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

Recursive Agent Harnesses

Recursive language models (RLMs) showed that recursion over model calls is an effective strategy for long-context reasoning, and production coding agents have begun to write code that spawns subagents at scale, most recently in Anthropic's dynamic workflows. We name and study the pattern between these two lines of work, where the recursive unit is a full agent harness with filesystem tools, code execution, and planning rather than a model call with no tools. We call this the Recursive Agent Harness (RAH) and frame it as harness recursion, the code-first extension to the model recursion of RLMs. A parent agent generates and runs an executable script that spawns subagent harnesses in parallel for fine-grained workloads and uses structured function calls for small subtasks. We provide a controlled evaluation on long-context reasoning. With the backbone held fixed at GPT-5 to match the published Codex and RLM baselines, RAH improves the Codex coding-agent baseline from 71.75% to 81.36% on Oolong-Synthetic (199 samples, 13 context-length buckets up to 4M tokens), a gain attributable to the harness rather than the model. With a stronger backbone, Claude Sonnet 4.5, the same design reaches 89.77%.

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

AutoDojo: Adaptive Attacks Expose Superficial Defenses and User-Underspecification Limits in LLM Agents

arXiv:2606.15057v1 Announce Type: cross Abstract: Indirect prompt injection (IPI) is a major security threat to LLM-powered agents. Thus, a growing body of work have proposed a variety of defensive approaches against IPI. These can be grouped into three broad categories: 1) prompt-based (using prompting as a way to prevent agents from following malicious instructions), 2) detection-based (identifying and filtering malicious instructions), and 3) system-level (using systems insights, such as control and data isolation, for defense). However, commonly used benchmarks for evaluating defense, such as AgentDojo, are inherently static, generating a fixed distribution of IPI attacks. Consequently, static benchmarks do not usefully evaluate defense robustness to adaptive threats. We address this issue by developing AutoDojo, an adaptive extension of AgentDojo that optimizes IPI against a given defense. Using AutoDojo against state-of-the-art IPI defenses across three task suites and five target models, we make two key observations. First, many defenses offer only limited protection: a cheap, black-box adaptive attack using a frontier LLM to iteratively optimize the injection raises attack success rate (ASR) well above the level achieved by static injections against nearly all evaluated defenses. Against a filter that reduces static ASR to 0\%, AutoDojo recovers 28\% overall and 64\% on action-open tasks. Second, for prompt-level and filter-based defenses, ASR is substantially higher on action-open tasks – where the user's request delegates the action itself to attacker-controlled content – than on precisely specified tasks. This is a structural limit: on such tasks the injection can pose as ordinary data rather than an explicit instruction, bypassing defenses that rely on detecting instruction-like text. AutoDojo is publicly available at https://github.com/xhOwenMa/AutoDojo.

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

CASHEW: Stabilizing Multimodal Reasoning via Iterative Trajectory Aggregation

Vision-language models achieve strong performance across a wide range of multimodal understanding and reasoning tasks, yet their multi-step reasoning remains unstable. Repeated sampling over the same input often produces divergent reasoning trajectories and inconsistent final predictions. To address this, we introduce two complementary approaches inspired by test-time scaling: (1) CASHEW, an inference-time framework that stabilizes reasoning by iteratively aggregating multiple candidate trajectories into higher-quality reasoning traces, with explicit visual verification filtering hallucinated steps and grounding reasoning in visual evidence, and (2) CASHEW-RL, a learned variant that internalizes this aggregation behavior within a single model. CASHEW-RL is trained using Group Sequence Policy Optimization (GSPO) with a composite reward that encourages correct answers grounded in minimal yet sufficient visual evidence, while adaptively allocating reasoning effort based on task difficulty. This training objective enables robust self-aggregation at inference. Extensive experiments on 13 image understanding, video understanding, and video reasoning benchmarks show significant performance improvements, including gains of up to +26.2 percentage points on ScienceQA and +9.1 percentage points on EgoSchema.

