Academic Intelligence · Curated Daily

Explore the Frontier of Global Academia

AcademicHub aggregates real-time literature from top journals and preprint platforms. Build your personal research radar and let large language models compile cross-disciplinary analysis briefings automatically.

01.
arXiv (CS.AI) 2026-06-12

ReSum: Synergizing LLM Reasoning and Summarization with Reinforcement Learning

arXiv:2606.13316v1 Announce Type: new Abstract: Reinforcement Learning with Verifiable Rewards (RLVR) is a central technique for improving long-horizon reasoning in Large Language Models (LLMs). However, existing RLVR methods often encourage unnecessarily long reasoning rollouts, which can degrade reasoning coherence and exhaust the available context budget. Existing approaches to long-context organization often depend on external mechanisms to organize rollouts, rather than enabling the model to manage its own reasoning trajectory. To address this limitation, we propose ReSum, a novel RLVR framework that enables LLMs to compress and organize their reasoning trajectories through self-summarization. Our pilot studies show that self-summarization stabilizes generation by lowering token-level entropy, and that introducing a ``summarization'' phrase can substantially mitigate errors propagated from an incorrect rollout prefix. Motivated by these findings, ReSum adopts a summarization-aware adaptive rollout mechanism that contrastively evaluates whether self-summarization benefits the ongoing reasoning process. Specifically, when the model spontaneously triggers self-summarization, ReSum masks the summarization phrase to create a contrastive branch; for non-summarization positions, it instead randomly injects the phrase to create a matched branch. We further design a summarization-aware advantage to enable finer-grained comparison between contrastive rollout trajectories. Extensive experiments show that ReSum improves performance at an average of 4\% while reducing rollout length by 18.6\%.

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

Asymptotically Optimal Sequential Testing with Markovian Data

arXiv:2602.17587v3 Announce Type: replace-cross Abstract: We study one-sided and $\alpha$-correct sequential hypothesis testing for data generated by an ergodic, finite-state Markov chain. The null hypothesis is that the unknown transition matrix belongs to a prescribed set $P$ of stochastic matrices, and the alternative corresponds to a disjoint set $Q$. We establish a non-asymptotic instance-dependent lower bound on the expected stopping time of any valid sequential test under the alternative, which is asymptotically tight. Our novel analysis improves the existing lower bounds, which are either asymptotic or provably sub-optimal in this setting. Our lower bound incorporates both the stationary distribution and the transition structure induced by the unknown Markov chain. We further propose an optimal test whose expected stopping time matches this lower bound asymptotically as $\alpha \to 0$. We illustrate the usefulness of our framework through applications to sequential detection of model misspecification in Markov Chain Monte Carlo and to testing structural properties, such as the linearity of transition dynamics, in Markov decision processes. Our findings yield a sharp and general characterization of optimal sequential testing procedures under Markovian dependence.

03.
arXiv (quant-ph) 2026-06-16

Quantum Measurement and Continuous Markov Processes

Authors:

arXiv:2606.15958v1 Announce Type: new Abstract: These are the lecture notes for a course on diffusive quantum measuring instruments. They were prepared and delivered at the Perimeter Institute on Mondays and Thursdays, from 2:30 to 4:00 PM, beginning October 27th, 2025 and ending December 11th, 2025. These lectures were recorded and can be found at https://pirsa.org/c25038.

