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

Localizing Credit at the Divergence: Path-Conditioned Self-Distillation for LLM Reasoning

arXiv:2606.15576v1 Announce Type: cross Abstract: Reinforcement learning from verifiable rewards assigns a single scalar to each rollout, leaving token-level credit assignment underspecified in long reasoning traces. On-policy self-distillation addresses this by letting the same model act as a teacher conditioned on privileged information, producing a dense per-token signal. But the common choice of a ground-truth answer is only an endpoint cue: on terse-answer tasks, the teacher falls silent at the intermediate positions where path-level guidance matters most. We propose Hindsight Self-Distillation (HSD), which conditions the teacher on a successful peer rollout drawn from the current training group. Such a peer is an exact sample from the success-conditioned policy, requiring no additional sampled rollouts. By providing a full successful continuation rather than only the final answer, the resulting credit signal concentrates at the divergence position between a failed rollout and a successful peer. Across Qwen3-8B and Qwen3-32B on math and code benchmarks, HSD obtains the best result against GRPO variants and on-policy distillation baselines, with the largest gains on terse-answer tasks such as AIME.

02.
arXiv (CS.CL) 2026-06-11

When Does Language Matter? Multilingual Instructions Reveal Step-wise Language Sensitivity in Vision-Language-Action Models

Vision-Language-Action (VLA) models have shown strong performance in language-conditioned robotic manipulation, yet their robustness to linguistic variation remains poorly understood. In this work, we present the first systematic multilingual evaluation of VLA models by translating the LIBERO benchmark into ten languages, revealing severe performance degradation under non-English instructions, with success rates dropping by 30-50%. Through fine-grained analysis of task executions, we find that language influence is highly non-uniform across steps: certain steps exhibit strong language dependence and dominate overall task failure, while others are largely language-agnostic. Based on this insight, we propose a step-wise inference-time intervention that aligns representations according to step language sensitivity, substantially improving performance under linguistic variation. Our results indicate that language robustness in VLA models is fundamentally a step-wise control problem, highlighting the importance of temporally structured analysis for reliable embodied agents.

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

S-Agent: Spatial Tool-Use Elicits Reasoning for Spatial Intelligence

Real-world spatial intelligence requires reasoning over a continuous and evolving 3D world, yet existing VLMs and tool-augmented agents largely remain tied to static, stateless inference from isolated visual observations. We introduce \textsc{S-Agent}, a spatial tool-use agentic paradigm for understanding and reasoning over continuous multi-view images and videos. By formulating spatial reasoning as spatio-temporal evidence accumulation rather than isolated frame-level prediction, \textsc{S-Agent} reshapes spatial perception into scene-centric understanding beyond frame-centric recognition. Specifically, \textsc{S-Agent} casts the VLM as a semantic planner that decides what evidence is needed, while a hierarchy of spatial tools and experts grounds objects in 2D, lifts them into 3D geometric evidence, and aggregates this evidence into high-level spatial knowledge (e.g., counting, measurement, orientation, and relative position). Additionally, a temporal memory mechanism, including Scene Memory for maintaining the evolving scene state and Agent Memory for accumulating reasoning context, enables evidence integration across frames and reasoning steps. Comprehensive experiments on multi-view and video spatial reasoning benchmarks show that \textsc{S-Agent} consistently improves both open-source and closed-source VLMs in a training-free manner. Beyond inference-time augmentation, supervised fine-tuning (SFT) on \textsc{S-Agent}-generated spatial trajectories \textsc{S-300K} yields \textsc{S-Agent-8B}, a compact spatial agent that significantly surpasses similar-scale baselines (e.g., Qwen3-VL-8B) and performs comparably to advanced closed-source models (e.g., GPT-5.4 and Gemini 3).

