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

MemToolAgent: Leveraging Memory for Tool Using Agents Based on Environment and User Feedback

Modern large language model (LLM) agents can use external tools to help users solve complex tasks. However, for problems that require learning from long-term historical events or from previous agent-environment interactions, LLM agents are required to use memory mechanisms to store and retrieve experiences. While sophisticated memory systems exist for dialogue agents, few studies have empirically examined how to improve agents' tool-using capabilities through past user-agent conversations. We propose MemToolAgent, a framework that improves tool use through memory management. Our approach contains a memory extraction module that processes past experiences into structured memory entries, and a retrieval module that dynamically selects a subset of the stored memory entries. This enables more personalized and accurate responses aligned with user preferences and feedback without requiring LLM fine-tuning. In summary, this work has three main contributions: (1) a unified memory entry format that improves both general-purpose and personalized tool use without LLM fine-tuning, (2) a reflection-based memory extraction that uses environment and user feedback to distill wrong executions into critiques to store, and (3) a retrieval module that chooses how many past experiences to use based on the memory similarity distribution. MemToolAgent achieves 29%, 80%, and 17% relative improvements compared to strong baselines on the WorkBench, NESTFUL, and PEToolBench benchmarks, respectively.

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

Examining the Limits of Word2Vec with Toki Pona

Word2Vec's effectiveness at generating semantic embeddings has been widely validated, yet it has been tested almost exclusively on languages with large vocabulary inventories. This study examines whether Word2Vec can successfully capture semantic relationships within an extremely reduced vocabulary using data from Toki Pona, a constructed language with approximately 130 words. We sourced 1.4 million sentences (7.95 million tokens) from the Toki Pona community for training. Approximately 23% of sentences in the corpus contain non-Toki Pona tokens such as named entities, loanwords, and neologisms. To investigate whether this linguistic noise enhances or hinders performance – a topic rarely addressed in word embedding literature – we trained two distinct models: one retaining these incidental tokens and another filtering them out completely. Evaluation was conducted using quantitative methods measuring word proximity to semantic category centroids, automated silhouette scores via agglomerative clustering, and qualitative analysis utilizing representational similarity matrices compared against English. The results indicate that while sparse, non-core tokens do not affect the relative structure of the learned embeddings, they actually draw similar words closer together in the vector space. Importantly, Word2Vec's effectiveness depends more on distributional patterns than lexicon size even at this extreme lower bound.

03.
arXiv (CS.CL) 2026-06-11

The Dynamics of Human and AI-Generated Language: How Semantics Fluctuates across Different Timescales

Spoken language, whether produced by humans or large language models (LLM), unfolds over time with varying semantic content. However, we still lack simple, interpretable time-series features that capture how generic versus specific content is distributed over time, and that can be used to compare human and AI-generated speech. We introduce a semantic-timescale analysis pipeline that turns word-level transcripts with timestamps into semantic time-series. For each spoken narrative, we compute (i) semantic specificity using WordNet-based word depth and (ii) contextual similarity using SBERT embeddings and quantify their temporal dependence using autocorrelation-window measures (ACW-0 and related metrics). We then compare original speech to multiple shuffled controls that selectively disrupt lexical identity, temporal order, and word duration. Across human-read autobiographical narratives, TTS readings, and LLM-generated texts rendered with TTS, we find that segments with longer ACW-0 in the semantic time-series tend to contain more generic vocabulary, whereas segments with shorter ACW-0 are enriched in more specific words. These associations are strongly attenuated or abolished when word order and timing are randomized, indicating that ACW-based measures capture non-trivial temporal organization of semantic content beyond static lexical distributions. Our results suggest that ACW-based semantic timescales are a useful family of features for analyzing and comparing the temporal structure of human and AI-generated speech.

