violations.

02.
arXiv (math.PR) 2026-06-16

Geometry of critical discrete structures: long-range percolation on the hierarchical lattice and the discrete torus

arXiv:2509.09589v2 Announce Type: replace Abstract: Consider (a) balls $\Lambda_n$ of growing volumes in the $d$-dimensional hierarchical lattice, and (b) the $d$-dimensional discrete torus $\mathbb{T}_n^d$ on $n^d$ vertices. Place edges independently between each pair of vertices $x\neq y\in\Lambda_n$ or $\mathbb{T}_n^d$ with probability $1-\exp(-\beta J(x, y) )$ where $J(x, y) \asymp \| x-y \|^{-\alpha}$ for some $0

03.
arXiv (CS.CL) 2026-06-16

SAAS: Self-Aware Reinforcement Learning for Over-Search Mitigation in Agentic Search

Agentic search enables LLMs to solve complex multi-hop questions through iterative reasoning and external search. Despite the effectiveness, these systems often suffer from a critical limitation in practice: agents fail to recognize their own knowledge boundaries, blindly triggering searches when internal knowledge suffices and failing to terminate search even when adequate evidence has been collected. The lack of self-awareness leads to severe over-search, incurring substantial inference latency and prohibitive computational cost. To this end, we propose SAAS, a novel RL framework designed to cultivate dynamic self-awareness that precisely regulates search behavior without compromising accuracy. SAAS introduces three key components: (i) a search boundary modeling mechanism, which identifies the search boundary under the evolving policy by contrasting search-disabled and search-enabled rollouts; (ii) a boundary-aware reward module, which translates this boundary awareness into trajectory-level penalties, suppressing unnecessary and redundant searches; and (iii) a stage-wise optimization strategy, which leverages a sequential curriculum to prioritize reasoning over search regularization, thereby avoiding reward hacking. Extensive experiments demonstrate that SAAS substantially reduces over-search, while maintaining accuracy. Our code and implementation details are released at https://github.com/XMUDeepLIT/SAAS.

04.
arXiv (CS.AI) 2026-06-17

Ensemble RL through Classifier Models: Enhancing Risk-Return Trade-offs in Trading Strategies

作者:

arXiv:2502.17518v3 Announce Type: replace-cross Abstract: This paper presents a comprehensive study on the use of ensemble Reinforcement Learning (RL) models in financial trading strategies, leveraging classifier models to enhance performance. By combining RL algorithms such as A2C, PPO, and SAC with traditional classifiers like Support Vector Machines (SVM), Decision Trees, and Logistic Regression, we investigate how different classifier groups can be integrated to improve risk-return trade-offs. The study evaluates the effectiveness of various ensemble methods, comparing them with individual RL models across key financial metrics, including Cumulative Returns, Sharpe Ratios (SR), Calmar Ratios, and Maximum Drawdown (MDD). Our original experimental results demonstrate that ensemble methods often outperform base models in terms of risk-adjusted returns, providing better management of drawdowns and overall stability. However, both the original analysis and the additional reproduction reported in this version show that ensemble performance is sensitive to the choice of variance threshold \(\tau\), classifier group, RL-agent pair, and market universe. The reproduction evidence strengthens the conclusion that classifier-assisted ensemble selection can improve robustness, while also clarifying that the advantage is conditional rather than automatic across all datasets. This study emphasizes the value of combining RL with classifiers for adaptive decision-making, with implications for financial trading, robotics, and other dynamic environments.

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) 2026-06-16

Evaluation of Alternative-Based Information Systems for Deliberative Polling using an Agentic Simulator