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

TUNI: Unifying Pre-training and Fine-tuning with Modality-Aware Mutual Learning and Rectification for RGB-T Semantic Segmentation

RGB-thermal (RGB-T) semantic segmentation improves the environmental perception of autonomous platforms in challenging conditions. Prevailing RGB-T segmentation frameworks suffer from suboptimal multi-modal feature extraction and fusion, unbalanced modality dependency, and inadequate utilization of thermal information. To address these challenges, we propose TUNI, a unified pre-training and fine-tuning framework for efficient and real-time RGB-T semantic segmentation. It pre-trains an RGB-T encoder that incorporates an RGB-T local module that selectively emphasizes salient consistent and distinct local features across modalities, thereby integrating cross-modal feature extraction and fusion in a unified manner. To alleviate the modality bias issue during RGB-T pre-training, modality-inverted contrastive mutual learning is introduced to enable knowledge exchange between two RGB-dominated and thermal-dominated encoders. In the fine-tuning phase, modality rectification learning fully exploits residual thermal information by focusing on correct yet divergent prediction regions between two modality-specific decoders. We further develop three TUNI variants, covering lightweight, balanced, and high-performance requirements. Extensive experiments on five RGB-T semantic segmentation datasets demonstrate that TUNI achieves superior accuracy, generalization, and compactness compared with 15 state-of-the-art models. The code is available at https://github.com/xiaodonguo/TUNI-v2.

05.
arXiv (CS.AI) 2026-06-12

ERTS: Adversarial Robustness Testing of Ethical AI via Semantic Perturbation in a Bounded Consequence Space

arXiv:2606.13282v1 Announce Type: new Abstract: As AI systems are deployed in high-stakes ethical contexts such as healthcare triage, autonomous vehicle control, and employment screening, formal methods for evaluating their robustness against adversarial manipulation of ethical reasoning remain underdeveloped. This paper introduces the Ethical Robustness Testing System (ERTS), a closed-pipeline framework that: (1) encodes ethical dilemmas into a 22-dimensional Ethical Consequence Space (ECS) grounded in established ethical theory; (2) applies 17 semantic perturbation functions subject to 6 validity constraint classes including a novel semantic coherence constraint; (3) measures decision deviation via a 4-component Ethical Instability Index (EII); and (4) produces domain-adaptive pre-deployment robustness assessment verdicts. We evaluate 4 structured baseline models and 2 production LLMs (Gemini 2.0 Flash and Llama 3.2) across 50 ethical scenarios spanning 8 deployment domains, generating 1,500 adversarial test cases. Results demonstrate that only 33% of models achieve assessment clearance, with the local Llama-3.2 model proving particularly vulnerable to fairness corruption and information degradation attacks (ERS = 0.737). To the best of our knowledge, no existing framework combines a bounded ethical consequence space, semantic coherence constraints, and domain-adaptive assessment in a single adversarial testing pipeline.

06.
arXiv (math.PR) 2026-06-12

Mixing times of one-sided $k$-transposition shuffles

arXiv:2112.05085v2 Announce Type: replace Abstract: We study mixing times of the one-sided $k$-transposition shuffle. We prove that this shuffle mixes relatively slowly, even for $k$ big. Using the recent ``lifting eigenvectors'' technique of Dieker and Saliola and applying the $\ell^2$ bound, we prove different mixing behaviors and explore the occurrence of cutoff depending on $k$.

07.
arXiv (CS.LG) 2026-06-16

Finite-Time Convergence of Distributionally Robust Q-Learning with Linear Function Approximation

arXiv:2510.01721v3 Announce Type: replace Abstract: Distributionally robust reinforcement learning (DRRL) seeks policies that perform well when the deployment transition model differs from the nominal model generating the data. Most finite-sample guarantees for DRRL are tabular, model-based, rely on generative access, or obtain function-approximation guarantees only under additional structure, such as linear-transition models or restrictive discount-factor conditions. We study discounted model-free robust Q-learning under an $(s,a)$-rectangular chi-square uncertainty set, with linear approximation of the robust Q-function, using only a single Markovian trajectory from an unknown nominal model. Our algorithm combines a target-network outer loop with a dual function-approximation scheme for the chi-square robust Bellman update. The dual procedure uses moment-tracking critics, suffix averaging, a fresh-evaluation stage for the variance-like moment, and a tunable smoothing parameter to have a Lipschitz-continuous chi-square dual gradient. We prove a finite-time convergence bound to the optimal robust Q-function up to approximation error, without imposing a small-discount-factor assumption. Our results help close a gap between the empirical use of robust RL algorithms and the non-asymptotic guarantees available for their non-robust counterparts.

