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

Automatic Summarization of Doctor-Patient Encounter Dialogues Using Large Language Model through Prompt Tuning

Automatic text summarization (ATS) is an emerging technology to assist clinicians in providing continuous and coordinated care. This study presents an approach to summarize doctor-patient dialogues using generative large language models (LLMs). We developed prompt-tuning algorithms to instruct generative LLMs to summarize clinical text. We examined the prompt-tuning strategies, the size of soft prompts, and the few-short learning ability of GatorTronGPT, a generative clinical LLM developed using 277 billion clinical and general English words with up to 20 billion parameters. We compared GatorTronGPT with a previous solution based on fine-tuning of a widely used T5 model, using a clinical benchmark dataset MTS-DIALOG. The experimental results show that the GatorTronGPT- 20B model achieved the best performance on all evaluation metrics. The proposed solution has a low computing cost as the LLM parameters are not updated during prompt-tuning. This study demonstrates the efficiency of generative clinical LLMs for clinical ATS through prompt tuning.

02.
arXiv (CS.AI) 2026-06-17

Prototype-Based Semantic Consistency Alignment for Domain Adaptive Retrieval

arXiv:2512.04524v4 Announce Type: replace-cross Abstract: Domain adaptive retrieval aims to transfer knowledge from a labeled source domain to an unlabeled target domain, enabling effective retrieval while mitigating domain discrepancies. However, existing methods encounter several fundamental limitations: 1) neglecting class-level semantic alignment and excessively pursuing pair-wise sample alignment; 2) lacking either pseudo-label reliability consideration or geometric guidance for assessing label correctness; 3) directly quantizing original features affected by domain shift, undermining the quality of learned hash codes. In view of these limitations, we propose Prototype-Based Semantic Consistency Alignment (PSCA), a two-stage framework for effective domain adaptive retrieval. In the first stage, a set of orthogonal prototypes directly establishes class-level semantic connections, maximizing inter-class separability while gathering intra-class samples. During the prototype learning, geometric proximity provides a reliability indicator for semantic consistency alignment through adaptive weighting of pseudo-label confidences. The resulting membership matrix and prototypes facilitate feature reconstruction, ensuring quantization on reconstructed rather than original features, thereby improving subsequent hash coding quality and seamlessly connecting both stages. In the second stage, domain-specific quantization functions process the reconstructed features under mutual approximation constraints, generating unified binary hash codes across domains. Extensive experiments validate PSCA's superior performance across multiple datasets.

03.
arXiv (CS.LG) 2026-06-19

Sparsity, Superposition, and Forgetting: A Mechanistic Study of Representation Retention in Continual Learning

arXiv:2606.20431v1 Announce Type: new Abstract: Continual learning (CL) systems often forget previously acquired knowledge, yet the mechanisms driving forgetting remain hard to isolate in practice because real datasets entangle many factors. We present a controlled, toy-world framework that makes these mechanisms observable and testable. Using a synthetic generator-separator pipeline, we define ground-truth latent features, build tasks with tunable sparsity and overlap, and introduce measurable quantities for representation strength and superposition (directional overlap among features). We then study retention dynamics-the temporal change of representation strength by fitting sparse dynamical relations (via SINDy) between retention, superposition, and exposure history. A complementary task-level analysis based on effective rank characterizes how representational capacity is allocated across tasks. Our controlled experiments yield three takeaways. (1) Superposition tends to increase over time with transient dips at task boundaries, suggesting boundary-specific interference rather than steady drift. (2) Higher feature sparsity induces more superposition yet does not inevitably cause forgetting; when representations remain strong, forgetting can be reduced despite overlap. (3) Task-level effective rank grows with sparsity, indicating broader capacity usage under sparse regimes. Together, these results nuance the common intuition that more superposition leads to more forgetting by showing that overlap interacts with representation strength and capacity allocation. Our toy analysis provides falsifiable hypotheses and diagnostic tools for CL.