arXiv:2606.11692v1 Announce Type: cross Abstract: Deliberative polling promises to improve collective decision-making by exposing shareholders to a broad range of arguments before they vote. Yet ensuring that every voter encounters a representative sample of the reason space, the coverage problem, remains an open challenge, particularly at scale and in adversarial or strategically motivated electorates. This paper introduces a way of evaluating solutions using the LLM-based Agentic Bipolar Argumentation Simulator, grounded in a framework which formalises a poll as a six-tuple of endorsing and opposing justifications, attack and enhance relations, and shareholder- and relation-weights. ABAS simulates N autonomous shareholder agents, each assigned a latent opinion according to desired distributions in [-1, 1], who sequentially vote, choose or author justifications, and optionally submit argumentation-graph links. The simulator implements recommendations that rank existing justifications by their observable endorsement mass. It evaluates the mechanism's success by coverage, namely the fraction of the corpus reason-tag set represented in the K recommendations presented to each shareholder, as a solution to the NP-hard Subsuming Justification Problem. Reported experiments characterise how creativity rate (pown), recommendation size (K), argumentation density (plinks), and population size (N) affect coverage and corpus diversity. In an authenticated electorate where Sybil attacks are impossible and only the relation graph is gameable, we stress-test the scoring with coordinated strategic voting attacks: a tag-flood attack collapses coverage, while author-count relation weighting through a reversed-PageRank rule resists the flood markedly better than uniform weights.

07.
arXiv (CS.CL) 2026-06-18

Application of integrated gradients explainability to sociopsychological semantic markers

Classification of textual data in terms of sentiment, or more nuanced sociopsychological markers (e.g., agency), is now a popular approach commonly applied at the sentence level. In this paper, we exploit the integrated gradient (IG) method to capture the classification output at the word level, revealing which words actually contribute to the classification process. This approach improves explainability and provides in-depth insights into the text. We focus on sociopsychological markers beyond sentiment and investigate how to effectively train IG in agency, one of the very few markers for which a verified deep learning classifier, BERTAgent, is currently available. Performance and system parameters are carefully tested, alternatives to the IG approach are evaluated, and the usefulness of the result is verified in a relevant application scenario. The method is also applied in a scenario where only a small labeled dataset is available, with the aim of exploiting IG to identify the salient words that contribute to building the different classes that relate to relevant sociopsychological markers. To achieve this, an uncommon training procedure that encourages overfitting is employed to enhance the distinctiveness of each class. The results are analyzed through the lens of social psychology, offering valuable insights.

08.
arXiv (quant-ph) 2026-06-11

Mathematical Basis for Analyzing Superconducting Phase Transitions Using Catastrophe Theory

arXiv:2606.11810v1 Announce Type: cross Abstract: We establish a rigorous mathematical bridge from quantum many-body path integrals to the cusp catastrophe model by Lyapunov-Schmidt reduction, which provides a theoretical foundation for analyzing superconducting phase transition using the catastrophe theory. First, it is proved that, near the critical point the infinite-dimensional effective action is diffeomorphic to a finite-dimensional catastrophe. Secondly, starting from Ginzburg-Landau free energy functional, the Euler-Lagrange partial differential equation can be reduced to the cusp catastrophe model. Thirdly, the fermionic imaginary-time path integral to the cusp catastrophe is derived through the Hubbard-Stratonovich transformation, Matsubara frequency expansion, and Grassmann algebra. Furthermore, we connect this framework with the adsorption potential theory we proposed, elucidating the catastrophic topological nature of the electron pairing mechanism in high-temperature superconductivity. The precise microscopic derivation of the adsorption potential from first-principles electronic structure calculations would strengthen the predictive power of the theory.

09.
arXiv (CS.CL) 2026-06-16

GRACE-DS: a Guarded Reward-guided Agent Correction Environment in Data Science

We introduce GRACE-DS, a Guarded Reward-guided Agent Correction Environment in Data Science for pre-deployment evaluation of LLM-powered AutoML agents. GRACE-DS is a set of evaluation metrics in an isolated environment that can be applied to tabular ML tasks specific to a particular organization. It exposes agents to realistic workflow stages, from planning and data inspection through feature engineering, model development, validation, and code repair to final submission, while hidden executable validators measure not only final predictive performance but also leakage avoidance, reproducibility, protocol validity, correction behavior, and reward alignment. The strongest structured regime, flexible iterative interaction (our approach), achieves higher end-to-end normalized hidden-test quality than single-shot generation, unstructured interaction, and restart-based baselines, while also improving protocol-valid completion. Validated across more than 7,000 episodes, these results establish GRACE-DS as a robust platform for assessing the capacity of LLM-based AutoML agents to execute machine learning workflows under production-like conditions and in accordance with organization-specific requirements.