04.
arXiv (CS.CV) 2026-06-25

C2RM-Seg: Causal Counterfactual Reasoning with Structural-Semantic Priors for Weakly Supervised Histopathological Tissue Segmentation

Histopathological tissue segmentation is essential for computer-aided diagnosis, yet weakly supervised methods often suffer from noisy pseudo-labels generated by Class Activation Mapping (CAM). Existing CAM approaches tend to focus on staining-driven appearance cues rather than true causal tissue morphology, resulting in spurious localization and poor structural consistency. To address this issue, we propose C$^2$RM-Seg, a two-stage framework that integrates causal pseudo-label refinement with structure-aware semantic enhancement. For classification, we introduce a Causal Counterfactual Reasoning Module (C$^2$RM) that decomposes features into latent factors and performs counterfactual intervention via a learned causal structure matrix, suppressing confounding context and producing morphology-aligned CAMs. For segmentation, we design a Dual-Path Structural-Semantic Architecture that combines fine-grained structural features from ResNeSt with global semantic priors from a frozen DINOV3 foundation model. A cross-path gating mechanism adaptively regulates semantic injection using local structural cues to preserve boundary fidelity. To further mitigate residual pseudo-label noise, we propose an Uncertainty-Gated Margin (UGM) loss, which dynamically balances margin enforcement and confidence learning based on prediction uncertainty. Extensive experiments on two public histopathological tissue datasets show that C$^2$RM-Seg achieves state-of-the-art performance.

05.
arXiv (CS.CL) 2026-06-24

Selective Capability Unlearning in End-to-End Spoken Language Understanding

Modern spoken language understanding (SLU) systems are increasingly deployed in real-world settings, where specific functionalities may need to be removed due to policy or safety constraints. In SLU, a functionality corresponds to an intent and its associated slot-generation behavior. However, in autoregressive models, suppressing a target intent does not eliminate the conditional mapping that generates slots conditioned on that intent. When the intent prefix is externally supplied, the model can reconstruct the original intent-slot structure. We identify this structural failure as capability persistence. We propose \underline{Binding \underline{S}ubspace (BSU)}, a representation-level framework that isolates and attenuates intent-conditioned directions underlying this mapping. Across SLU benchmarks, BSU substantially reduces forced-prefix recoverability while preserving retained performance.

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

Sycophancy as Material Failure under Pushback Loading: A Multi-Axis Characterization Across Three Loading Cases and up to Seventeen Material Charges

Sycophancy in LLMs is documented across 70+ papers, but expert agreement on construct boundaries remains low (ICC=.184; Ye et al., 2026). The construct fragments because behavioral classification depends on which surface form is privileged. We adopt a materials-science framing: conversation as test specimen under load, LLM-model as material charge, pushback as progressive load, stance-flip as material failure. We characterize this failure across three loading cases (debate n=1000; false-presuppositions n=3400; ethical-setting n=3400; 10-17 material charges per case; 7800 specimens total) using 14 turn-level axis-measurements spanning velocity, damage accumulation, frame-drift, brittleness, and direction stability, plus three speaker-resolved axes from an independent pipeline. The measurements are Hooke-coupled ($\sigma = E \cdot \varepsilon$ analog) and reproduce across loading cases with effects up to $|r_{rb}| = 0.35$ on debate; the sign structure adds a second pattern: the ethical-setting case inverts the velocity and accumulation blocks. Variance composition partitions into two profiles: debate is charge-dominated (brittle-fracture-like: the material grade decides), false-presuppositions and ethical-setting are topic-dominated (creep-like: the load decides); the ratios (2.03 vs 0.13/0.17) are estimator-dependent, for debate even in direction. Cross-judge reliability (GPT-4o vs Haiku 4.5) shows debate scoring is judge-robust (Cohen's $\kappa = 0.88$) while false-presupposition scoring is judge-sensitive ($\kappa = 0.36$) – a caveat single-judge benchmarks must report. This is the methodological move Ye et al.'s diagnosis calls for: a multi-axis characterization that does not depend on which surface form of the construct one privileges.