04.
arXiv (CS.CL) 2026-06-24

MMed-Bench-IR: A Heterogeneous Benchmark for Multilingual Medical Information Retrieval

Retrieval-augmented generation (RAG) in clinical settings increasingly requires multilingual retrieval against predominantly English evidence corpora. Multilingual medical retrieval demands three capabilities: cross-lingual alignment, concept discrimination, and evidence retrieval. However, existing benchmarks evaluate these only in isolation, leaving the interaction between biomedical expertise and multilingual coverage unmeasured. We introduce MMed-Bench-IR, a benchmark designed to disentangle these axes across 6 languages and three structurally heterogeneous tasks: (1) cross-lingual medical QA retrieval with 6,127 queries grounded in the Unified Medical Language System (UMLS), (2) concept discrimination over 4,975 confusion sets at three difficulty tiers, and (3) multilingual evidence retrieval for RAG with 2,040 quality-assured queries. The three tasks share zero concept and query overlap by design, ensuring that aggregate scores reflect genuine capability breadth. Evaluation of ten systems across six paradigm families reveals severe cross-lingual failure: biomedical encoders that score 0.818 nDCG@10 in English drop to 0.056 in Japanese, a gap that English-only benchmarks cannot detect.

05.
arXiv (CS.AI) 2026-06-16

ChatPlanner: A Large Language Model Framework for Personalized Public Transit Routing

arXiv:2606.15315v1 Announce Type: new Abstract: Personalized public transit routing in public transit systems remains challenging due to the difficulty of capturing and integrating diverse user preferences into routing algorithms. This paper presents ChatPlanner, a novel framework that leverages Large Language Models (LLMs) to enable preference aware public transit routing. Our approach employs fine-tuned LLMs with Retrieval-Augmented Generation (RAG) to extract routing parameters and interpret nuanced user preferences from natural language queries, subsequently integrating these preferences into the objective function of a public transit routing algorithm. This study designs preference aware datasets incorporating eight personas and five contexts to establish scoring standards for both fine-tuning and RAG. This work conducted three experiments to validate the solutions' feasibility, extraction of routing information and preferences, and solution set quality and completeness. Results demonstrate that ChatPlanner generates feasible solutions reliably. Fine-tuning enforces the required output structure and learns general preference patterns, while RAG provides query-specific context to resolve imprecise or conversational expressions and calibrate continuous scores. The combination of both achieves the highest accuracy in routing information extraction and user preference interpretation. Results based on selected case studies show that by capturing user preferences, ChatPlanner identifies valuable solutions across different dimensions that existing route planners overlook, generating more valuable route alternatives. This research establishes a new paradigm for integrating natural language understanding into transportation optimization.

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

Uncertainty Decomposition for Clarification Seeking in LLM Agents

Recent position papers argue that the classical aleatoric/epistemic uncertainty framework is insufficient for interactive large language model (LLM) agents and call for underspecification-aware, decomposed, and communicable uncertainty representations that can unlock new agent capabilities such as proactive clarification seeking and shared mental-model building. Practical deployment constraints – black-box APIs, interactive latency budgets, and the absence of labeled trajectories – rule out logprob-based, multi-sampling, and training-based methods, leaving prompt-based estimation as the most viable family for surfacing such signals at deployment time. We answer this call with a simple prompt-based decomposition that separates action confidence from request uncertainty (u), enabling the agent to ask for clarification when the task specification is ambiguous. To evaluate it, we introduce two clarification-augmented benchmarks (WebShop-Clarification and ALFWorld-Clarification) in which 50% of tasks are deliberately underspecified, and systematically compare the proposed decomposition against ReAct+UE and Uncertainty-Aware Memory (UAM) across five LLM backbones (GPT-5.1, DeepSeek-v3.2-exp, GLM-4.7, Qwen3.5-35B, GPT-OSS-120B) on these variants together with the standard WebShop, ALFWorld, and REAL benchmarks for fault detection. Averaged across the five backbones, the proposed decomposition improves clarification F1 on ALFWorld-Clarification by 73% over ReAct+UE and by 36% over UAM, and leads clarification F1 on every backbone on WebShop-Clarification and on four of five backbones on ALFWorld-Clarification, indicating that the gains generalize beyond a single LLM.