08.
arXiv (CS.AI) 2026-06-16

GIST-CMTF: Goal-State Inference for Causal Minimal Tool Filtering in LLM Agents

arXiv:2606.16813v1 Announce Type: new Abstract: Tool-augmented LLM agents rely on runtime filtering to decide which tools should be visible at each step. Causal Minimal Tool Filtering (CMTF) reduces tool-choice confusion by exposing only the next causally necessary tool frontier, but it assumes that the user request has already been mapped to a symbolic goal state. In practice, requests such as "handle my appointment" or "take care of this email" may correspond to multiple possible goals. This creates wrong-goal execution, where an agent follows a valid causal tool path for an unintended objective. We introduce GIST-CMTF, a goal-state inference layer that predicts candidate symbolic goals over the same state-transition vocabulary used by CMTF, estimates ambiguity, and either applies CMTF or exposes clarification as a causal action that produces missing goal or state variables. We evaluate GIST-CMTF across seven model backends, six filtering methods, and 120 controlled tool-use tasks. GIST-CMTF achieves 97.0% task success, compared with 80.1% for top-goal CMTF and 82.9% for semantic-goal CMTF. It reduces wrong-goal execution from 19.4% under top-goal CMTF to 2.5%, while preserving the one-tool exposure of causal filtering and using substantially fewer tokens than all-tools exposure. These results suggest that reliable tool-augmented agents should validate goal state, not only tool relevance, before exposing external actions.

09.
bioRxiv (Bioinfo) 2026-06-16

RetroMol: Parsing a shared encoding from natural products and their biosynthetic gene clusters

Natural products such as polyketides and nonribosomal peptides (NRPs) are important sources of bioactive compounds, including many antibiotics. Many of them are assembled by modular enzyme complexes and further modified and diversified by tailoring reactions encoded by biosynthetic gene clusters (BGCs). Although natural products and their coding BGCs describe different data modalities of the same biochemical process, a unified language to jointly describe their biochemistry is lacking. Here we introduce a sequence-based representation of the core biosynthesis of modular natural products, which we call primary sequences, that bridges chemical structures and BGCs. We also present RetroMol, an algorithm that parses either natural product structures or their encoding BGCs into their primary sequences of natural product building blocks. RetroMol allows for similarity scoring between natural products and BGCs, enabling the retrieval of compounds, BGCs, and a combination of the two, based on their biosynthetic similarity. This can, for instance, be used to retrieve biosynthetically similar but structurally dissimilar compounds, or link natural products to candidate coding BGCs in large experimental datasets. We demonstrate the latter by rediscovering the nocardichelin B BGC as a proof of principle. We also exemplify the utility of biosynthetic similarity by showing various pairs of biosynthetically similar compounds with low structural similarity. Together, these results establish primary sequences as a shared biosynthetic encoding for natural product comparison and BGC prioritization.

10.
bioRxiv (Bioinfo) 2026-06-13

Testing the reliability of AI-generated protein structures

Although AlphaFold2 and its competitors have demonstrated remarkable abilities to predict protein structure, more work is needed to explore the limitations of these methods. Here we investigated the reliability of AlphaFold2 and ColabFold by creating a set of realistic but false protein sequences, using ColabFold to predict their structure, and then asking how often the program produces a high-scoring structure for a sequence that does not represent a protein. We determined that AlphaFold2 has a very small but non-zero false positive rate, estimated here at approximately 1 in 435 if one uses a threshold pLDDT score of 70 to define positive predictions. We also discovered, serendipitously, that some high-scoring sequences in the human genome were not false positives, but instead were previously unknown and un-annotated pseudogenes. These latter findings indicate that some well-established human annotations of protein-coding genes may have incorrectly extended the 5-prime untranslated regions too far. They also suggest that the false positive rate of AlphaFold2 is low enough that almost any high-scoring structure, even in a noncoding region, is worthy of further investigation.