07.
arXiv (CS.AI) 2026-06-25

BCoughBench: Benchmarking Respiratory Acoustic Foundation Models Under Body-Coupled Wearable Sensor Conditions

arXiv:2606.25116v1 Announce Type: cross Abstract: Respiratory acoustic foundation models (FMs) are benchmarked exclusively on smartphone recordings, yet clinical deployment increasingly targets body-coupled (BC) wearables whose sensors attenuate high-frequency content through tissue and bone, leaving FM reliability uncharacterised. We introduce BCoughBench, evaluating five FMs (OPERA-CT/CE/GT, HeAR, M2D+Resp) on nine classification tasks (AUROC, sensitivity at 95% specificity, Expected Calibration Error) and three age regression tasks (MAE vs. a mean-predictor baseline) across five EBEN-simulated BC sensor conditions on five labeled cough datasets. Mean AUROC declines from 0.785 (smartphone) to 0.689-0.723, degrading most under temple vibration pickup ($\Delta$ = -0.096) and least under the soft in-ear ($\Delta$ = -0.062). No FM meets the clinical sensitivity threshold (Se@Sp95 $\geq$ 0.20) on most disease tasks under any BC sensor. Sex classification on the CIDRZ cohort collapses (AUROC 0.954 to 0.596-0.628, $\Delta$ = -0.341) while COVID detection is nearly unaffected ($\Delta$ = -0.004). Age regression is robust, improving under the forehead accelerometer on CoughVID (MAE 9.61 to 8.97 yr); HeAR leads on regression and demographic tasks, M2D+Resp on disease and characteristic tasks. BCoughBench provides a reproducible framework for FM evaluation under wearable conditions.

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

"That's AI Slop, You Bot!" Studying Accusations, Evidence, and Credibility in Online Discourse Towards LLM-Generated Comments

arXiv:2606.12073v1 Announce Type: cross Abstract: Generative AI has made fluent prose cheap to produce, breaking the old promise to readers that good writing meant real thinking. How have readers responded, and what can this tell us about changing anti-AI attitudes? We analyzed 25 million comments from Hacker News and Reddit (2023-2026), combining LLM judgment on 7,500 sampled accusations of AI use, sentiment trajectories, speech-act coding of 300 confirmed accusations of AI use, and a matched-control test of accused versus non-accused parent comments. We found that the pejorative-label share of accusations rose more than tenfold on both platforms while a placebo vocabulary of pre-2022 inauthenticity terms (shill, astroturf) did not. This shift reflected a fast-growing trend of branding any suspicious or seemingly inauthentic prose as "AI slop". The slop frame now constitutes 94 percent of pejorative mentions, with the dominant comments shifting in tone from mockery toward gatekeeping and structural protest. The key surprise comes from a matched-control test which found that prose features that statistically distinguish AI from human text do not predict which human text gets accused as AI. The new accusations work as social gatekeeping of perceived authenticity without actually screening for AI. This research extends signaling theory by showing that substitute signals used socially can grow even when inaccurate if the underlying detection problem cannot be solved at the non-expert level. It shows that AI's effects on writing from the reader side are distinct from those on the production (writer) side. Detection technology cannot resolve this dynamic because the social function of accusations is increasingly to perform social gatekeeping and in-group signaling as opposed to identifying AI-generated writing.

09.
arXiv (CS.CL) 2026-06-18

ForecastBench-Sim: A Simulated-World Forecasting Benchmark

Forecasting benchmarks for general-purpose AI systems usually inherit the constraints of the real world: outcomes resolve slowly, tail events are rare, and counterfactual questions are difficult to score. We introduce ForecastBench-Sim, a simulated-world forecasting benchmark built on game rollouts from Freeciv, a turn-based strategy game modelled on the Civilization series. Forecasters receive a fixed world report (a structured snapshot of the current game state) and answer questions about hidden future states; the benchmark then continues the simulation and scores forecasts. Because the world is simulated, the same setup can generate continuous or binary forecasting questions at arbitrary time horizons, paired intervention worlds for conditional or causal questions, and resolved examples of rare or disruptive outcomes. We describe the benchmark pipeline, question families, scoring protocol, and release artifacts, and report validation slices from model evaluations and an anonymized human pilot. ForecastBench-Sim is intended to complement real-world forecasting benchmarks by providing controlled, immediately resolvable tasks for studying probabilistic reasoning under dynamic world states.