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

Normative Robustness as a Frontier for Non-Verifiable Reasoning in LLMs

arXiv:2606.12731v1 Announce Type: new Abstract: As LLMs increasingly serve in advisory and deliberative roles, users rely on them for non-verifiable reasoning in domains lacking objective ground truths. However, traditional evaluations of LLM reasoning focus almost exclusively on fact-based domains, such as mathematics and science, leaving uncertainty over whether and to what degree models can handle ambiguous, subjective, or value-laden problems over time. To address this concern, we propose moral reasoning as a paradigmatic subdomain of non-verifiable reasoning. We define moral robustness as a model's capacity to exhibit sound moral reasoning across time and contexts, and we introduce a scalable, adversarial, multi-turn evaluation framework to empirically measure this capability. We simulate 48,000 user-agent moral deliberations across four frontier LLMs, varying premise relevance, premise order, conversation duration, and the user's stated moral view. We find that models successfully ignore morally-irrelevant distractors, but shift their reasoning by up to 6.5%, on average, towards the user's stated preferred moral view, and varying their reasoning depending on factors such as order (altering moral judgments by order in 13-22% of the cases) and duration (altering moral judgments between single-turn and multi-turn in 10-24% of the cases). Our analysis indicates that models tailor not just their final verdicts but their underlying justifications to align with a user's moral viewpoint - a failure mode we characterize as moral deliberative sycophancy.

08.
arXiv (CS.AI) 2026-06-11

FreeBridge: Variational Schrödinger Bridges for Cellular Transition Dynamics

arXiv:2606.11286v1 Announce Type: cross Abstract: High-content imaging assays quantify cellular responses to chemical and genetic perturbations, yet continuous trajectories of individual cells are unobservable because cells are chemically fixed at acquisition. Perturbation modeling therefore reduces to inferring stochastic transport between control and treated populations observed only as separate marginals. While recent generative models achieve strong end-point alignment, boundary consistency does not determine intermediate evolution: multiple stochastic processes may connect identical marginals while traversing regions unsupported by observed single-cell morphologies. We introduce FreeBridge, a Schrödinger Bridge formulation for single-cell transition modeling under endpoint-only supervision. FreeBridge defines atomic states as instance-segmented single-cell representations, establishing a fixed cellular manifold, and learns stochastic transport constrained within this geometry via empirical latent support regularization. Across BBBC021, RxRx1, and JUMP, FreeBridge maintains competitive or improved endpoint fidelity and mechanism-of-action retention under a unified evaluation protocol; on BBBC021, it further reduces intermediate support violations. These findings highlight the importance of geometric grounding for biologically interpretable perturbation dynamics. Project page: https://y-research-sbu.github.io/FreeBridge/.

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

DriveJudge: Rethinking Autonomous Driving Evaluation with Vision-Language Models

Autonomous driving has shifted towards end-to-end policy learning, where reliable, interpretable policy evaluation is a fundamental challenge as driving quality is highly context-dependent. Commonly used rule-based driving metrics like EPDMS are interpretable but lack context-awareness, while recent VLMbased evaluations are context-aware but limited by ambiguous VLM outputs and weak physical grounding. To evaluate driving in a manner that is both interpretable and context-aware, we introduce DriveJudge. DriveJudge is a driving evaluation agent that combines rule-grounded evaluation with Vision-Language Model (VLM) reasoning and selectively invokes physically-grounded deterministic rule functions after interpreting the environmental context. To train and evaluate DriveJudge, we curate a large-scale dataset of 33,577 challenging driving samples with human annotations on whether the driving behavior is reasonable in the given scenario. With this dataset, we address the underexplored problem of driving metric evaluation, and introduce two human-aligned benchmark tasks: Driving Quality Classification and Trajectory Preference Selection. DriveJudge outperforms EPDMS for driving quality classification by 21.23 AUC, and the recent VLM-based DriveCritic for trajectory preference selection by 6.5%, setting a new standard for interpretable and precise driving evaluation.