10.
arXiv (CS.LG) 2026-06-19

A deep learning framework for jointly solving transient Fokker-Planck equations with arbitrary parameters and initial distributions

arXiv:2604.06001v2 Announce Type: replace-cross Abstract: Efficiently solving the Fokker-Planck equation (FPE) is central to analyzing complex parameterized stochastic systems. However, current numerical methods lack parallel computation capabilities across varying conditions, severely limiting comprehensive parameter exploration and transient analysis. This paper introduces a deep learning-based pseudo-analytical probability solution (PAPS) that, via a single training process, simultaneously resolves transient FPE solutions for arbitrary multi-modal initial distributions, system parameters, and time points. The core idea is to unify initial, transient, and stationary distributions via Gaussian mixture distributions (GMDs) and develop a constraint-preserving autoencoder that bijectively maps constrained GMD parameters to unconstrained, low-dimensional latent representations. In this representation space, the panoramic transient dynamics across varying initial conditions and system parameters can be modeled by a single evolution network. Extensive experiments on paradigmatic systems demonstrate that the proposed PAPS maintains high accuracy while achieving inference speeds four orders of magnitude faster than GPU-accelerated Monte Carlo simulations. This efficiency leap enables previously intractable real-time parameter sweeps and systematic investigations of stochastic bifurcations. By decoupling representation learning from physics-informed transient dynamics, our work establishes a scalable paradigm for probabilistic modeling of multi-dimensional, parameterized stochastic systems.

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

SDFLoRA: Selective Decoupled Federated LoRA for Privacy-preserving Fine-tuning with Heterogeneous Clients

arXiv:2601.11219v3 Announce Type: replace-cross Abstract: Federated learning (FL) for large language models (LLMs) has attracted increasing attention as a privacy-preserving approach for adapting models over distributed data, where parameter-efficient methods such as Low-Rank Adaptation (LoRA) are widely adopted to reduce communication and memory costs. However, practical deployments often exhibit rank and data heterogeneity: clients operate under different low-rank budgets and data distributions, making direct aggregation of LoRA updates biased and unstable. Existing approaches either enforce a unified rank or align heterogeneous updates into a single shared subspace, which tends to mix transferable and client-specific directions and consequently undermines personalization. Moreover, under differential privacy (DP), perturbing such structurally mixed updates injects noise into directions that should remain purely local, leading to unnecessary utility degradation. To address these issues, we propose Selective Decoupled Federated LoRA (SDFLoRA), a structure-aware LoRA framework that decouples each client update into a shared component for aggregation and a private component that preserves client-specific semantics. Only the shared component participates in subspace alignment, while the private component remains local and uncommunicated, making the training DP-compatible and stabilizing aggregation under rank heterogeneity. By injecting noise only into the aggregated shareable update, this approach avoids perturbations to local directions and improves the utility-privacy trade-off. Experiments on multiple benchmarks demonstrate that SDFLoRA outperforms federated LoRA baselines and achieves a strong utility-privacy trade-off.

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

T-Mem: Memory That Anticipates, Not Archives

Long-term memory is essential for conversational agents to remain coherent across extended dialogues, follow through on commitments made many sessions earlier, and adapt their behaviour to each user. Current LLM-backed long-term conversational memory, however, is reachability-bounded by the similarity between a query and stored content, both lexical and dense-vector. The approach is effective when query and memory share surface features such as wording or named entities (we call this descriptive). But it misses another, equally valuable class of cases, where query and memory do not share surface features and are tied only by a latent semantic arc (associative). On this regime prevailing long-term memory systems collectively fail. Covering this other half is what allows an assistant, for the first time, to actively draw on past dialogue as a semantic asset. On the memory side, this is the engineering counterpart of what cognitive science calls episodic future thinking: rehearsing past experience for the future contexts under which it will need to be found. We call these write-time rehearsals triggers. We propose T-Mem, the first long-term conversational memory architecture that covers both descriptive and associative recall. At each of two evidence granularities, single facts and full exchanges, T-Mem instantiates one descriptive trigger family and one associative trigger family, so that every memory remains reachable from both surface-similar and relevance-bound queries. As empirical validation, T-Mem reaches state-of-the-art on both LoCoMo and LoCoMo-Plus.