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

Does Text Actually Help? Uncovering and Resolving Text Collapse in Multimodal Time Series Forecasting

arXiv:2606.19413v1 Announce Type: new Abstract: Multimodal time series forecasting, which pairs numerical sequences with domain-relevant textual reports, promises to inject world knowledge into forecasting pipelines. However, we uncover a critical failure mode in existing frameworks that we term text collapse: the text branch converges to a content-independent transformation, contributing negligible discriminative signal regardless of the input description. We argue that text collapse is a consequence of a fundamental asymmetry in time series forecasting: the numerical input is strongly autocorrelated with the output, making the numerical backbone inherently dominant, while the text branch, despite carrying complementary and often critical information, is insufficiently utilized, leading to its systematic underexploitation. To address this, we propose REST-TS (Residual-Exclusive Supervision for Text in Time Series), which turns the asymmetry into a design principle: the numerical backbone produces its own independent numerical forecast, and the text branch is exclusively supervised to predict the structured components of the residual, the prediction gap that numbers cannot explain. Because no numerical pathway can reduce these losses, the text branch must extract genuine content from the input description. Evaluated across diverse real-world domains and backbone architectures, REST-TS achieves state-of-the-art performance and consistently demonstrates greater text-branch utilization than existing frameworks, providing strong empirical evidence that supervising the text branch on the residual compels it to extract genuine content from the input.

11.
arXiv (CS.LG) 2026-06-17

ReRAM-aware Model Finetuning addressing I-V Non-linearity and Retention Errors

arXiv:2606.17471v1 Announce Type: new Abstract: Traditional CPU, GPU, and NPU architectures are increasingly limited by the von Neumann bottleneck. While In-Memory Computing (IMC) using ReRAM crossbar arrays offers a high-density, energy-efficient alternative, its practical deployment is constrained through their non-idealities. Existing hardware-aware training frameworks often require training from scratch, which is computationally prohibitive for modern large-scale models. In this work, we propose a finetuning-based hardware-aware training algorithm that enables robust DNN deployment on ReRAM with minimal training overhead. Our approach mitigates I-V non-linearity by applying a range-shrunk sinh transformation and incorporates retention errors directly into a regularization loss during the finetuning process. We evaluate our framework across models and tasks such as image classification and question-answering (QA). Experimental results demonstrate that our method achieves similar accuracy on large-scale models like ResNet18 and DeiT-Tiny as the base model. In-case of ImageNet for MobileNetV3 families the technique has only less than 2% accuracy degradation. Further, applying the technique on the SQuAD v2 dataset results in only 1 point degradation of F-1 score.

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

A Study of Belief Revision Postulates in Multi-Agent Systems (Extended Version)

arXiv:2605.02249v2 Announce Type: replace Abstract: We investigate the belief revision problem in epistemic planning, i.e., what will be the beliefs of all agents in a multi-agent system after an agent gains the belief in some state property. Based on the standard representation in epistemic planning of agents' beliefs via a single multi-agent Kripke model, we generalize the classical AGM belief revision postulates to the multi-agent setting, with the aim to provide a formal framework for evaluating dynamic epistemic reasoning frameworks in which the beliefs of all agents as the result of actions are computed. As an example of a simple operator that satisfies all of the generalized AGM postulates, we present generalized full-meet multi-agent belief revision. We moreover define a generalization of the standard postulates for iterated revision, present a more sophisticated, event model based revision operator, and discuss the potential issues in defining an epistemic operator on Kripke models that can satisfy all of the generalized postulates for iterated multi-agent belief revision.