11.
arXiv (CS.CL) 2026-06-18

STARE: Surprisal-Guided Token-Level Advantage Reweighting for Policy Entropy Stability

Reinforcement Learning with Verifiable Rewards algorithms like GRPO have emerged as the dominant post-training paradigm for complex reasoning in LLMs, yet commonly suffer from policy entropy collapse during training. We conduct a first-order gradient analysis of token-level entropy dynamics under GRPO and identify a token-level credit assignment mismatch: the per-token entropy variation decomposes into the product of the trajectory-level advantage and an entropy sensitivity function over the next-token distribution, yielding an advantage-surprisal four-quadrant structure and a near-criticality property. Motivated by it, we propose STARE (Surprisal-guided Token-level Advantage Reweighting for policy Entropy stability), which identifies entropy-critical token subsets via batch-internal surprisal quantiles, selectively reweights their effective advantages, and incorporates a target-entropy closed-loop gate for stable entropy regulation. Across model scales from 1.5B to 32B and three task families (Short CoT, Long CoT, and Multi-Turn Tool Use), STARE sustains stable RL training over thousands of steps while maintaining policy entropy within the target band. On AIME24 and AIME25, STARE outperforms DAPO and other competitive baselines by 4%-8% in average accuracy, with reflection tokens and response length growing in tandem, indicating sustained exploration-exploitation balance that further unlocks RL training potential.Code is available at https://github.com/hp-luo/STARE.

12.
arXiv (CS.LG) 2026-06-11

Neuro-Relational Programs: Unifying Queries and Neural Computation over Structured Data

arXiv:2606.11946v1 Announce Type: cross Abstract: The conventional approach to deep learning over relational databases applies neural models, such as Graph Neural Networks (GNNs), to a graph representation of the database. Recent approaches instead operate on databases directly, associating tuples with embeddings and extending query mechanisms to jointly process embeddings and relational content. Inspired by these developments, we introduce Neuro-Relational Programs (NRPs), a declarative query language for relational databases whose facts carry numeric vector embeddings. NRPs extend Datalog-style rules with operations that combine, aggregate, and transform embeddings, thereby interleaving relational reasoning and learnable neural components within a single formalism. This yields a general approach to neural computation over relational data: an NRP can be read both as a query plan with trainable components and as a neural architecture with relational structure built in. Natural syntactic fragments of NRPs recover existing architectures and query formalisms. Zero-ary NRPs correspond to non-adaptive query algorithms; monadic NRPs generalize GNN-style message passing and precisely capture Deep Homomorphism Networks, a connection that we extend to frontier-guarded NRPs over databases with row-ids. We characterize the expressive power of unrestricted NRPs with ReLU-FFN transformations by FOCQ, an extension of first-order logic with counting interpreted over real-weighted structures, yielding a precise connection with uniform TC$^0$ over ordered databases. Together, these results establish NRPs as a broad declarative framework for querying and neural computation over relational data.

13.
arXiv (math.PR) 2026-06-18

A Stochastic ISCS Markov Model for Fake News Propagation

arXiv:2606.18282v1 Announce Type: cross Abstract: This paper studies the propagation of fake news through a stochastic rumor spreading model based on Markov chains. Inspired by classical epidemiological SIR models, we consider a generalization of the Daley-Kendall framework for rumours that incorporates fact-checkers, following the Ignorant/Spreader/Checker/Stifler model introduced in Piqueira (2020). The model analyzes the influence of checkers on fake news dynamics. Numerical simulations are used to illustrate the behavior of the system and the impact of fact-checkers.

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

Analyzing Visual Aircraft Representations with Sparse Autoencoders

Vision models can achieve strong performance on classification tasks, but the internal representations supporting their predictions are often difficult to interpret. This work investigates whether sparse autoencoders can decompose intermediate representations of a vision model into interpretable features. We train a ConvNeXt classifier on the FGVC-Aircraft dataset, extract spatial activations from its final feature stage, and train a sparse autoencoder on these activations. The learned sparse features are analyzed using top-activating image patches, activation strength, and class selectivity. Qualitative visual inspection reveals that several features correspond to recognizable aircraft structures and visual patterns. We evaluate a subset of selected features using input-space and feature-space ablations, measuring how blurring image patches and suppressing sparse features affect class logits, classification margins, and prediction confidence. The results suggest that sparse autoencoders can reveal partially interpretable, class-relevant visual features associated with aircraft recognition, while also exposing limitations such as polysemanticity and coarse spatial localization.