10.
bioRxiv (Bioinfo) 2026-06-10

GEOAgent: An AI-driven Autonomous Framework for Intelligent GEO Data Retrieval and Standardized Preprocessing

Datasets in the Gene Expression Omnibus (GEO) remain difficult to reuse at scale because sample annotations are heterogeneous and raw sequencing data require assay-specific preprocessing. We present GEOAgent, an AI-driven autonomous framework designed for intelligent dataset retrieval and standardized preprocessing by coupling autonomous semantic governance with an automated Nextflow pipeline named bioStream. Metadata from 181,760 sequencing series and 84,756 associated PubMed records were organized in a relational database and semantic index to support natural-language dataset retrieval. The framework automatically determines assay modalities, resolves experimental design pairings, and standardizes sample naming to minimize manual curation overhead. Based on these parsed attributes, the framework generates deployment-ready manifests to automatically execute containerized workflows across bulk and single-cell omics modalities. In expert-curated benchmarks, the workflow achieved 96% retrieval precision alongside 100% accuracy in assay classification and sample relationship resolution. The web platform is publicly accessible, while the source code and associated databases are openly available via GitHub and Zenodo.

11.
arXiv (math.PR) 2026-06-19

A Cycle Walk for Sampling Measures on Spanning Forests for Redistricting

arXiv:2509.08629v2 Announce Type: replace-cross Abstract: We introduce the Cycle Walk, a new Markov chain Monte Carlo method for sampling distributions on balanced graph partitions, motivated by applications in political redistricting. The method operates on spanning forests and combines two types of updates: local "cycle" moves within districts and global moves that exchange population between adjacent districts while preserving balance constraints. This construction enables efficient Metropolis–Hastings correction while allowing proposals at multiple spatial scales. We show that the Cycle Walk naturally interpolates between existing approaches based on local updates and a class of global update methods derived from recombination (RECOM). Through a range of numerical experiments on synthetic graphs and real-world precinct data, we demonstrate that the Cycle Walk exhibits improved empirical convergence diagnostics for distributions that place weaker weight on spanning-tree counts, a regime that is challenging for existing methods. In particular, the algorithm remains effective when incorporating alternative compactness measures that more closely reflect policy-relevant criteria. These results suggest that the Cycle Walk provides a flexible and computationally efficient framework for sampling from a broader class of redistricting distributions than previously accessible with MCMC techniques.

12.
arXiv (CS.LG) 2026-06-17

Tight $L_\infty$ Sample Complexity for Low-Degree and Sparse Boolean Polynomials

arXiv:2606.17319v1 Announce Type: cross Abstract: Motivated by the optimization of bounded binary black-box functions, we study the problem of learning polynomial surrogates over the Boolean hypercube. To ensure that optimizing the surrogate yields good solutions for the underlying objective, we require uniform $L_\infty$-error guarantees rather than the usual $L_2$-type guarantees. We characterize the minimax sample complexity of uniform estimation under subgaussian noise for two classes of bounded polynomials. First, for polynomials of degree at most $d$ on $n$ variables, the sample complexity scales as $n^{d+1}$. Second, for $s$-sparse Fourier-Walsh polynomials with $s \leq n$, it scales as $ns^2$. These rates differ structurally from the noiseless setting, where uniform exact recovery scales as $n^d$ and $ns$, respectively. Our lower bounds hold even for arbitrary adaptive learners, showing that the additional factors are intrinsic to the noisy cases. Standard Fourier-analysis tools for the $L_2$-norm do not naturally extend to the $L_\infty$-setting in a way that yields uniform guarantees. Our proofs overcome this difficulty by relying on suitably chosen auxiliary norms that serve as proxies for controlling the $L_\infty$-error. Together, our results provide a tight characterization of the sample complexity of learning optimization-safe polynomial surrogates.

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

The algebra of Krom logic programs

arXiv:2606.15719v1 Announce Type: cross Abstract: This paper investigates the algebraic structure of Krom logic programs, consisting only of facts and rules with at most one body atom. We show that sequential composition endows the class of Krom programs with a natural monoid structure and that this structure admits rich algebraic extensions to Krom seminearrings, Krom quemirings, Krom-Conway seminearrings, and Krom-Conway omegaseminearrings. Furthermore, we establish explicit generating sets and canonical decompositions, study the associated ${}^\omega$-operator, characterize the Kleene star in graph-theoretic terms, and relate finite Krom monoids to transformation monoids and finite-state automata. These results provide new connections between logic programming, algebraic automata theory, and algebraic graph theory.