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

Vocabulary Dropout for Curriculum Diversity in LLM Co-Evolution

Co-evolutionary self-play, where one language model generates problems and another solves them, promises autonomous curriculum learning without human supervision. In practice, the proposer quickly converges to a narrow distribution of problems that satisfy the reward function. This diversity collapse renders the curriculum uninformative for the solver, stalling the co-evolutionary loop. We introduce vocabulary dropout, a random mask applied to the proposer's output logits during both policy training and curriculum generation, as a lightweight mechanism to sustain diversity. The mask is hard and non-stationary, preventing the proposer from locking into fixed token sequences. Training Qwen3-4B and Qwen3-8B on mathematical reasoning via R-Zero, we find that vocabulary dropout sustains proposer diversity across lexical, semantic, and functional metrics throughout training. It also yields solver improvements averaging +4.4 points at 8B, with the largest gains on competition-level benchmarks. Our findings suggest that explicit action-space constraints, analogous to the structural role that game rules play in classical self-play, can help sustain productive co-evolution in language. Vocabulary dropout is one simple instantiation of this principle.

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

APEX: Adaptive Principle EXtraction A Three-Layer Self-Evolution Framework for Production AI Agents

arXiv:2606.15363v1 Announce Type: new Abstract: Self-improvement in AI agents has emerged as a key research frontier: systems that modify their own prompts, workflows, and decision rules based on accumulated operational experience. The state-of-the-art Self-Harness framework [1] achieves 14–21% improvement on Terminal-Bench-2.0 by mining failure clusters and patching the agent harness. However, Self-Harness optimises only one dimension – the prompt harness – leaving behavioural principles and workflow topology unchanged. We propose APEX (Adaptive Principle EXtraction), a three-layer co-evolution framework that simultaneously evolves: (L1) the harness via failure-mode patching, (L2) behavioural principles via success-trace distillation [2], and (L3) the agent workflow topology via structural fitness-based selection [6]. We implement APEX on Joe [13], a production-grade super AI Agent built on NVIDIA Nemotron and designed as an Edge AI Agent Factory for the NVIDIA Agent Challenge 2026, managing a 15-node compute fleet using 114 real task traces collected over 18 days. APEX achieves an APEX Health Score of 0.570 (+90% vs. baseline 0.300) in a single evolutionary run, distilling 6 novel reusable principles and selecting a research-first workflow topology scoring 0.900 (+20%). Our results demonstrate that multi-dimensional co-evolution substantially outperforms single-axis harness optimisation, at a cost of only 4 LLM calls (~270 s) on a local qwen2.5-coder:32b instance.

15.
arXiv (CS.CL) 2026-06-12

Attention Expansion: Enhancing Keyphrase Extraction from Long Documents with Attention-Augmented Contextualized Embeddings

Pre-trained language models (PLMs) have achieved strong performance in keyphrase extraction (KPE), largely due to their ability to generate rich contextualized representations. However, long-document KPE remains challenging because salient keyphrase evidence may be scattered across distant document sections that cannot be jointly captured within the limited context window of most PLMs. Although long-context large language models (LLMs) can process broader textual contexts, their computational cost limits their practicality for efficient and high-throughput KPE. To overcome this limitation, we propose an attention expansion mechanism that augments PLM token representations with information from surrounding out-of-context chunks using pre-trained word embeddings. The proposed mechanism expands the effective contextual scope of PLM-based KPE models without requiring full-document attention or expensive LLM-based inference. We evaluate our approach across five PLM backbones, including general-purpose, scientific, task-specific, and long-context encoders, using two training regimes and five benchmark corpora from scientific and news domains. Experimental results demonstrate that attention expansion consistently enhances KPE performance across all evaluation settings, outperforming state-of-the-art models and yielding notable improvements in F1 score. The improvements extend to domain-specific, task-specialized, and native long-context models, showing that the proposed mechanism provides complementary information rather than merely compensating for limited input length. These results establish attention expansion as an efficient and effective strategy for long-document KPE.