04.
arXiv (CS.CL) 2026-06-11

Hubs or Fringes: Pretraining Data Selection via Web Graph Centrality

The performance of modern language models depends critically on pretraining data composition. Yet existing data selection methods rely on auxiliary classifiers for document scoring or mixture optimization, adding computational overhead and dependence on labeled data. We propose WebGraphMix, a lightweight data selection framework that computes structural centrality scores over the Common Crawl host-level web graph and uses them to vary the proportion of central versus peripheral documents in the pretraining mixture. We hypothesize that central hosts expose models to reusable abstractions, while peripheral hosts encode specialized, long-tail knowledge. WebGraphMix computes centrality scores efficiently at web scale, requiring no model training, labeled data, or downstream supervision. We integrate WebGraphMix into the DataComp-LM pipeline and train models at 400M and 1B parameter scales with 8B and 28B tokens respectively, evaluating on 23 tasks ranging from factual knowledge to symbolic reasoning. Our experiments show that central and peripheral web regions encode complementary capabilities. Mixture combining both at a ratio of 1:1 achieves 41.4% on average, compared to 39.8% for uniform sampling. Combining structural scores with document-level quality classifier scores further improves performance to 43.8%. These findings demonstrate that web graph topology is a meaningful axis for pretraining data curation, capturing information that is largely orthogonal to existing content-based approaches.

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

Prediction of Runtime Parameters of Parallel Chemistry Applications via Active and Generative Learning

arXiv:2606.16226v1 Announce Type: new Abstract: In this work, we develop two main Machine Learning based approaches to predict the runtime parameters of highly scalable parallel chemistry computations.These approaches employ active and generative learning together with the empirically determined gradient boosted regression tree models chosen among a rich suite of machine learning models. When evaluated on Coupled-Cluster with Singles and Doubles computations, our models achieve a mean absolute error percentage (MAPE) as low as 0.023 and a coefficient of determination as high as 99.9%. Furthermore, when combined with active learning to mitigate the lack of large amounts of training data, our models score a MAPE about 0.2 with 20-25% of the original dataset.

06.
arXiv (quant-ph) 2026-06-19

Vine Codes: Low-Overhead Quantum LDPC Codes on a Planar Square Grid

arXiv:2606.20263v1 Announce Type: new Abstract: The surface code is a promising route towards large-scale quantum computing, requiring only nearest-neighbour gates amenable to superconducting hardware. However, surface codes incur large qubit overheads. Novel quantum low-density parity check (qLDPC) codes promise to reduce overheads but require long-range connections that are difficult to achieve on superconducting platforms. Here, we introduce "Vine Codes" - qLDPC codes that are implementable on a planar square grid through nearest-neighbour, two-qubit gates native to superconducting platforms (iSWAP and CZ). Our approach generalises "Directional Codes" recently introduced by Gehér et. al. (2025) which are constrained to a torus. In contrast, vine codes have open boundary conditions constructed with the aid of routing qubits. We perform extensive numeric searches and find promising candidate vine codes, e.g. [[121,4,6]], [[221,6,7]], and [[234,9,6]] codes. We verify the circuit distances and show that data and measure qubits required can be reduced by up to ~28% relative to the surface code at a circuit distance of 7. Even including routing qubits, vine codes require fewer total qubits than the surface code (e.g. ~18% reduction at circuit distance 10) and benefits are expected to increase at higher distances. We perform circuit-level noise simulations to demonstrate that under a realistic noise model and at a near-term noise rate of $10^{-3}$, vine codes can perform better than the surface code while using fewer qubits. We give an exhaustive list of all unique vine codes up to stabiliser-weight 9. We additionally introduce "Flip-Vine Codes" which possess single-qubit transversal Clifford gates useful for fault-tolerant logic and magic state cultivation. We furthermore construct examples of generalised open boundaries for vine codes that go beyond the familiar X/Z boundaries of the surface and tile codes.