13.
arXiv (quant-ph) 2026-06-16

Bright Emission from Dark Sources in Hyperbolic Media

arXiv:2606.16071v1 Announce Type: cross Abstract: Hyperbolic media enable ultra-strong light-matter interactions through their extreme field localization and small mode volumes, but low-loss realizations are fundamentally limited to the mid-infrared, owing to the long lifetimes of optical phonons in high-quality crystals. Here we show that bright emitters operating at visible or near-infrared frequencies can be used to generate radiation in this regime by inducing mid-infrared population dynamics, thereby creating a source in the hyperbolic frequency band without a corresponding dipole transition. We demonstrate that even a source with vanishing dipole and higher multipole moments - strictly non-radiating in any isotropic medium - becomes radiatively active in a hyperbolic environment. This enables visible and near-infrared control of light-matter interactions in polaritonic hyperbolic materials, establishing a new low-loss solid-state quantum optics platform.

14.
arXiv (CS.AI) 2026-06-15

Hy-Embodied-0.5-VLA: From Vision-Language-Action Models to a Real-World Robot Learning Stack

arXiv:2606.14409v1 Announce Type: cross Abstract: In this report, we present Hy-Embodied-0.5-VLA, abbreviated as HyVLA-0.5, an end-to-end system that spans the full robot learning stack: data collection, model design, continued pre-training and supervised fine-tuning, RL post-training, and real-world deployment. Each component serves a distinct role in this stack.

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

DDTNet: Degradation Disentanglement and Transfer Network for Test-Time All-in-One De-weathering Adaptation

All-in-one adverse weather image restoration aims to remove multiple degradations, such as rain, haze, and snow, using a single unified model. Despite their broad applicability, existing methods typically compromise performance, delivering balanced but suboptimal results for individual degradation types. This issue becomes more pronounced when a domain gap exists between training and testing data. Motivated by the observation that modeling degradation patterns is more feasible than recovering clean content, we propose the Degradation Disentanglement and Transfer Network (DDTNet), which focuses specifically on degradation transfer. By disentangling degradation patterns from target-domain degraded images and transferring them to source domain clean images, DDTNet generates domain-adaptive paired training data. These pairs are then used to fine-tune restoration models, significantly enhancing their adaptability across diverse weather conditions and domains. The core of DDTNet is the Degradation Disentanglement Module (DDM), which comprises Degradation Coupled Attention (DCA) to capture both general and weather-specific features, thereby enabling effective disentanglement and transfer of degradation patterns. Experimental results demonstrate that DDTNet significantly and consistently improves existing all-in-one models across real-world deraining, desnowing, and dehazing datasets.

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

Configurable Clinical Information Extraction with Agentic RAG: What Works, What Breaks, and Why

arXiv:2606.19602v1 Announce Type: new Abstract: Patient contexts span hundreds of heterogeneous documents and thousands of structured data points, yet the document-level metadata that AI systems need for retrieval and triage is absent or incomplete. Standard retrieval-augmented generation fails on this data, mishandling temporal reasoning, cross-document dependencies, and missing metadata. We deploy ACIE (Agentic Clinical Information Extraction) at University Medicine Essen: an on-premise agentic RAG pipeline that reasons over complete patient contexts and grounds every answer in source passages for clinician verification. We quantify the metadata gap, trace the architectural decisions it shaped, and evaluate extraction alongside an independent retrospective lymphoma registry study, in which nuclear-medicine physicians verify every extracted value against its cited sources. Across 7,326 judgments, clinicians accepted 96.5\% of extractions, with per-type acceptance ranging from 80\% to 99\%.