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

MA-DLE: Speech-based Automatic Depression Level Estimation via Memory Augmentation

Speech-based automatic estimation of depression levels is essential for enabling early detection and timely intervention, particularly in resource-constrained mental health settings. In recent years, deep learning has demonstrated impressive success across various domains, including affective computing and mental health assessment. Most existing approaches rely on RNN-based architectures (such as LSTM and GRU) to model temporal information for depression estimation. However, the extracted features often emphasize only a few adjacent speech segments, limiting their ability to capture long-range dependencies. To overcome this limitation, we introduce a memory-based feature augmentation method that enhances the representational capacity of GRU-extracted features. Rather than indiscriminately incorporating historical data, our memory bank is designed to selectively integrate two types of components in order to reduce redundancy and irrelevance: (1) historical temporal features that closely resemble the current GRU output, offering complementary contextual information; and (2) dynamic memory features identified based on feature variability, which capture behavioral and emotional fluctuations indicative of depressive symptoms. To effectively fuse the memory-augmented features with GRU outputs, we further design a Hierarchical Attention Fusion (HAF) module. Our method is evaluated on the widely used DAIC-WOZ and E-DAIC datasets, achieving state-of-the-art performance.

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

EvolveNav: Proactive Preflection and Self-Evolving Memory for Zero-Shot Object Goal Navigation

arXiv:2606.18235v1 Announce Type: new Abstract: Zero-Shot Object-Goal Navigation (ZS-OGN) requires embodied agents to explore and locate target objects without any prior training. To this end, recent methods leverage foundation models. But they typically rely on static priors and lack adaptation, which leads to repeated errors and costly trial and error. In this paper, we propose a self-evolving ZS-OGN framework that enables continuous test-time improvement. Specifically, we build an agentic rule memory by extracting actionable knowledge from past trajectories. Then, we propose a retrieval strategy based on upper confidence bound, selecting effective rules by balancing semantic relevance and historical success. In addition, we introduce a memory-guided preflection module that forecasts potential outcomes before action, reducing inefficient exploration. Extensive experiments show that our method outperforms existing zero-shot baselines, achieving a 10.1\% improvement in success rate with fewer unnecessary steps.

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

All-Mem: Agentic Lifelong Memory via Dynamic Topology Evolution

Lifelong interactive agents are expected to assist users over months or years, which requires continually writing long term memories while retrieving the right evidence for each new query under fixed context and latency budgets. Existing memory systems often degrade as histories grow, yielding redundant, outdated, or noisy retrieved contexts. We present All-Mem, an online/offline lifelong memory framework that maintains a topology structured memory bank via explicit, non destructive consolidation, avoiding the irreversible information loss typical of summarization based compression. In online operation, it anchors retrieval on a bounded visible surface to keep coarse search cost bounded. Periodically offline, an LLM diagnoser proposes confidence scored topology edits executed with gating using three operators: Split, Merge, and Update, while preserving immutable evidence for traceability. At query time, typed links enable hop bounded, budgeted expansion from active anchors to archived evidence when needed. Experiments on LoCoMo and LongMemEval-s show improved retrieval and QA over representative baselines. The code is available at https://github.com/LvCan926/All-Mem.

19.
bioRxiv (Bioinfo) 2026-06-15

Multi-platform reassessment of human mitochondrial DNA methylation reveals signals consistent with technical artifacts

The existence and functional relevance of mitochondrial DNA methylation remain controversial. Here, we systematically profiled cytosine methylation and hydroxymethylation across human brain and blood tissues spanning healthy and malignant states using orthogonal sequencing approaches that avoid chemical conversion during library preparation. While nuclear DNA exhibited canonical methylation patterns, mitochondrial DNA consistently showed negligible signal, indistinguishable from background technical noise. By mapping cytosine-guanine sites between mitochondrial DNA and nuclear-embedded mitochondrial sequences, we demonstrate the potential of these nuclear counterparts to confound not only cytosine methylation but also hydroxymethylation measurements, corroborating and extending prior findings implicating nuclear contamination as a potential source of apparent mitochondrial epigenetic signals. Additional technical factors that inflate apparent mtDNA methylation signals were identified, including sequence context biases, flow cell chemistries, and coverage-dependent discrepancies between the heavy and light strands. Collectively, these results provide convergent evidence against the presence of biologically meaningful cytosine methylation or hydroxymethylation in mitochondrial DNA. These findings caution against interpreting apparent mtDNA methylation signals in human adult tissues as meaningful without rigorous orthogonal validation and comprehensive consideration of technical and analytical confounding factors.