07.
bioRxiv (Bioinfo) 2026-06-23

Early Tracheal and Salivary miRNAs in Extremely Preterm Infants Predict BPD-related Pulmonary Hypertension

Pulmonary hypertension (BPD-PH) associated with bronchopulmonary dysplasia (BPD) in preterm infants associates with high morbidity and mortality within the first two years of life. In a previous unbiased study, we identified a panel miRNAs in tracheal aspirates (TA) that were differentially expressed in extremely low gestational age newborns (ELGANs) with BPD-PH compared to those with BPD but no PH. To explore the predictive potential of these miRNAs, we studied TA exosomes from 7 days old ELGANs and analysed a curated panel of 16 miRNAs through logistic regression and calculated the predictive AUROC to diagnose BPD-PH at 36 weeks PMA. AUROC of TA miRNAs was 0.76 with sensitivity and specificity of 53% and 93%, respectively. Adding sex and gestational age to the variables improved the AUROC to 0.78 with sensitivity and specificity of 61 and 87% respectively. Due to challenges of obtaining TA in non-invasively ventilated infants, we collected saliva samples from ELGANs at 7 days of age and compared the log expression of these 16 miRNAs in both biofluids and found significant correlation in their expression (pearson r=0.92, p

08.
arXiv (math.PR) 2026-06-24

Gradient Mean-Field Dynamics with Measure-Valued States: Well-Posedness, Chaos, and Long-Time Stability

arXiv:2606.24385v1 Announce Type: new Abstract: We study a stochastic mean-field interacting particle system whose state space is $\Y = \Tt^d \times \cP(U)$, where the first component represents a spatial variable and the second one is a probability measure over a compact metric space $U$. The dynamics are driven by locally Lipschitz drift operators: the spatial component evolves according to a Brownian diffusion, while the measure-valued component is perturbed by a projected cylindrical noise acting in the Arens–Eells space. We first establish existence and uniqueness of strong solutions for both the $N$-particle system and the associated nonlinear McKean–Vlasov equation under locally Lipschitz and linear growth assumptions on the drift coefficients. We then prove propagation of chaos: as $N\to\infty$, the empirical measure converges in expectation in Wasserstein–1 distance towards the unique McKean–Vlasov solution. Further, we investigate exponential convergence of the nonlinear McKean–Vlasov dynamics towards a unique invariant measure.

09.
arXiv (CS.CL) 2026-06-12

A Context-Aware Dataset for Stance Detection in Bioethical Controversies on Reddit

Bioethical debates increasingly unfold on social media, yet stance detection research lacks large-scale, domain-specific resources for modeling such context-dependent discourse. We present BioStance, a context-aware dataset of 39,600 annotated Post-Comment pairs from Reddit bioethical discussions. BioStance covers six controversial targets across three dimensions of bioethical controversy: fundamental value conflicts, individual liberty versus collective responsibility, and technological uncertainty. Each instance preserves hierarchical conversational context and is labeled by three independent annotators using a three-class stance scheme: Favor, Against, and None. The annotations achieve a mean Krippendorff's $\alpha$ of 0.82, indicating substantial reliability. By combining thematic diversity, conversational structure, and high-quality human annotation, BioStance supports research on context-aware stance detection, argument mining, and computational analysis of bioethical discourse.

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

Thermodynamic Signatures of Reasoning: Free-Energy and Spectral-Form-Factor Diagnostics for Hallucination Detection in Large Language Models

Authors:

Hallucination detection in large language models (LLMs) is deployment-critical, and recent work shows that the spectrum of attention-derived graph Laplacians carries strong signal about reasoning quality. Prior spectral diagnostics, however, summarize the Laplacian spectrum by a handful of eigenvalues or hand-picked scalars, leaving most of its structure unused. We propose Free-Energy Signatures (Fes), a spectral descriptor that treats each layer's attention Laplacian as a Hamiltonian and extracts its thermodynamic potentials partition function, free energy, spectral entropy, heat capacity together with the random-matrix-theory (RMT) spectral form factor. We prove three results: (i)~Lipschitz stability of Fes under attention perturbation; (ii)~an expressiveness result showing that Fes enriches finite spectral summaries and approximates moment-derived spectral functionals under explicit regularity and grid-resolution assumptions; and (iii)~a finite-sample PAC bound on the AUROC of a training-free detector built from Fes. Empirically, across six open-weight LLMs and six benchmarks, a lightweight probe on Fes descriptors achieves the strongest aggregate AUROC among attention-spectral baselines, improving over LapEig by $+6.5$ AUROC points and over GoR-4 by $+2.4$ points on average, while requiring no update to the underlying LLM. In the fully unsupervised setting, an RMT-deviation score achieves mean AUROC $0.71$, providing a label-free but weaker detector. A complementary RMT analysis shows that correct generations exhibit more Wigner-Dyson like spectral statistics, whereas hallucinations exhibit more Poisson-like statistics. The anonymized code and config are provided in the supplementary material.