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

Graph Grounded Cross Attention Transformer Neural Network for Structurally Constrained Full Event Sequence Generation in Predictive Process Monitoring

arXiv:2606.18726v1 Announce Type: cross Abstract: Structurally constrained event sequence generation remains challenging because generated paths must preserve transition feasibility, temporal order, termination, and attribute consistency. In predictive process monitoring (PPM), this challenge appears as full event sequence generation, whereas existing work mainly addresses component tasks such as next activity, remaining time, outcome, and attribute prediction. This paper proposes the Graph Grounded Cross Attention Transformer Neural Network (GGATN) for this unified PPM task. GGATN uses a global process graph as structured activity memory, contextualizes sequence positions through Transformer self attention, and injects process topology through graph grounded cross attention. Unlike autoregressive decoding, GGATN generates activities, timestamps, length, and event level and sequence level attributes in a single pass, followed by Viterbi style graph constrained decoding for feasible paths and explicit termination. Experiments on six benchmark event logs show more reliable generation quality than local instruction prompted LLM baselines. GGATN achieves strong performance on sequence similarity, Damerau Levenshtein similarity, bigram based control flow similarity, and duration distribution, while maintaining zero hallucinated activities and zero sequence level attribute inconsistency. Ablation analyses confirm the global graph encoder as a stable structural prior. Interpretability analyses show how graph structure, sequence context, feedback refinement, and constrained decoding shape generation.

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

Neural Slack Variables for Shape Constraints

arXiv:2606.13803v1 Announce Type: new Abstract: Enforcing functional inequality constraints such as monotonicity and convexity in neural networks is a fundamental challenge in many industrial and scientific applications. Classical one-sided penalty methods, along with primal-dual methods gated by complementary slackness, provide constraint gradients only at violated locations, resulting in fragile satisfaction. Architectures that guarantee feasibility by construction, on the other hand, remain largely limited to elementary cases and impose additional inductive biases. We introduce neural slack variables, a deep learning native primal-side approach that converts constraint enforcement into a regression problem by coupling the primary network with a jointly learned auxiliary network. The auxiliary network serves as a valid target for the primary network's constraint quantities, inducing feasibility and regularity. Neural slack variables achieve zero measured violations on dense-grid monotonicity and convexity test cases, where penalty and primal-dual baselines leave residual violations, and enable arbitrage-free learning of volatility surfaces, an open industrial challenge in quantitative finance.

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

LLM4RTL: Tool-Assisted LLM for RTL Generation

arXiv:2606.15500v1 Announce Type: cross Abstract: Large language models (LLMs) have facilitated impressive progress in software engineering, code generation, tooling, and systems. Concurrently, a significant body of research has developed which explores a growing variety of methods and systems for applying LLMs to hardware and chip design (e.g., systems for RTL code generation based on functional description). However, when it comes to open Verilog/RTL code-generation, we need high-quality training samples to build specialized and more effective LLM systems through fine-tuning or low-rank adaptation. Here, we propose a ``judge-renew-check-renew-check'' (JRCRC) pipeline which updates a current public dataset using a hierarchy of state-of-the-art commercial LLM models differing in their costs and capabilities in RTL code generation. This approach achieves a cost-effective mechanism for filtering and refining code-generation samples into a higher-quality training dataset. Our experiments also identify some common weaknesses of LLMs in rule-based reasoning and logic, and consequently, in RTL code-generation. Having identified these weaknesses, we develop an architecture for incorporating pre-processing tools to dynamically assist the LLMs in inferring logical relationships from tabular data formats. With our tools-assisted architecture for RTL code generation, we achieve significant overall performance gains in the VerilogEval benchmark and outperform many state-of-the-art methods. Our LLM4RTL system achieves performance comparable to that of GPT-4O using a significantly much smaller LLM.

07.
arXiv (CS.LG) 2026-06-15

MOSIC: Model-Agnostic Optimal Subgroup Identification with Multi-Constraint for Improved Reliability