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

SHARD: Safe and Helpful Alignment via Self-Reframing Distillation

Large language models often struggle with sensitive prompts. They may refuse outright, provide generic safety boilerplate, or fail to address the user's legitimate informational needs that can be answered safely. We introduce SHARD, a self-reframing distillation method to improve safe-helpfulness. It first rewrites sensitive prompts to surface benign intent using philosophical guidelines, then reframes its original responses into safe, more helpful ones, and finally fine-tunes the model on its self-reframed responses. Across DNA and the English subset of LINGUASAFE, SHARD improves helpfulness for most model families while preserving safety. It also remains competitive with distillation from a larger teacher model, suggesting that models can internalize safe and helpful behavior elicited from their own. Warning: This paper contains content that may be offensive or harmful.

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

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

arXiv:2606.18506v1 Announce Type: new Abstract: Objective sleep assessment relies on polysomnography (PSG), yet clinical impact is often better reflected in patient-reported outcomes (PROs) such as sleepiness and fatigue. Existing summary indices, including the Apnea-Hypopnea Index (AHI), provide limited insight into the multidomain physiology underlying functional recovery. We propose an interpretable, causal-discovery–guided framework for deriving a hierarchical Sleep Recovery Score (SRS) from multimodal PSG. Using two large population cohorts (MESA: n=1540; MrOS: n=825), we apply directed acyclic graph (DAG) learning to identify candidate physiological drivers spanning respiratory burden, hypoxic burden, sleep fragmentation, sleep architecture, and autonomic regulation. Although derived from clinical PSG, these domains map naturally to sensing streams increasingly available in connected health technologies, including wearable ECG, oximetry, and sleep-stage estimation devices. To preserve mechanistic plausibility, we introduce a two-stage screening process that combines physiology-based constraints with constrained LLM-assisted auditing to identify and remove structural confounders and construct-overlapping variables. Across cohorts, these five domains emerge as recurrent physiological domains associated with recovery, and the resulting SRS shows up to 2.5$\times$ stronger alignment with perceived recovery than AHI. By linking multimodal sleep physiology to patient-centered outcomes through an interpretable, bias-aware, and domain structured framework, this work provides a practical foundation for recovery modeling across both clinical sleep studies and emerging smart and connected health settings.

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

Unified Multimodal Autoregressive Modeling with Shared Context-Visual Tokenizer is Key to Unification

Unified Multimodal Modeling aims to integrate visual understanding and generation within a single system. However, existing approaches typically rely on two disparate visual tokenizers, which splits the representation space and hinders truly unified modeling. We propose UniAR, a unified autoregressive framework where a single discrete visual tokenizer serves as the key bridge between understanding and generation, enabling a shared context in which the model can directly interpret its own generated visual tokens without additional re-encoding. UniAR adapts a pretrained vision encoder with multi-level feature fusion and a lookup-free bitwise quantization scheme, preserving both high-level semantics and low-level details while scaling the effective visual vocabulary at minimal cost. Building on this, the unified autoregressive model adopts parallel-bitwise-prediction to jointly predict spatially grouped, multi-level visual codes, substantially reducing visual sequence length and accelerating generation. Finally, a diffusion-based visual decoder operates on discrete visual tokens to decode high-fidelity images. Through large-scale pre-training, followed by supervised fine-tuning and reinforcement learning, UniAR achieves state-of-the-art performance on image generation and image editing while remaining competitive on multimodal understanding benchmarks. The project page is available at https://sharelab-sii.github.io/uniar-web.

20.
arXiv (quant-ph) 2026-06-12

More efficient Clifford+T synthesis for small-angle rotations and application to Trotterization