11.
arXiv (quant-ph) 2026-06-12

Generalized Exact Fractional Quantum Information Model with Memory Effects

arXiv:2606.13525v1 Announce Type: new Abstract: In this paper, we analyze quantum information measures in fractional quantum mechanics using the Riemann-Liouville derivative formalism adopted here. In this case, we initially reconsider the conventional definitions of Shannon entropy and Fisher information, subsequently extending them to fractional quantum systems described by nonlocal differential operator frameworks adopted. Within this generalized formulation, fractional expressions of Shannon entropy and Fisher information are constructed and their mathematical structures examined thoroughly. Also, the formalism is then applied to the quantum harmonic oscillator, yielding explicit analytical expressions derived as functions of the fractional parameter therein. The obtained results demonstrate that fractional derivatives alter the localization properties of probability densities and generate nontrivial variations in information content and sensitivity across system behavior. In this context, the fractional parameter plays a central role in controlling deviations from the standard quantum information measures framework. Also, the study establishes a consistent framework for describing information-theoretic properties of quantum systems governed by nonlocal dynamics.

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

Pix2Fact: When Vision Is Not Enough – Benchmarking Fine-Grained VQA with Web Verification on High-Resolution Real-World Scenes

Despite progress on general tasks, vision-language models (VLMs) still struggle with challenges that demand both fine-grained visual grounding and external knowledge, a synergy overlooked by existing benchmarks that evaluate these abilities in isolation. To fill this void, we introduce Pix2Fact, a visual question-answering benchmark designed to assess expert-level visual perception and knowledge search. Pix2Fact comprises 1,000 high-resolution (4K+) images spanning eight scenarios. Its questions and answers are meticulously crafted by PhD-holding annotators from top global universities across diverse disciplines. Each question requires detailed visual grounding and the integration of external knowledge. Evaluating ten state-of-the-art VLMs, including proprietary models such as Gemini-3.1-Pro and GPT-5.4, we find that Pix2Fact poses a formidable challenge: the most advanced model (Gemini-3.1-Pro) achieves only 51.7% average accuracy, even with access to visual ground truth and search tools. Our analysis attributes this low accuracy to three factors, frequent visual grounding errors even with visual ground truth, shallow search harnessing, and VLM's inability to retrieve long-tail, unstructured local information. This striking gap exposes the limitations of current models in assisting humans with real-world scenarios that demand overwhelming visual comprehension. We believe Pix2Fact will serve as a critical benchmark to drive the next generation of language-vision agents that seamlessly integrate fine-grained perception with robust knowledge search.

13.
PLOS Medicine 2026-06-04

Beyond associations: Navigating the safety of non-steroidal anti-inflammatory drugs (NSAIDs) in early pregnancy

by Andrew S. C. Yuen, Kenneth K. C. Man Pain and fever in pregnancy require treatment, but fetal safety concerns complicate analgesic choice. A recent PLOS Medicine study presents new evidence on the safety of first-trimester NSAID use and congenital malformation risk, but interpreting findings across studies is challenging. In this Perspective, Kenneth Man and Andrew Yuen highlight a recent PLOS Medicine study that presents new evidence on the safety of first-trimester NSAID use and congenital malformation risk, but discuss why interpreting findings across studies is challenging.