arXiv:2504.20908v3 Announce Type: replace Abstract: Current subgroup identification methods typically follow a two-step approach: first estimate conditional average treatment effects and then apply thresholding or rule-based procedures to define subgroups. While intuitive, this decoupled approach fails to incorporate key constraints essential for real-world clinical decision-making, such as subgroup size and propensity overlap. These constraints operate on fundamentally different axes than CATE estimation and are not naturally accommodated within existing frameworks, thereby limiting the practical applicability of these methods. We propose a unified optimization framework that directly solves the primal constrained optimization problem to identify optimal subgroups. Our key innovation is a reformulation of the constrained primal problem as an unconstrained differentiable min-max objective, solved via a gradient descent-ascent algorithm. We theoretically establish that our solution converges to a feasible and locally optimal solution. Unlike threshold-based CATE methods that apply constraints as post-hoc filters, our approach enforces them directly during optimization. The framework is model-agnostic, compatible with a wide range of CATE estimators, and extensible to additional constraints like cost limits or fairness criteria. Extensive experiments on synthetic and real-world datasets demonstrate its effectiveness in identifying high-benefit subgroups while maintaining better satisfaction of constraints.

08.
Nature (Science) 2026-06-08

Fifty years since a simple equation described the chaos of biology

An exploration of chaos theory in population dynamics showed that unpredictable systems can often be modelled using surprisingly simple mathematics. An exploration of chaos theory in population dynamics showed that unpredictable systems can often be modelled using surprisingly simple mathematics.

09.
arXiv (quant-ph) 2026-06-24

Syndrome aware mitigation of logical errors

arXiv:2512.23810v2 Announce Type: replace Abstract: Broad applications of quantum computers will require error correction (EC). However, hardware roadmaps indicate that physical qubit numbers will remain limited in the foreseeable future, leading to residual logical errors that constrain the size and accuracy of achievable computations. Recent work suggested logical error mitigation (LEM), which applies known error mitigation (EM) methods to logical errors, eliminating their effect at the cost of a runtime overhead. We introduce syndrome-aware logical error mitigation (SALEM), which mitigates logical errors conditioned on the error syndromes measured during error correction. The runtime overhead of SALEM is exponentially lower than that of LEM schemes which do not make use of syndrome data, enabling substantially larger circuit volumes that can be executed accurately. Compared to the routinely used combination of error correction and syndrome rejection (post-selection), SALEM increases the size of reliably executable computations by orders of magnitude. In the practical setting where space and time overheads are fixed and error reduction methods are compared by their resulting estimation errors, we observe a surprising phenomenon: SALEM, which tightly combines EC with EM, can outperform physical EM even above the standard fault-tolerance (pseudo) threshold. Thus, SALEM can make use of EC in regimes of physical error rates where EC is commonly deemed useless.

10.
bioRxiv (Bioinfo) 2026-06-18

novelBGC: An interactive dual-score framework for biosynthetic gene cluster novelty assessment and candidate prioritisation

Genome mining now yields tens of thousands of putative biosynthetic gene clusters (BGCs) per project, yet, separating genuinely novel candidates from rediscoveries of known compounds remains the rate-limiting step before experimental validation. Single-axis prioritisation tools, antiSMASH similarity, BiG-FAM GCF distance, and self-resistance-enzyme (SRE) filters such as ARTS, each surface a different facet of evidence, yet their isolated use systematically over-ranks rediscovery-prone BGCs and overlooks genuinely orphan clusters. We present novelBGC, a web-hosted framework that converts these disparate outputs into two deliberately non-inverse continuous metrics per BGC, a Novelty (N) and a Reference Similarity (RS) score which together define a 2D decision plane that resolves rediscoveries, divergent family members, contig-edge artefacts, and uncharted chemistry with interactive visualisations, with all component weights user-tuneable at submission. Retrospective validation across three independent experimental datasets demonstrates the utility of the framework for candidate prioritization. Within the first 186-BGC SRE-guided cloning study, every confirmed bioactive product fell within the low-to-mid N band whereas 55 high-N (N [≥] 0.50) BGCs were never selected. Moreover, in the other two studies, it correctly prioritised the fully orphan lariocidin BGC of Paenibacillus sp. M2 and the divergent within-family indanopyrrole-A idp BGC of Streptomyces sp. CNX-425. Together, these case studies demonstrate that the joint (N, RS) space facilitates prioritization decisions that are difficult to achieve using any single criterion alone. from identical input data. novelBGC requires no command-line expertise, no local tool installation, and no manual integration of intermediate output formats, addressing a well-documented accessibility barrier for wet-laboratory researchers engaging with genome-mining workflows. novelBGC is freely available at https://project.iith.ac.in/sharmaglab/novelbgc/.