15.
Nature (Science) 2026-06-10

Gene ancestries reveal diverse microbial associations during eukaryogenesis

The origin of eukaryotes remains a central enigma in biology1. Continuing debates agree on the pivotal role of a symbiosis between an alphaproteobacterium and an Asgard archaeon2,3. However, the nature, timing and contributions of other potential bacterial partners4–6 and the role of interactions with viruses7–9 remain contentious. To address these questions, we used advanced phylogenomic approaches and comprehensive datasets spanning the known diversity of cellular life and viruses. Our analysis provided a revised reconstruction of the last eukaryotic common ancestor (LECA) proteome, in which we traced the phylogenetic origin of each protein family. We found compelling evidence for multiple waves of horizontal gene transfer from diverse bacterial donors, with some likely to have preceded mitochondrial endosymbiosis. We inferred plausible traits of the major donors and their functional contributions to the LECA. Our findings support a contribution of horizontal gene transfers to shaping the proteomes of pre-LECA ancestors and suggest a facilitating role of Nucleocytoviricota viruses. Taken together, our results suggest that ancient eukaryotes may have originated within complex microbial ecosystems through a succession of diverse associations that left a footprint of horizontally transferred genes. Phylogenomic reconstruction of the proteome of the last eukaryotic common ancestor sheds light on the origin of eukaryotes, indicating an important role of horizontal transfer of genes from diverse bacterial and viral donors.

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

FP8 is All You Need (Part 1): Debunking Hardware FP64 as the HPC Holy Grail (June 13th version)

arXiv:2606.06510v2 Announce Type: replace-cross Abstract: Conventional HPC holds that native hardware FP64 is the irreducible foundation of scientific computing. On AI-optimized GPUs of the NVIDIA B300 generation and beyond, native FP64 throughput has collapsed to ~1.3 TFLOPS even as FP8 tensor throughput has grown to multiple PFLOPS. We argue something stronger than that this is survivable: the FP8 tensor-core matrix-multiply is the sole computational primitive on which double-precision scientific computing needs to be built. Every canonical kernel – dense and sparse linear algebra, spectral transforms, stencils – and every application composing them reduces, via the Chinese Remainder Theorem-based Ozaki Scheme II, to sequences of FP8 matrix operations; the only non-FP8 arithmetic is a bounded, fixed-width integer accumulation at reconstruction. Native FP64 is thereby demoted from a hardware requirement to a derived accuracy guarantee obtained by composition over the FP8 primitive. We organize the claim as a five-layer hierarchy – the FP8 op, Ozaki II, the basic kernels or Berkeley "dwarfs", composite solvers, and full applications – and, because the dwarf taxonomy already spans scientific computing, establish it by exhibiting the reduction for every dwarf rather than a sample. The claim is falsifiable, and we build the instrument that tests it: a Tensor-Memory Equilibrium (TME) model extending the Roofline with emulation parameters (alpha, beta, gamma). We identify register-level fusion as the mechanism that keeps emulation memory-bound, project recovered FP64 performance across B300 and Rubin against an H100 baseline, and close the kernel coverage with a companion FFT analysis and compensated reductions. The model could have returned a negative verdict; instead it passes across the dwarfs and their compositions. This is the analytical half of a two-part program, with a follow-on implementation to validate the thesis on real silicon.

17.
arXiv (math.PR) 2026-06-11

Integrated expectile-based measures of inequality

arXiv:2606.12333v1 Announce Type: cross Abstract: Expectiles provide a class of asymmetric location functionals that incorporate the magnitude of deviations and admit a natural geometric interpretation. Building on their structural consistency with the convex stochastic order, this paper introduces a family of integrated expectile functionals for measuring risk, dispersion, and inequality. The proposed functionals admit analytical representations as integrals of expectiles across asymmetry levels. For a distinguished subclass of these constructions, a geometric representation is available: the resulting quantities can be expressed as weighted areas of star-shaped sets encoding the distributional asymmetry of a random variable. This approach yields a new class of expectile-based inequality indices, constituting a natural counterpart to classical Gini-type measures while preserving desirable monotonicity and consistency properties. Empirical counterparts are derived in closed form and admit explicit decompositions over finite samples. The framework extends naturally to multivariate settings through directional expectile constructions, leading to measures capable of capturing genuinely joint forms of multivariate dispersion and inequality.