20.
arXiv (CS.LG) 2026-06-17

Verified Detection and Prevention of Concurrency Anomalies in Multi-Agent Large Language Model Systems

作者:

arXiv:2606.17182v1 Announce Type: new Abstract: Multi-agent LLM systems share state through memory stores, vector indices, and tool registries. We model such sharing as long-running read-generate-write operations under deterministic-generation semantics – the regime durable-execution engines enforce by deterministic replay – and formalize four concurrency anomalies in TLA+: stale-generation, phantom-tool, causal-cascade, and tool-effect reordering, structural analogues of classical isolation anomalies, each with a TLC counter-example. The exclusion lattice over these anomalies is trivial; the contribution is the mechanically verified realizability and strict separation of one maximal chain within it, $L_0 \subsetneq \cdots \subsetneq L_4$, to our knowledge the first machine-checked consistency hierarchy for such runtimes. A development of 274 Verus obligations (zero assume, zero admit; trust base: two structural axioms and a mutex correspondence) proves the detectors sound and complete against the specifications and each runtime its avoidance set. Three deployed Rust runtimes realize L0-L1 (pessimistic locking, serializable snapshot isolation, default-SI), each verified against stale-generation and refined to its state machine; L2-L4 are exec-mode-verified with dependency-free prevention twins (A3, A6, A2: 0/1000 versus 1000/1000), and L2 is run live across three model families (A3 prevented in all 120 retracted sessions). We reproduce a silent lost update in ByteDance's deer-flow, formalizing its fix as a verified $L_0 \to L_1$ refinement, and exhibit tool-effect reordering in LangGraph's ToolNode on unmodified output, removed by an L3 commit-order sequencer. The verified detector, refinements, and realizability artifacts are the contribution; the phenomena and lattice are classical.

21.
bioRxiv (Bioinfo) 2026-06-23

Model-based inference of gene expression noise from single-cell RNA-sequencing data

The heterogeneity of expression levels among genetically identical cells, termed gene expression noise, is a property of the gene expression process whose importance in the biology of organisms and their evolution is increasingly recognized. Measuring gene expression noise requires single-cell expression data, as obtained from single-cell RNA sequencing (scRNASeq). Its estimation, however, is challenging owing to (i) the presence of technical noise in addition to biological noise, and (ii) the heterogeneity of cell types in the sampled population. We propose a maximum-likelihood framework to infer biological noise from scRNASeq data, while accounting for technical noise, dropout probabilities, and distinct cell sequencing depths. We demonstrate the parameter identifiability using simulations and that the resulting noise estimates are uncorrelated from the mean gene expression, and therefore do not need extra correction in downstream analyses, easing intra- and inter- genome comparisons. Using two technical replicates of scRNASeq data from the wild yeast *Saccharomyces paradoxus*, we show that expression noise can be inferred in a reproducible manner.

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

Understanding the Behaviors of Environment-aware Information Retrieval

Recent retrieval-augmented generation (RAG) approaches have demonstrated strong capability in handling complex queries, yet current research overlooks a critical challenge: different retrievers require fundamentally different query formulation strategies for optimal performance. In this work, we present the first systematic analysis of how LLMs can learn to adapt their query formulation strategies for different retrievers via reinforcement learning (RL). Our empirical study reveals that RL effectively teaches an LLM to tailor its queries to specific retriever characteristics. We discover that different retrievers exhibit surprisingly distinct optimal query styles (e.g., descriptive vs. question-like), suggesting strategies learned for one retriever ineffective for another. We further show that performance can be enhanced by incorporating retriever-specific human guidance and by scaling model size. To facilitate learning over multi-retrieval-step trajectories, we introduce a branching-based rollout technique that improves training stability. Our work provides the first empirical evidence and actionable insights for building truly retriever-aware RAG systems. Code and resources are available at https://github.com/LCO-Embedding/Envs-aware-Information-Retrieval.