11.
arXiv (CS.CV) 2026-06-25

Efficient Remote Sensing Instance Segmentation with Linear-Time State Space Distilled Visual Foundation Models

The computational complexity of Transformers scales quadratically with the number of tokens, which significantly constrains the efficiency of vision models, particularly recent ViT-based foundation models in dense prediction tasks. Instance segmentation, a typical dense visual prediction task in the remote sensing field, faces similar challenges. In this paper, inspired by the recent advances of knowledge distillation in large language models, we introduce RS4D - a new remote sensing instance segmentation method with linear computational complexity, which addresses the inefficiency of long sequence modeling through distilled state space modeling (SSM). We propose an adaptive noise and masking knowledge distillation training method for pre-training lightweight SSM backbones, which effectively compresses knowledge from the vast self-attention space into a compact, dense linear state space. We also design a remote sensing image instance segmentation architecture based on this lightweight visual encoder, where we explore variants of three different backbones and two segmentation heads. Extensive experiments are conducted on multiple benchmark datasets, including SSDD, WHU, and NWPU. Compared to ViT-based approaches, our proposed SSM backbone achieves an 8x reduction in parameters and a 9x reduction in FLOPs while maintaining comparable or superior accuracy to both ViT- and CNN-based instance segmentation methods. The implementation codes have been publicly available at https://github.com/QinzheYang/RS4D.

12.
arXiv (CS.AI) 2026-06-25

Evaluating Scene-based In-Situ Item Labeling for Immersive Conversational Recommendation

arXiv:2604.09698v2 Announce Type: replace-cross Abstract: The growing ubiquity of Extended Reality (XR) is driving Conversational Recommendation Systems (CRS) toward visually immersive experiences. We formalize this paradigm as Immersive CRS (ICRS), where recommended items are highlighted directly in the user's scene-based visual environment and augmented with in-situ labels. While item recommendation has been widely studied, the problem of how to select and evaluate which information to present as immersive labels remains an open problem. To this end, we introduce a principled categorization of information needs into explicit intent satisfaction and proactive information needs and use these to define novel evaluation metrics for item label selection. We benchmark IR-, LLM-, and VLM-based methods across three datasets and ICRS scenarios: fashion, movie recommendation, and retail shopping. Our evaluation reveals three important limitations of existing methods: (1) they fail to leverage scenario-specific information modalities (e.g., visual cues for fashion, meta-data for retail), (2) they present redundant information that is visually inferable, and (3) they poorly anticipate users' proactive information needs from explicit dialogue alone. In summary, this work provides both a novel evaluation paradigm for in-situ item labeling in ICRS and highlights key challenges for future work.

13.
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.

14.
arXiv (quant-ph) 2026-06-16

Comparative Performance Analysis of NIST PQC Standards: From STM32 Software Limitations to FPGA-SoC Acceleration

arXiv:2606.15744v1 Announce Type: new Abstract: The rapid advancement of quantum computing poses a significant threat to classical public-key cryptographic systems, necessitating the transition to Post-Quantum Cryptography (PQC). This study investigates the implementation challenges of NISTstandardized signature schemes on resource-constrained embedded hardware. We present a comparative analysis of SPHINCS+ and CRYSTALS-Dilithium on an ARM Cortex-M4 (STM32F407G) microcontroller. Our findings reveal that SPHINCS+ is practically unusable in this software-only environment, with impractical execution times. Furthermore, the reference Dilithium implementation failed to execute entirely on the MCU due to severe RAM and timing constraints. To overcome these hardware limitations, we integrated a hardware-accelerated Dilithium core onto a Xilinx Zynq-7000 ZedBoard SoC. By implementing a specialized Number Theoretic Transform (NTT) accelerator in the FPGA fabric, we achieved successful execution with performance rates for key generation and signature generation at millisecond levels. These results demonstrate that while pure software PQC is non-viable for standard microcontrollers, a hardware-software codesign approach provides the necessary efficiency for quantumresistant embedded systems.