18.
PLOS Computational Biology 2026-06-01

Supervised deep learning with gene functional annotation for cell classification

作者:

by Zhexiao Lin, Yuanyuan Gao, Wei Sun Gene-by-gene differential expression analysis is a widely used supervised approach for interpreting single-cell RNA-sequencing (scRNA-seq) data. However, modern scRNA-seq datasets often contain large numbers of cells, leading to the identification of many differentially expressed genes with extremely small p-values but negligible effect sizes, thus making biological interpretation difficult. To overcome this challenge, we developed Supervised Deep learning with gene functional ANnotation (SDAN), a method that integrates gene functional annotation information (e.g., protein-protein interaction) with gene-expression profiles through a graph neural network. SDAN identifies functionally coherent gene sets that optimally classify cells, and the resulting cell-level classification scores can be aggregated to make individual-level predictions. We evaluated SDAN alongside three representative existing methods in three real-data applications aimed at identifying gene sets associated with severe COVID-19, dementia, and cancer immunotherapy response. Across all applications, SDAN consistently outperformed the alternative approaches by achieving two objectives simultaneously: accurate outcome classification and clear assignment of genes to functionally related gene sets.

19.
arXiv (CS.LG) 2026-06-15

Conformal calibration and look-elsewhere effect in anomaly detection for new-physics searches

arXiv:2606.13780v1 Announce Type: cross Abstract: Machine-learned anomaly detection is reshaping searches for new physics, but it has outrun the statistics used to interpret it. A raw anomaly score has no calibrated meaning, a model that scans many regions inflates the look-elsewhere effect, and the asymptotic significances the field relies on are blind to the background mismodelling that anomaly detectors are especially prone to. We propose a calibration layer, built on conformal prediction, that turns any anomaly score into a defensible significance with distribution-free, finite-sample guarantees. Conformal prediction converts scores into valid local p-values, weighted and Mondrian variants repair the sideband-to-signal-region exchangeability failures that resonant searches suffer, and a Gross-Vitells step carries the result through to a look-elsewhere-aware global significance. The layer does two things at once. It exposes miscalibration that the standard pipeline cannot see, and it corrects it without retraining the detector. On public LHC Olympics data, a classifier develops a substructure-mass correlation that makes sideband-calibrated background p-values anti-conservative. Taken at face value, this manufactures a $\sim 46\sigma$ excess from background sculpting alone, which the label-free weighted correction removes, restoring an honest null. When run as a blind wide-mass bump hunt, the standard asymptotic and unweighted procedures fabricate $\gtrsim10\sigma$ excesses and $\approx5\sigma$ excesses even in signal-free windows, while the conformal layer raises no false alarms and its global false-positive rate is verified on background-only pseudoexperiments. The result is an auditable, detector-agnostic path from an uncalibrated score to a trials-factor-aware significance, ready to be folded into experimental anomaly searches.

20.
PLOS Computational Biology 2026-06-17

Deciphering cell type-specific causal genetic effects on brain imaging-derived phenotypes and disorders with single-cell Mendelian randomization

作者:

by Anyi Yang, Xingzhong Zhao, Xing-Ming Zhao, Yucheng T. Yang Reconstructing causality routes from genetic effects to complex phenotypes in particular cell types is crucial for understanding biological mechanisms underlying the brain-associated phenotypes including imaging-derived phenotypes (IDPs), and brain disorders and behaviors (DBs). Here, we develop a single-cell Mendelian randomization framework to infer cell type-specific causal relationships between gene expression and diverse brain-associated complex phenotypes by integrating single-cell expression quantitative trait loci (cis-eQTLs) and genome-wide association study findings. We identifiy a set of 254 and 217 cis-eQTL target genes (eGenes) that may have causal effects on 112 IDPs and 26 DBs in eight cell types, respectively. These causal eGenes exhibit strong cell type specificity and varied pleiotropy among different types of brain-associated phenotypes. Further integrative analysis reveals putative causality routes among cell type-specific causal eGenes and brain-associated complex phenotypes. Finally, we characterize the spatiotemporal expression patterns of these causal eGenes, and highlight the coordinated associations of the brain-associated phenotypes based on the expression of their causal eGenes. Overall, our study presents a large-scale analysis of the genetic effects of brain structures, disorders and behaviors, providing a catalog of cell type-specific causal eGenes.