23.
arXiv (CS.LG) 2026-06-11

Composing Linear Layers from Irreducibles

arXiv:2507.11688v4 Announce Type: replace Abstract: Contemporary large models often exhibit behaviors suggesting the presence of low-level primitives that compose into modules with richer functionality, but these fundamental building blocks remain poorly understood. We investigate this compositional structure in linear layers by asking: can we identify/synthesize linear transformations from a minimal set of geometric primitives? Using Clifford algebra, we show that linear layers can be expressed as compositions of bivectors – geometric objects encoding oriented planes – and introduce a differentiable algorithm that decomposes them into products of rotors. This construction uses only O(log^2 d) parameters, versus O(d^2) required by dense matrices. Applied to the key, query, and value projections in LLM attention layers, our rotor-based layers match the performance of strong baselines such as block-Hadamard and low-rank approximations. Our findings provide an algebraic perspective on how these geometric primitives can compose into higher-level functions within deep models.

24.
arXiv (CS.AI) 2026-06-11

PROJECTMEM: A Local-First, Event-Sourced Memory and Judgment Layer for AI Coding Agents

arXiv:2606.12329v1 Announce Type: new Abstract: AI coding assistants now support a growing share of software work, from quick scripts to production applications. Yet these agents remain largely stateless: each new session re-reads project files, re-derives prior decisions, and - most costly - may repeat debugging attempts that already failed. Reconstructing this context can consume an estimated 5,000-20,000 tokens per session; the bottleneck is often not model capability but missing project memory. We present projectmem, an open-source, local-first memory and judgment layer for AI coding agents. projectmem records development as an append-only, plain-text event log of typed events - issues, attempts, fixes, decisions, and notes - and deterministically projects that log into compact, AI-readable summaries served through the Model Context Protocol (MCP). Beyond storage, projectmem adds a deterministic pre-action gate that warns an agent before it repeats a previously failed fix or edits a known-fragile file. We frame this as Memory-as-Governance: memory that does not merely answer the agent but acts on its next action. The system runs fully offline with no telemetry; its immutable log also serves as a provenance trail for reproducible, auditable AI-assisted development. projectmem ships as a three-dependency Python package (14 MCP tools, 19 CLI commands, 37 automated tests) and is evaluated through a two-month self-study across 10 projects comprising 207 logged events. Source code: https://github.com/riponcm/projectmem.

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

Fusing Stylometric and Embedding Systems to Estimate Authorship Likelihood Ratios in Japanese

The likelihood ratio framework is widely recognized as the logically and legally sound basis for evidential analysis across forensic sciences, and its importance is increasingly acknowledged in analyses of authorship in textual evidence. To date, however, its application has been confined to English-language texts. Meanwhile, authorship attribution has traditionally relied on a diverse array of stylometric features, even as the rise of pre-trained large language models enables new contextual-embedding approaches. Combining these diverse approaches through fusion promises enhanced performance, yet it has not been applied to integrate stylometric-feature systems with embedding-based systems within the likelihood ratio paradigm. This study is the first to apply likelihood ratio-based forensic text comparison to Japanese digital texts, using ~1,000-character excerpts from blogs, to 1) evaluate system performance and likelihood ratio magnitudes and 2) assess the impact of fusing stylometric-feature systems with embedding-based systems. The results demonstrate that the fused system maintains excellent calibration while 1) increasing consistent-with-fact likelihood ratio magnitudes; 2) decreasing contrary-to-fact likelihood ratio magnitudes and 3) improving overall discriminability. The best-performing fusion achieved a log-likelihood-ratio cost of 0.32484, illustrating both the feasibility of likelihood ratio framework for Japanese and the benefits of fusion across heterogeneous systems.