15.
arXiv (quant-ph) 2026-06-12

Exotic critical states as fractional Fermi seas in the one-dimensional Bose gas

arXiv:2602.17656v2 Announce Type: replace-cross Abstract: Critical quantum field theories occupy a central position in modern theoretical physics for their inherent universality stemming from long-range correlations. As an example, the Tomonaga-Luttinger liquid (TLL) describes a wealth of one-dimensional quantum systems at low temperatures. Its behavior is deeply rooted in the emergence of an effective Fermi sea, leading to power-law correlations and Friedel oscillations. A promising direction to realize systems exhibiting novel universal behavior beyond TLL is through the generalization of the underlying Fermi sea. In this Letter, we show that fractional Fermi seas with reduced occupancy arise in an integrable Bose gas driven out of equilibrium by cyclic changes in interactions from repulsive to attractive. The correlation functions feature signatures of criticality incompatible with a conventional TLL, suggesting a novel critical phase. Our predictions, based on Generalized Hydrodynamics, are directly relevant to cold atoms.

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

TouchThinker: Scaling Tactile Commonsense Reasoning to the Open World with Large-scale Data and Action-aware Representation

arXiv:2606.11637v1 Announce Type: new Abstract: Touch is a key modality for embodied agents to understand the physical world. Although recent work has incorporated tactile signals into language systems for tactile commonsense reasoning, scaling such systems to realistic open-world settings remains challenging due to two key bottlenecks: (1) current tactile reasoning datasets remain limited in format and scale, providing insufficient supervision for reasoning from tactile observations to physical commonsense and hindering the learning of transferable tactile commonsense; (2) Tactile signals are inherently redundant and action-specific, yet existing methods often overlook these properties, resulting in inefficient representations with limited semantic expressiveness. To address these limitations, we propose TouchThinker, a tactile-language framework that scales tactile commonsense reasoning to the open world from both data and representation perspectives. First, we construct TouchThinker-1M, a million-scale, multi-source tactile reasoning dataset covering 415 objects, 8 scenarios, and 7 sensor types, providing a solid data foundation for open-world generalization. We further introduce TouchThinker-Bench, an open-world benchmark with more realistic and diverse tasks. Then, we propose action-aware modeling mechanism to improve tactile representation efficiency and enable efficient reasoning. Experimental results demonstrate that TouchThinker achieves competitive performance against state-of-the-art models across multiple datasets. Our code and dataset will be made available at: https://github.com/lvkailin0118/TouchThinker.

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

X-MADAM-RAG: Diagnosing and Handling Chinese-English Evidence Conflict in Retrieval-Augmented Generation

Retrieval-augmented generation (RAG) systems may receive evidence that is not merely noisy but mutually contradictory. This issue becomes particularly salient in multilingual settings, where retrieved Chinese and English evidence may support incompatible answer candidates. We study this problem through X-RAMDocs-ZHEN, a controlled Chinese-English benchmark derived from RAMDocs for diagnosing evidence conflict in RAG. The benchmark contains 300 examples across six balanced conditions, including monolingual support, bilingual agreement, reversed conflict directions, and conflict with optional noise. We further examine X-MADAM-RAG, an interpretable pipeline that decomposes evidence handling into per-document candidate extraction, visible-evidence repair, deterministic candidate grouping, and conflict-aware aggregation. On the original controlled benchmark with Qwen2.5-7B-Instruct, X-MADAM-RAG achieves 0.9667 strict accuracy and 0.9767 conflict-aware success, outperforming an evidence-normalized single-call baseline. However, a zero-call rule-only extractor reaches 1.0000 on the same benchmark, revealing strong template regularity. To probe this limitation, we construct a deterministic naturalized stress test that removes explicit answer templates while preserving candidate strings. On its 100-sample subset, rule-only extraction falls to 0.0000, but X-MADAM-RAG also drops to 0.3000 strict accuracy, below both naive and evidence-normalized baselines. A privileged oracle remains perfect, indicating that document-level extraction is the main bottleneck. These findings position X-RAMDocs-ZHEN and X-MADAM-RAG as diagnostic tools for controlled evidence conflict rather than as evidence of general hallucination detection or robustness to natural retrieval.