14.
arXiv (CS.CV) 2026-06-12

ReFoCUS: Reinforcement-guided Frame Optimization for Contextual Understanding

Recent progress in Large Multi-modal Models (LMMs) has enabled effective vision-language reasoning, yet the ability to video understanding remains constrained by suboptimal frame selection strategies, albeit with the rapid development of video-specialized LMMs. Prior works attempted to solve this with static heuristics or external retrieval modules to feed frame-level information, but these approaches often fail to capture visual cues grounded to the given user queries conflating raw visual dynamics with true semantic relevance. In this paper, we introduce ReFoCUS (Reinforcement-guided Frame Optimization for Contextual UnderStanding), the first framework to integrate online policy-gradient reinforcement learning into frame-level optimization for video-LLMs. ReFoCUS aims to learn a frame selection policy, leveraging reward signals derived from reference models to capture their underlying scoring behavior over frame combinations that best support temporally grounded responses. To efficiently explore the large combinatorial frame space, we employ an autoregressive and query-conditional selection architecture that ensures contextual consistency while reducing complexity. Our policy learning removes the need for explicit frame-level supervision, as it implicitly discovers optimal and semantically consistent frame compositions. ReFoCUS consistently improves reasoning accuracy across multiple video QA benchmarks, demonstrating the advantage of aligning frame selection with model-internal utility.

15.
arXiv (CS.AI) 2026-06-17

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

Authors:

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.

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

Steady-State Noise Signatures of Lindbladian Exceptional Points

arXiv:2606.13377v1 Announce Type: new Abstract: Exceptional points (EPs) are non-Hermitian degeneracies at which two or more eigenvalues and their corresponding eigenvectors coalesce. In open quantum systems, exceptional points can arise in the Lindbladian governing the dissipative dynamics. Their signatures have so far been mainly identified in finite-time observables, such as transient currents, while steady-state average currents generally provide no direct evidence of the underlying exceptional-point structure. In this work, we demonstrate that signatures of Lindbladian EPs can nevertheless be accessed in the steady-state regime through current noise. We derive general expressions for current correlation functions within a Lindblad master-equation framework and show, in particular, how exceptional points affect their behaviour as a function of the time delay. We illustrate these results with the paradigmatic example of two interacting qubits coupled to two reservoirs, where the steady-state noise clearly distinguishes overdamped, underdamped, and critical regimes. Our results establish current correlation functions as a steady-state probe of Lindbladian EPs in open quantum systems.

17.
arXiv (CS.AI) 2026-06-15

Where's the Plan? Locating Latent Planning in Language Models with Lightweight Mechanistic Interventions

arXiv:2605.07984v2 Announce Type: replace-cross Abstract: We study planning site formation in language models – where internal representations of structurally-constrained future tokens form during the forward pass, and whether they causally drive generation. Using rhyming-couplet completion as a clean test of forward-looking constraint, we apply two lightweight methods (linear probing and activation patching) across Qwen3, Gemma-3, and Llama-3 at more than ten scales. Probing shows that future-rhyme information is linearly decodable at the line boundary, with signal that strengthens with scale in all three families. Activation patching reveals that only Gemma-3-27B causally relies on this encoding, exhibiting a handoff in which the causal driver migrates from the rhyme word to the line boundary around layer 30. Every other model we test conditions on the rhyme word throughout generation, with near-zero causal effect at the line boundary despite strong probe signal. We localize the Gemma-3-27B handoff to five attention heads through two-stage path patching that recover ~90% of the rhyme-routing capacity at the newline.