21.
arXiv (CS.CL) 2026-06-12

Operads for compositional reasoning in LLMs

Question decomposition, i.e. breaking a complex query into simpler sub-queries whose answers are composed to produce a final answer, is a widely used strategy for improving LLM reasoning, yet it currently lacks a rigorous mathematical foundation. In this paper, we propose operads, mathematical structures that model many-in, one-out operations and compositions thereof, as a natural framework for describing question decomposition. We define the questions operad $Q$, in which operations correspond to question templates and composition corresponds to substitution of sub-answers, and show how QA models can be interpreted as algebras over $Q$. Beyond reframing existing practice, this operadic perspective points toward new methods, in particular a notion of operadic consistency, which measures whether a QA model's answers agree across the partial collapses of a question decomposition tree. Empirical evaluation of operadic consistency is reported in our companion paper (Bottman, Liu, and Richardson, 2026), which finds it strongly correlated with accuracy across twelve LLMs and four multi-hop QA datasets and outperforming standard temperature-based self-consistency baselines. We argue that operads are the natural mathematical home for question decomposition, and that invariants such as operadic consistency open new directions for analyzing and improving the reliability of multi-step reasoning.

22.
bioRxiv (Bioinfo) 2026-06-21

DeepCDS: Ab initio coding sequence prediction in prokaryotic short reads

Accurate coding sequence prediction in short prokaryotic metagenomic reads remains challenging due to sequence fragmentation, unknown sequence origins, and sequencing errors. Here we introduce DeepCDS, a deep learning-based ab initio coding sequence predictor trained on short prokaryotic sequences with and without simulated Illumina-like sequencing errors. DeepCDS integrates ESM-2 protein language model embeddings with nucleotide-level information to predict complete and fragmented coding sequence regions. Benchmarking on 215 phylogenetically diverse prokaryotic organisms demonstrates that DeepCDS consistently outperforms current state-of-the-art methods in coding sequence detection, start and stop codon localization, and robustness to different sequencing error profiles, while remaining operational at shorter sequence lengths than existing tools support. These findings demonstrate that protein language models capture distinct signals relevant for nucleotide-level coding sequence detection, especially at very short lengths. Ultimately, DeepCDS may help uncover the functional potential of the vast microbial diversity that remains genomically uncharacterized.

23.
arXiv (CS.AI) 2026-06-16

Multi-agent Framework for Time-Sensitive Complementary Collaboration in Minecraft

arXiv:2606.15684v1 Announce Type: new Abstract: We present TickingCollabBench, a Minecraft-based multi-agent benchmark for a novel class of time-sensitive complementary collaboration tasks. Our benchmark reflects four core characteristics of real-world collaboration: agent heterogeneity, mandatory collaboration, dynamic environments, and strict real-time constraints with failure risks. To enable this, we develop the TickingCollab framework, which supports the generation of diverse dynamic environments and abstracts Minecraft's primitive APIs to enable declarative YAML task specifications for composing these events. Building on this, we design a feasibility-aware automated benchmark generation pipeline, where an LLM drafts structurally diverse task configurations and feasibility verifier filters out invalid ones using approximate constraints. Evaluations demonstrate that lang latency and inherent difficulty of coordinating under partial observability and agent heterogeneity cause LLMs to frequently fail under dynamic environments and fall significantly short of a global-knowledge oracle.

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

TriFlow: Generating Artist-Like 3D Mesh Topology via Nearest-Vertex Vector Fields

We present TriFlow, a new generative approach for producing compact 3D meshes with artist-like triangle topology directly from input geometry conditions such as signed distance fields. Our key insight is to represent mesh topology as a nearest-vertex vector field (NVF) defined over the surface, where each point encodes its association to the nearest triangle vertex in the local barycentric frame. We train a latent flow-matching model to synthesize this field, enabling topology generation conditioned on the input geometry. To extract a coherent mesh, we cluster surface regions using the generated NVF and guide a constrained quadric error metric (QEM) mesh simplification with topology-aware optimization. This yields output meshes that closely match the input geometry while exhibiting structured, artist-like connectivity. Experiments demonstrate that TriFlow achieves stronger generalization and significantly improved topology quality compared to state-of-the-art learning-based approaches, alongside 90% lower Chamfer Distance and an 8x speedup.