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

Encode Errors: Representational Retrieval of In-Context Demonstrations for Multilingual Grammatical Error Correction

Grammatical Error Correction (GEC) involves detecting and correcting the wrong usage of grammar. While large language models (LLMs) with in-context learning (ICL) capabilities have shown significant progress on various natural language processing (NLP) tasks, their few-shot performance on GEC remains suboptimal. This is mainly due to the challenge of retrieving suitable in-context demonstrations that capture error patterns instead of semantic similarity. In this paper, we demonstrate that LLMs can inherently capture information related to grammatical errors through their internal states. From these states, we extract the Grammatical Error Representation (GER), an informative and semantically neutral encoding of grammatical errors. Our novel GER-based retrieval method significantly boosts performance in ICL settings on multilingual GEC datasets, improving the precision of correction. For high-resource languages, our results on 8B-sized open-source models match those of closed-source models such as Deepseek2.5 and GPT-4o-mini. For low-resource languages, our $F_{0.5}$ scores surpass the baseline by up to a factor of 1.20. This method provides a more precise and resource-efficient solution for multilingual GEC, offering a promising direction for interpretable GEC research.

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

Variable Bound Tightening for Nash Equilibrium Computation in Multiplayer Imperfect-Information Games

Authors:

arXiv:2606.25997v1 Announce Type: cross Abstract: There has been significant recent progress in algorithms for approximation of Nash equilibrium in large two-player zero-sum imperfect-information games and exact computation of Nash equilibrium in multiplayer strategic-form games. While counterfactual regret minimization and fictitious play are scalable to large games and have convergence guarantees in two-player zero-sum games, they do not guarantee convergence to Nash equilibrium in multiplayer games. Recently, an approach has been presented for exact computation of Nash equilibrium in multiplayer imperfect-information games that solves a quadratically constrained program based on a nonlinear complementarity problem formulation derived from the sequence-form game representation. This formulation was solved using Gurobi's nonconvex quadratic solver, which employs spatial branch-and-bound to iteratively refine variable bounds by solving convex relaxations of bilinear terms via McCormick envelopes. During presolve, Gurobi introduces auxiliary variables and, in some cases, binary variables, leading to an internal MIQCP reformulation. This approach was demonstrated to outperform prior algorithms from the Gambit software suite and quickly solve three-player Kuhn poker after removal of dominated actions; however, the algorithm was not able to solve the full version of the game within 24 hours. In this paper, we derive finite bounds on slack and multiplier variables in the nonlinear complementarity formulation. These bounds strengthen the convex relaxations used within spatial branch-and-bound and lead to substantial computational improvements. We demonstrate the impact of the proposed bounds on exact Nash equilibrium computation in three-player Kuhn poker.