arXiv:2605.31544v2 Announce Type: replace Abstract: Clifford+T synthesis of rotation gates is an important routine in fault-tolerant quantum compilation. While Clifford+T synthesis is scalable, it has a high overhead of tens of T gates per rotation in practice, translating to high resource estimates for many fault-tolerant algorithms. However, these well-known results, including those using probabilistic mixtures [Quantum 7, 1208 (2023)], are independent of the rotation angle $\theta$, requiring $O(\log 1/\delta)$ T gates. We show that it is possible to do much better for small angles, reducing the T cost to $\tilde{O}(\theta^2/\delta)$, and returning to existing $O(\log1/\delta)$ results in the worst case. This is particularly important since many algorithms, such as Trotterization, are dominated by small-angle rotations. Further, we perform a detailed theoretical and numerical study of quasi-probabilities, which can further reduce the total T cost of large circuits by orders of magnitude with only a small overhead in sample complexity. We also develop a scheme based on quasi-probability mixtures of Clifford+T fallback channels. We derive new $\theta$-dependent formulas that can be used for resource estimation of fault-tolerant quantum algorithms. As an application of our results, we show that the gate cost of Trotterization circuits compiled to a Clifford+T gate set is constant in the small Trotter step size limit, and can be reduced by orders of magnitude even for large step sizes. The cost of fault-tolerant Trotterization for a variety of applications should be re-examined in light of these results. Our work dispels the widely-stated claim that Clifford+T rotation synthesis has a high cost independent of $\theta$, and further develops a scalable quasi-probability method for rotation synthesis. We also expect our results to bring forward useful early fault-tolerant quantum computing by reducing required magic state resources.

21.
arXiv (CS.AI) 2026-06-16

Theorem-Grounded Execution Ontologies for Interpretable Machine Reasoning

arXiv:2606.16010v1 Announce Type: cross Abstract: Large language models have achieved impressive performance on reasoning tasks spanning mathematics, science, programming, and commonsense inference. Despite these advances, their reasoning processes remain largely latent, making them difficult to interpret, verify, replay, debug, and transfer across domains. Existing approaches such as chain-of-thought, tree-of-thoughts, graph-of-thoughts, and tool-augmented reasoning expose intermediate reasoning artifacts but typically lack explicit execution semantics, formal state representations, and verifiable reasoning structures. We introduce Theorem-Grounded Execution Ontologies (TGEO), a framework that models reasoning as an executable state-transition process rather than a sequence of generated tokens. Given an input problem, TGEO identifies relevant theorem families, binds the problem to a domain ontology, discovers semantic objects, instantiates states and operators, constructs predicates and contracts, and synthesizes an executable reasoning graph. The resulting graph provides an interpretable, replayable, and auditable representation of reasoning in which every state transition, operator application, and validation step is explicitly represented. TGEO integrates five architectural components: (1) theorem-grounded reasoning priors, (2) executable ontologies, (3) operator-mediated state transitions, (4) predicate and contract-based execution validation, and (5) architectural auditing and failure localization. We evaluate TGEO on theorem-intensive reasoning tasks derived from mathematical benchmark domains and a curated Golden Execution Suite. Our findings demonstrate the value of executable reasoning representations for interpretable, verifiable, and reproducible AI reasoning systems.

22.
arXiv (CS.AI) 2026-06-11

End-to-End Machine Learning for Depressive State Classification via EEG and fNIRS

arXiv:2606.11555v1 Announce Type: cross Abstract: The escalating demand for mental healthcare, driven by rising societal stress, highlights the limitations of traditional psychiatric diagnostics. Conventional methods - relying primarily on clinical interviews and patient self-reports - are inherently vulnerable to subjective bias and the varying empirical judgment of practitioners. To address the need for quantitative evaluation, biological signal-based detection, including electroencephalography (EEG) and functional near-infrared spectroscopy (fNIRS), has emerged as a promising objective alternative. Such technology is particularly vital for identifying latent depressive states that may be unrecognized by the subjects themselves. Furthermore, in aging populations, the high comorbidity between depression and dementia necessitates early differentiation to prevent mutual symptom exacerbation and maintain Quality of Life (QoL). This pilot study of eleven healthy students establishes a framework for biological signal-based depression detection, serving as a foundational step toward automated, objective diagnostic tools for clinical use.