14.
arXiv (CS.LG) 2026-06-17

Eigen-Spike Emergence and Quadratic Equivalents for Conjugate Kernels on Nonlinearly Separable Data

arXiv:2605.29669v2 Announce Type: replace-cross Abstract: Recent work in random matrix theory (RMT) has developed the notion of deterministic equivalents: typically linear surrogate models that approximate the spectral behavior of large nonlinear random matrices, such as nonlinear feature maps in neural networks (NNs). Such equivalents make theoretical predictions tractable by reducing a complex model to a simpler one with properties that fall under the umbrella of classical RMT tools. However, this leaves open the question of whether this idealized linear equivalence remains meaningful for classification of high-dimensional nonlinearly separable data. Motivated by this, we consider the conjugate kernel (CK), which is the nonlinear feature map of a one-layer feedforward NN, under a canonical nonlinearly separable dataset for the XOR problem; and we use the study of informative outlier eigenvalues in the CK and whether their corresponding eigenvectors asymptotically align with XOR labels as a proxy for nonlinear learnability. We develop a robust quadratic equivalent of the CK matrix that enables a precise analysis of emergent informative spikes, as one modifies various knobs common in ML practice: sample complexity, signal-to-noise ratio (SNR), nonlinear activation choice, and pretrained features. We identify regimes in which these knobs move the CK beyond the linear equivalent and produce BBP-type transitions to label-aligned outlier eigenspaces. Our analysis helps bring deterministic-equivalence tools from RMT to bear on problems of practical relevance in ML.

15.
medRxiv (Medicine) 2026-06-15

Automated AI-Based Ventricular Subcompartment Segmentation and Volumetry in Idiopathic Normal Pressure Hydrocephalus

Purpose In idiopathic normal pressure hydrocephalus (iNPH), longitudinal monitoring of ventricular size is important for diagnosis and treatment follow-up. This study aimed to validate a fully automated AI model for CT ventricular volumetry with subcompartments and to compare AI-derived volume changes with routine radiology assessments. Methods This retrospective, single-center study included 88 patients with iNPH and 456 non-contrast-enhanced head CT examinations. The model was trained on 38 manually labeled CT scans with 12 ventricular subcompartments. Outcomes included segmentation accuracy, correspondence between AI-derived longitudinal ventricular volume changes and radiology report categories (decreased, unchanged, increased), radiologist detection thresholds for ventricular change, and paired pre- and postoperative volume changes in 22 patients with ventriculoperitoneal shunt. Results Mean segmentation accuracy was high (Dice, 0.83). 91% of 100 segmentations were rated as excellent by an expert neuroradiologist. AI-derived ventricular volume changes corresponded well to radiology report categories (median total ventricular volume changes of -17% in cases reported as decreased, 0% in unchanged cases, and +22% in increased cases; all p < 0.001). Radiologists reported ventricular volume change in 50% of cases at an AI-measured relative volume change of +/-6%, and in 90% of cases at +21% for enlargement and -18% for decrease. After shunt placement, ventricular volume decreased by -8% (median), with the largest relative reductions observed in the right temporal and occipital horns. Conclusions Automated AI-based ventricular segmentation on CT enables accurate and reproducible assessment of ventricular volume changes in iNPH and complements routine radiological evaluation for longitudinal and postoperative monitoring.

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

CrossMaps: Confidence-Aware Open-Vocabulary Semantic Mapping for Rover Navigation

arXiv:2606.16935v1 Announce Type: cross Abstract: Rovers rely on perception to maintain spatial maps that encode both objects and sensor quality (e.g., range reliability, lighting artifacts, data density), guiding data fusion, embedding updates, and navigation under partial observability. To study these coupled perception-navigation processes, we present CrossMaps, a real-time confidence-aware open-vocabulary semantic mapping pipeline that constructs language-queryable maps from RGB-D data. Building on VLMaps-style approaches, CrossMaps integrates multi-scale CLIP embeddings with confidence-aware fusion and a dual-memory architecture consisting of Short-Term Memory (STM) and Long-Term Memory (LTM). The STM aggregates noisy visual observations using geometric, semantic, and temporal confidence cues, while confident and coherent cells are promoted to the LTM as persistent semantic landmarks. Designed for deployment with a Jetson Orin-powered UGV alongside SLAM, CrossMaps runs in real time and produces semantic heatmaps that can be queried with natural language to guide rover navigation.