20.
bioRxiv (Bioinfo) 2026-06-16

OmicOS: A Comprehensive Omics Ecosystem Infrastructure and Agent System for the AI Era

Biology has accumulated a vast ecosystem of omics methods, but much of this ecosystem remains built for expert humans rather than scientific agents. Methods are scattered across Python packages, R/Bioconductor and CRAN workflows, command-line tools, incompatible data containers and implicit object states, making even routine analyses difficult for an AI system to choose, execute and verify reliably. Here we introduce OmicOS, a comprehensive omics ecosystem infrastructure and agent system that turns OmicVerse V2, an open-source omics community, into an executable foundation for agentic biology. OmicVerse V2 provides the community substrate: scalable AnnDataOOM-compatible rust backends, agent-friendly Python algorithms for single-cell, spatial, bulk and multi-omics analysis, interfaces to single-cell foundation models, and Python-native reconstructions of historically R-centred Bioconductor/CRAN-style workflows. OmicOS makes this substrate actionable by registering analytical functions as state-aware capability contracts, allowing agents to inspect live data objects, select valid methods, execute controlled workflows and record provenance. The result is not a fixed pipeline, but a programmable omics environment in which agents compose real analyses from verified community methods rather than inventing tools. Across external and purpose-built benchmarks, OmicOS ranked first among the evaluated systems, reaching 81.2% on BiomniBench. Adding OmicVerse to a minimal agent improved task completion by up to 34.2 percentage points with qwen-3.6-35b, and controlled ablations showed that the gains came from registry-grounded execution rather than from larger models, documentation retrieval or unrestricted tool exposure. The same infrastructure scaled to atlas-sized data, reproduced R-centred workflows in Python and converted external pathology software into agent-usable skills. In a discovery task starting from a whole-body spatial map and the term Alzheimer disease, OmicOS composed a non-canonical workflow that integrated spatial expression, genetic association, eQTL and colocalization evidence to nominate a colon epithelial risk axis centred on PICALM, CD2AP and CR1. Together, OmicVerse and OmicOS define an open foundation for AI-era omics, showing how a community of biological methods can be transformed into a reliable, extensible and agent-operable system for discovery.

21.
arXiv (CS.LG) 2026-06-18

Everywhere Valid Bounds on False Discovery Proportions in Conformal Inference

arXiv:2605.20726v2 Announce Type: replace-cross Abstract: Modern applications of conformal inference to multiple testing problems, such as outlier detection and candidate selection, often involve selecting test samples whose conformal p-values fall below a threshold. The quality of such methods is often measured by the false discovery proportion (FDP), defined as the fraction of incorrect selections. Existing approaches typically control the expected value of the FDP, using methods such as the Benjamini-Hochberg procedure. This approach fails to provide high-probability bounds on the realized false discovery proportion and invalidates statistical guarantees if the rejection threshold is selected after inspecting the data. This paper establishes finite-sample, distribution-free upper bounds on the FDP that hold simultaneously over all possible rejection thresholds, enabling arbitrary post hoc selection of the threshold. Simultaneous validity is achieved by constructing a high-probability envelope for the empirical distribution function of null conformal p-values by sampling from their joint distribution. Furthermore, our framework allows practitioners to modulate the envelope's shape, thereby producing tight bounds in rejection regions of primary interest. We use this flexible approach to derive simultaneous FDP upper bounds for both outlier detection and conformal selection. We demonstrate through synthetic and real-data experiments that the resulting bounds are both valid and substantially less conservative than those derived from existing approaches.

22.
arXiv (quant-ph) 2026-06-12

Accidental Symmetry in the Tavis-Cummings Model via the Schwinger Boson Representation

arXiv:2606.12813v1 Announce Type: new Abstract: The Jaynes-Cummings (JC) Hamiltonian is a paradigmatic model of light-matter interaction and, more generally, qubit-boson interactions, widely used across atomic, optical, and superconducting qubit platforms. In the multi-qubit setting, where n qubits are identically coupled to a single boson mode, this interaction is known as the Tavis-Cummings (TC) Hamiltonian. The structure of the TC model is usually understood in terms of two standard symmetries: permutation invariance of the qubits and a U(1) symmetry associated with conservation of the total excitation number. Here we identify an additional, independent "accidental" symmetry of the TC Hamiltonian and construct the corresponding conserved observable. We show that, for n>2 qubits, this symmetry imposes strong constraints on the realizable unitary transformations. These constraints persist in the presence of the global $J_z$ Hamiltonian, but are removed by adding $J_z^2$, even though $J_z^2$ preserves both permutation invariance and the U(1) symmetry. Finally, we explain the origin of this previously unnoticed symmetry using Schwinger's boson representation of angular momentum. These restrictions have important implications for controllability of the TC system and for its applications to quantum computing, which are investigated further in a companion paper.