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

PEC-Home: Interpretation of Progressively Elliptical Commands in Smart Homes

Recent advancements in Large Language Models (LLMs) have empowered home assistants with natural language interaction capabilities. However, current assistants overlook the progressive omission that occurs in human dialogue as shared context accumulates, leading to more elliptical expressions for efficient communication. Thus, current assistants still struggle to interpret such elliptical expressions accurately, which limits their effectiveness in real-world applications. In practical smart home scenarios, assistants face two major challenges caused by elliptical commands: (1) referential ambiguity caused by different environmental expectations among multiple users; and (2) intention ambiguity resulting from user preferences that evolve over time or change with the environment. To address these challenges, we introduce PEC-Home, the first simulated home dataset specifically designed for interpreting progressively elliptical commands in smart homes. Extensive experiments on various LLMs, including GPT-4o, show that existing home assistants struggle to execute user-intended operations based solely on elliptical commands. Even when equipped with tools for storing and retrieving user dialogue history, execution accuracy remains below that achieved with complete commands.}.

19.
arXiv (CS.CL) 2026-06-11

Context-Aware Multimodal Claim Verification in Spoken Dialogues

Every day, millions absorb claims from podcasts and streams that no fact-checker ever sees. Spoken misinformation is built through conversation, where credibility comes not from facts alone but from how claims are framed, reinforced, or left unchallenged across turns. Yet fact-checking has focused on isolated text, leaving dialogue audio under-studied. We introduce MAD2, a new Multi-turn Audio Dialogues benchmark for spoken claim verification, containing 1,000 two-speaker dialogues with 3,368 check-worthy claims and approximately 10 hours of audio, and propose calibrated multimodal fusion of a context-aware audio encoder and a dialogue-aware text model. Across settings, adding dialogue context improves verification, but the gains depend on scenario type. Using only preceding context often matches offline performance, supporting live-moderation settings, and audio contributes most when transcript-based models are destabilized by additional context. Overall, conversational structure matters more for verification than misinformation framing.

20.
arXiv (CS.AI) 2026-06-18

Fully Geometric Multi-Hop Reasoning on Knowledge Graphs with Transitive Relations

arXiv:2505.12369v2 Announce Type: replace Abstract: Multi-hop logical reasoning on knowledge graphs requires faithfully mapping the logical semantics to latent space. Current geometric embedding methods show to be useful on this task by mapping entities to geometric regions and logical operations to latent transformations. While a geometric embedding can provide a direct interpretability framework for query answering, current methods have only leveraged the geometric construction of entities, failing to map logical operations to pure geometric transformations and, instead, using neural components to learn these operations. On the other hand, purely neural-based methods outperform geometric methods, but they lack interpretability in the latent space. We introduce GeometrE, a geometric embedding method for multi-hop reasoning, that maps every logical operation to a purely geometric operation in the latent space. Additionally, we introduce a transitive loss function and show that, unlike existing methods, it can preserve the logical rule for all a,b,c: r(a,b) and r(b,c) -> r(a,c). Our experiments show that GeometrE outperforms current state-of-the-art geometric methods and remains competitive with existing neural-based methods on standard benchmark datasets.

21.
bioRxiv (Bioinfo) 2026-06-08

TRACEY: an updated resource for SNARE protein domain annotation with improved HMMs and expanded sequence coverage

Motivation: SNARE proteins catalyse membrane fusion across the eukaryotic endomembrane system, from synaptic vesicle exocytosis to intracellular trafficking, endosomal and vacuolar transport, and autophagy, and their accurate domain annotation depends on the quality of profile models and the sequence diversity behind them. The original SNARE domain classification predates the recent expansion of eukaryotic sequence data, leaving its HMM profiles and subgroup coverage unable to resolve divergent and lineage-specific paralogs. Results: We present an updated release of TRACEY built on a resynchronized, non-redundant collection of 18,915 curated SNARE proteins spanning 1,188 species, together with a consolidated set of 83 HMM profiles, including 43 models for newly defined subgroups, reconstructed through an iterative, mixture-model-driven procedure. In direct comparison with the legacy models, at least ~75% of sequences in every overlapping group scored better with the new HMMs, indicating systematic gains in domain detection. A redesigned web interface adds multiparameter querying, FASTA download, and direct scanning of user-submitted sequences against the curated profiles. Availability and implementation: TRACEY is freely available at https://tracey.unil.ch.