17.
medRxiv (Medicine) 2026-06-10

Human genetic evidence links serine biosynthesis to diabetic peripheral neuropathy

Diabetic peripheral neuropathy (DPN) is a common and disabling condition for which no disease-modifying therapies are available. Glycemic and metabolic drivers do not fully explain why only a subset of individuals with diabetes develop DPN, and genetic contributors remain poorly defined. We aimed to perform a multi-population genome-wide association study (GWAS) of DPN to highlight potential new etiological pathways and therapeutic targets. Methods We performed a multi-population GWAS of neuropathy in people with and without diabetes using the VA Million Veteran Program and UK Biobank, followed by replication in the All of Us Research Program (AoU), and gene-based and gene-set analyses to identify implicated pathways. Causal relationships between circulating serine levels and DPN were further tested using two sample Mendelian randomization. To further evaluate pathogenic potential, we analyzed rare, high impact variants in GWAS implicated genes among individuals with unresolved inherited neuropathies using the GENESIS platform. Findings Among individuals with type 2 diabetes, we identified seven genome wide significant loci (p

18.
medRxiv (Medicine) 2026-06-15

Neural Correlates of Human Food Memory link to Microbial, Homeostatic, and Hedonic Signals: Evidence from a Prebiotic Randomized Clinical Trial

Background Homeostatic and hedonic brain circuits regulate eating behavior but also shape how food memories are encoded and retrieved. Objective We examined neural correlates during food memory encoding and retrieval during functional MRI before and after a 14-day prebiotic intervention in a preregistered, double-blind crossover trial (NCT03829189). Design 55 healthy adults with overweight (19 females, age 28{+/-}6.5, BMI 25-30 kg/m2) underwent 3 Tesla task-based functional MRI before and after dietary intervention of prebiotic (30g inulin/day) or equicaloric placebo for 14 days. Peripheral metabolic, short-chain fatty acids (SCFA), and microbial markers using 16S rRNA analysis were assessed in fasting blood and feces. Results Food memory was enhanced by assigned reward value and engaged brain activity in hedonic regions, including the nucleus accumbens, orbitofrontal cortex, caudate, cingulate, dorsomedial prefrontal cortex, and ventral tegmental area, as well as homeostatic and memory-related such as the hypothalamus and the hippocampus. Higher neural activations during food encoding were related to higher Actinobacteriota abundance, fecal SCFA acetate, and creatinine levels, and lower ghrelin levels. Activations in reward-related and homeostatic brain areas partially correlated with insulin, glucagon-like peptide-1, leptin, and thyroid-stimulating hormone levels. Neural activations related to food memory decreased after prebiotic intervention. The prebiotic supplementation induced decrease of hippocampal activity during food encoding related to changes in gut microbiota Firmicutes abundance. Conclusions This study indicates that neuronal food-related memory processes depend on homeostatic and hedonic brain signals modulated by the gut-brain axis. Our findings raise implications for the treatment of obesity and substance use disorder.