23.
arXiv (CS.AI) 2026-06-15

Adversarial Concept Search: Predicting Compositional Errors From Feature Geometry

arXiv:2606.13934v1 Announce Type: new Abstract: Humans cannot always intuit what scenarios are most challenging to LLMs. Hoping to capture challenging edge cases, developers either design problems to be difficult for humans or curate extensive benchmarks. What if we could instead anticipate which scenarios a model will fail on? In this paper, we use an LLM's representational geometry to predict which concept combinations it will fail on. We attribute this compositional failure to interference between salient features. In tasks that require systematic composition - toy programmatic settings, multihop reasoning, multilingual factual recall - we find that when a pair of concepts is encoded near-orthogonally, the model reliably composes them. When their linear encodings are close, producing interference, the model fails to compose them. Our method reliably anticipates failure modes across different compositional tasks, without evaluating specific inputs. These results lay the groundwork to use representational geometry to identify high-risk examples, construct targeted stress tests, and provide a scalable foundation for active learning in real-world deployment.

24.
arXiv (CS.CL) 2026-06-12

An End-to-End Hybrid Framework for Rumour Detection in Low-Resources Algerian Dialect

The rapid growth of social media has intensified the spread of rumours. This issue is more challenging in the Algerian context due to the informal and code-switched nature of dialectal content, the scarcity of annotated resources, and the limited effectiveness of standard Arabic NLP tools on dialect text. This paper presents an end-to-end rumour detection hybrid framework for Algerian dialect social media content. We build a domain-specific annotated dataset by combining real social media posts, synthetic data, and the FASSILA corpus, with automatic labeling based on a similarity-based annotation process. A transliteration pipeline is also introduced to generate parallel datasets in Arabic script and Arabizi. We evaluate multiple approaches, including classical machine learning, deep learning, transformers, and hybrid models. Experimental results show that a hybrid approach combining transformer embeddings with a classical classifier achieves the best performance, reaching an F1-score of 0.84. We also find that domain-specific pre-training is more important than model size, with social media-trained models outperforming larger models trained on formal Arabic corpora. These results demonstrate the feasibility of rumour detection in low-resource Algerian dialect settings.

25.
arXiv (CS.CL) 2026-06-15

Trusted Uncertainty in Large Language Models: A Unified Framework for Confidence Calibration and Risk-Controlled Refusal

Deployed language models must decide not only what to answer but also when not to answer. We present UniCR, a unified framework that turns heterogeneous uncertainty evidence including sequence likelihoods, self-consistency dispersion, retrieval compatibility, and tool or verifier feedback into a calibrated probability of correctness and then enforces a user-specified error budget via principled refusal. UniCR learns a lightweight calibration head with temperature scaling and proper scoring, supports API-only models through black-box features, and offers distribution-free guarantees using conformal risk control. For long-form generation, we align confidence with semantic fidelity by supervising on atomic factuality scores derived from retrieved evidence, reducing confident hallucinations while preserving coverage. Experiments on short-form QA, code generation with execution tests, and retrieval-augmented long-form QA show consistent improvements in calibration metrics, lower area under the risk-coverage curve, and higher coverage at fixed risk compared to entropy or logit thresholds, post-hoc calibrators, and end-to-end selective baselines. Analyses reveal that evidence contradiction, semantic dispersion, and tool inconsistency are the dominant drivers of abstention, yielding informative user-facing refusal messages. The result is a portable recipe of evidence fusion to calibrated probability to risk-controlled decision that improves trustworthiness without fine-tuning the base model and remains valid under distribution shift.