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

PaperJury: Due-Process Review for Bounded LaTeX Revision

Pre-submission hardening of human-authored LaTeX computer science papers differs from drafting assistance because it requires adversarial whole-paper review, explicit no-fix outcomes, and bounded artifact-safe revision. Existing writing assistants, critique generators, and judge-centered loops lack durable issue identity across rounds, deterministic routing from critique to adjudication, and manuscript control that can reject invalid concerns or defer author-dependent ones. We present PaperJury, a closed-loop review-verdict-revise-verify system built on a deterministic-versus-semantic split: deterministic orchestration manages decomposition, a frozen claim spine, a durable ledger, routing, stopping, and exact-once patch application, while semantic agents are limited to bounded review, judgment, and repair. PaperJury combines bounded holistic review, contestability-based routing, a due-process trial, and risk-proportional guard chains for anchor-bounded edits, yielding terminal outcomes of invalid-drop, valid-fixable, and author-required. In a two-arm expert-review evaluation on held-out Vision, natural language processing, and machine learning papers against four baselines, we assess issue quality, verdict and routing quality, edit safety, convergence behavior, and cost, supporting the thesis that load-bearing safety and completion logic should reside in deterministic orchestration rather than model discretion. PaperJury is available at https://github.com/u7079256/paperjury.

23.
Nature (Science) 2026-06-17

The ancestors of eukaryotic cells contained a mix of genes from various microbes

Authors: Unknown Author

Reconstruction of the ancestral gene repertoire of eukaryotic cells reveals traces of a series of close, long-term interactions with diverse microorganisms, and a role of viruses in gene exchange. The findings challenge the view that eukaryotic cells evolved from a simple merger of just two organisms. A series of gene-transfer events might have taken place in complex microbial communities.

24.
arXiv (CS.AI) 2026-06-19

AI-enhanced tuning of quantum dot Hamiltonians toward Majorana modes

arXiv:2601.02149v4 Announce Type: replace-cross Abstract: We propose a neural network-based model capable of learning the broad landscape of working regimes in quantum dot simulators, and using this knowledge to autotune these devices - based on transport measurements - toward obtaining Majorana modes in the structure. The model is trained in an unsupervised manner on synthetic data in the form of conductance maps, using a physics-informed loss that incorporates key properties of Majorana zero modes. We show that, with appropriate training, a deep vision-transformer network can efficiently memorize relation between Hamiltonian parameters and structures on conductance maps and use it to propose parameters update for a quantum dot chain that drive the system toward topological phase. Starting from a broad range of initial detunings in parameter space, a single update step is sufficient to generate nontrivial zero modes. Moreover, by enabling an iterative tuning procedure - where the system acquires updated conductance maps at each step - we demonstrate that the method can address a much larger region of the parameter space.

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

Library-Aware Doubles and Iterative Repair for Large Language Model-Generated Unit Tests in OpenSIL Firmware

arXiv:2606.19725v1 Announce Type: cross Abstract: Validating changes in low-level C firmware is expensive because unit tests (UTs) are fragile under strict build constraints, where missing headers, unresolved symbols, and dependency mismatches frequently prevent compilation and linking. This study introduces an automated UT authoring workflow for the Open-Source Silicon Initialization Library (openSIL) firmware codebase maintained by Advanced Micro Devices (AMD) that reduces manual effort through a large language model (LLM) guided multi-agent pipeline. The workflow combines automated generation of test scaffolds, library-aware creation or reuse of stubs, mocks, and fakes, and an iterative compile-dispatch repair loop driven by build logs and line-coverage feedback. We evaluate the approach using compilation success, repair iterations, dispatch success, and line coverage, with time, cost, and token usage as secondary measures. Across 76 functions under test, the workflow generated compilable UTs for 73 functions. In a configuration without line coverage guidance or retrieval augmentation, mean line coverage reached 73.9%. On a 48-function subset evaluated under both configurations, mean line coverage reached 98.8% with line-coverage guidance alone and reached 94.7% when combined with vector-database retrieval. Results show that automated generation-and-repair pipelines can substantially improve UT creation efficiency and coverage for constrained firmware environments while reducing manual debugging effort.