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

Grounded Chess Reasoning in Language Models via Master Distillation

arXiv:2603.20510v2 Announce Type: replace Abstract: Language models often lack grounded reasoning capabilities in specialized domains where training data is scarce but bespoke systems excel. We introduce a general framework for distilling expert system reasoning into natural language chain-of-thought explanations, enabling compact models to acquire domain expertise and the ability to generate faithful, grounded explanations. Rather than distilling only final outputs, we capture the full reasoning process, transforming opaque expert computations into transparent, step-by-step explanations. We demonstrate this approach in chess, a canonical reasoning domain where language models continue to underperform. Our 4B parameter model, C1, advances from a near-zero baseline to 48.1\% accuracy, outperforming all open-source models and most frontier proprietary systems. Notably, C1 surpasses its distillation teacher and generates solutions in two orders of magnitude fewer tokens than baselines. Unlike prior neural chess approaches that predict only best moves, C1 generates explainable solutions revealing strategic reasoning. Our pipeline combines supervised fine-tuning and reinforcement learning with theme-balanced data sampling for comprehensive tactical coverage. Master Distillation demonstrates how to inject expert-level knowledge into compact models for under-optimized domains, offering a recipe for unlocking RLVR where LLMs lack sufficient base capabilities.

20.
bioRxiv (Bioinfo) 2026-06-18

Accounting for allelic diversity and multicopy gene detection improves the accuracy of antibiotic resistance genotypic determination

Background Genomic prediction of antimicrobial resistance (AMR) relies on the accurate detection of resistance genes or allelic variants of core genes from raw or assembled genomes sequences. For several bacterial species and antibiotics, AMR genotype-phenotype discrepancies are common, indicating that important sources of error remain unresolved. For Enterococcus faecium, we focused on identifying the sources of discrepancies for tetracycline resistance, for which genotypic detection had shown particularly low accuracy. We investigated the effect of structural variation in antibiotic resistance genes (ARGs), including gene duplications, truncations, interruptions, and mixed configurations of complete and partial gene copies, as a source of genotype-phenotype discrepancies from short-read data. We conduct further extended investigations to other antibiotic families and into another bacterial species: Escherichia coli. Methods We analyzed collections of E. faecium and E. coli genomes, integrating high-quality complete assemblies, simulated Illumina short reads, and matched AMR phenotypic data. The integrity, copy number, and allelic diversity of ARGs were examined for multiple antibiotic classes, and their impact on ARG detection and accuracy of AMR determination was assessed using several commonly used bioinformatic tools (SRST2, ARIBA and AMRFinderPlus). Results For E. faecium, after ruling out the effect of specific tet allelic variants on tetracycline susceptibility, we found that the integrity and copy number of tet(M) had a major effect on detection accuracy. Duplicated and incomplete ARGs are also common in E. faecium genomes, particularly for macrolides (erm(B)) and aminoglycosides (ant(6)-Ia and aph(3')-IIIa). In E. coli, similar patterns were observed for tet(A), erm(B) and aminoglycoside-associated genes (aph(3')-IIIa and ant(6)-Ia). Across ARGs in both species, short-read mapping methods wrongly reported interrupted genes as complete in some instances, while assembly-based methods often failed to resolve complete copies of duplicated genes. Detection accuracy improved when tools were adapted to account for gene integrity and when extended AMR databases incorporating species-specific alleles were included. Conclusions Our findings reveal that bioinformatic limitations in dealing with ARG copy number and completeness, and in accounting for allelic variation, underly a substantial source of genotype-phenotype errors, highlighting the need for improved AMR databases and bioinformatic tools that consider these factors to achieve reliable genomic prediction of AMR.

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

LLM-as-Code Agentic Programming for Agent Harness

arXiv:2606.15874v1 Announce Type: new Abstract: Every major LLM agent framework gives the LLM the role of orchestrator; the model decides what to do next, when to call tools, and when to stop. We argue that token explosion, control-flow hallucination, and unreliable completion are not implementation bugs but architectural consequences of assigning the deterministic work of looping, branching, and sequencing to a probabilistic system. A better prompt or a stronger model cannot guarantee the reliability of the LLM agent. We therefore propose Agentic Programming, in which the program governs all control flow, and the LLM is itself part of it, an adaptive component we call LLM-as-Code and invoke only where a task calls for reasoning or generation. Within each call the model keeps full flexibility, but it cannot alter the program's execution path. With control in the program, the LLM's context is built from the execution history's call tree and forms a directed acyclic graph (DAG). Each call's context length is then determined by its call depth rather than by accumulation over steps. A case study of computer-use agents shows that the design is practical, not just a theoretical stance, substantially improving the stability of long visual operation sequences.