23.
bioRxiv (Bioinfo) 2026-06-16

Better data, better trees: GenBank-GISAID deduplication and source-specific artifact masking in viral genomics

GenBank and GISAID are the primary repositories for viral genomic data, but integrating records across them remains a challenge. The same sequence could be made available in both databases without any cross-reference linking the two entries. Consequently, there is no systematic way to identify this redundancy, which compromises the compilation of representative, non-redundant large-scale datasets. In parallel, the growth of viral genomic data has increased the risk of systematic technical artifacts introduced during sequencing or assembly. These artifacts can inflate substitution rate estimates and degrade temporal signal, biasing evolutionary rate estimates. To address both challenges, here we present a formal, reproducible workflow integrating two newly developed complementary tools: G2G matcher for cross-repository harmonization and Lab-Specific Bias FILTer (LSBFILT) for masking of laboratory-specific artifacts. Using the Eastern/Central/South African (ECSA) chikungunya virus lineage as a proof-of-concept, we demonstrate that our integrated workflow restores temporal signal and provides a robust, curated dataset for downstream phylodynamic analyses. Critically, restricting masking of homoplastic sites to specific sequences reduces the substitution rate estimate from an inflated 8.517 x 10e-4; to 5.078 x 10e-4; substitutions/site/year and increases the coefficient of determination (R2) of the root-to-tip regression analysis from 0.353 to 0.677. By enabling systematic cross-repository harmonization and source-specific artifact masking, we provide the molecular epidemiological community with scalable tools to reconcile fragmented genomic data and reduce technical biases, fostering more accurate and reproducible phylogenetic analysis. G2G matcher is available at https://github.com/andrezaleite/G2G-Matcher, and LSBFILT at https://github.com/khourious/LSBFILT.

24.
bioRxiv (Bioinfo) 2026-06-14

Generative design of antigen-specific T-cell receptor sequences with a conditional diffusion model

T cell receptor (TCR)-based immunotherapy holds immense potential for treating cancers and infectious diseases, where highly antigen-specific TCR recognition is crucial for adaptive immunity against tumors and pathogens. Engineering or de novo generation of the complementarity-determining region 3 (CDR3) loops of TCRs using artificial intelligence offers a powerful alternative to designing reactive TCRs rather than laborious experimental screening. However, current in silico approaches are constrained by weak conditional guidance, limited flexibility, and a lack of rigorous functional validation. To address these limitations, we introduce TCRDiff, a generative diffusion framework for designing antigen-specific TCRs conditioned on peptide-MHC (pMHC) targets and germline-encoded variable genes. By leveraging pre-trained knowledge from massive T-cell repertoires and TCR-pMHC recognition data, TCRDiff generates CDR3{beta} sequences with state-of-the-art fidelity to native binding TCRs through a denoising diffusion process. Furthermore, incorporating the interface geometry features generated TCR-pMHC complexes with superior structural plausibility. As a proof of concept, we deployed TCRDiff in a systematic pipeline to design candidate TCRs for immunotherapy. In vitro activation assays validated that TCRDiff-generated TCRs specifically recognize the MAGE-A3 epitope with minimized off-target cross-reactivity. Together, TCRDiff establishes a powerful, validated computational paradigm to accelerate the development of TCR-based immunotherapies.

25.
arXiv (CS.CV) 2026-06-16

OneFocus: Enabling Real-World X-ray Security Screening with a Unified Vision-Language Model

X-ray contraband detection is critical for security in large-scale logistics and transportation, yet conventional detectors struggle to adapt to emerging contraband types and lack fundamental visual understanding. Vision-language models (VLMs) offer strong generalization but are hindered by the scarcity of high-quality X-ray image-caption data. To bridge this critical gap, we present MMXray, a meticulously curated benchmark of 52,124 image-caption pairs spanning 28 fine-grained classes of X-ray contraband. To enrich MMXray with realistic occlusion patterns, we further introduce CleanDET, a dedicated synthesis dataset containing clean foreground contraband images from 28 categories and background images with diverse density levels, together with AnyContraSyn, a controllable synthesis method designed to operate on CleanDET. We also develop OnePipe, an extensible pipeline for systematic data curation. Built on MMXray, we propose OneFocus, a unified VLM that supports four core tasks: visual question answering, contraband localization, classification, and image understanding. OneFocus achieves state-of-the-art performance in X-ray contraband understanding and demonstrates robust cross-domain generalization, establishing a strong vision-language baseline for security screening.