22.
arXiv (CS.CL) 2026-06-17

Priors Persist Through Suppression: A Stroop Paradigm for Lexical Override

Authors:

Glossaries, technical specifications, and system prompts routinely ask language models to use familiar words in unfamiliar ways. When this works, the local rule does not install the new meaning on top of the old one; the pretrained prior keeps operating underneath, and its strength still shows through. We test this with a Stroop-style paradigm: a remapping rule (doctor means forest) pitted against the query word's lexical-prior distractor (hospital), with matched neutral controls. Across 11 open-weight models spanning four families and 1B-9B parameters, lexical-prior strength predicts interference even after item-level controls for answer prior, frequency, tokenization, and prompt wording. Activation patching on five aligned models locates a source-position triplet (definition subject, definition target, query word) that nearly fully recovers the conflict effect (aggregate $R \in [0.92, 1.06]$); a definition-target swap shows the triplet performs binding rather than identity matching. Dissociation experiments isolate target preservation as the binding-specific signature: distractor suppression occurs under matched, swap, and item-mismatched conditions alike, whereas target logit collapse occurs only when the definition-target position is corrupted. Behavior and mechanism converge on the same channel: the prior's strength both predicts which overrides fail and marks where the causal repair lands.

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

Generation of Maximal Snake Polyominoes Using a Deep Neural Network

Maximal snake polyominoes are difficult to study numerically in large rectangles, as computing them requires the complete enumeration of all snakes for a specific rectangle size, which corresponds to a brute force algorithm. This hinders the study of maximal snakes in larger rectangles. Moreover, most enumerable snakes lie in small rectangles, obscuring large-scale patterns. In this paper, we investigate the contribution of a deep neural network to the generation of maximal snake polyominoes from a data-driven training, where the maximality and adjacency constraints are not encoded explicitly, but learned. To this extent, we experiment with a denoising diffusion model, which we referred as Structured Pixel Space Diffusion (SPS Diffusion). We find that SPS Diffusion generalizes from small rectangles to larger ones, generating valid snakes up to 28x28 squares and producing maximal snake candidates on squares close to the current computational limit. The model is, however, prone to errors such as branching, cycles, or multiple snake components. Overall, the diffusion model is promising and suggests that complex combinatorial objects can be understood by deep neural networks, which is useful in their investigation.

24.
arXiv (CS.CL) 2026-06-16

SciOrch: Learning to Orchestrate Expert LLMs for Solving Frontier Multimodal Scientific Reasoning Tasks

Frontier scientific reasoning remains a major challenge for large language models (LLMs), where even the strongest commercial systems fall short of expert-level performance. A closer look at model behavior reveals substantial complementarity that single-model evaluation hides: different frontier models excel on different question types, and no single model captures the full picture. We present SciOrch, a framework that trains a lightweight 8B model to orchestrate frontier LLMs for scientific reasoning. The orchestrator decomposes each question, delegates sub-problems to selected commercial models through API calls, and synthesizes a final answer. Training such an orchestrator is fundamentally harder than conventional agentic RL: each action triggers an API call that is expensive in both dollar cost and latency, making standard online rollouts infeasible. We address this with MCTS-based approach, producing diverse orchestration trajectories, extracting per-node single-turn samples, and optimizing the orchestrator with GRPO-style training. On a 240-question test set spanning SGI-Reasoning and Scientists' First Exam, SciOrch reaches 56.66% average accuracy, outperforming the strongest single commercial model by 3.74% and the strongest multi-agent baseline by 3.33%. It also attains the best accuracy on both SGI and SFE with less than half the API cost of typical multi-agent methods.

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

LatentGym: A Testbed For Cross-Task Experiential Learning With Controllable Latent Structure

arXiv:2606.15306v1 Announce Type: cross Abstract: We envision continually learning agentic systems that become more useful over time: as they encounter sequences of related tasks, they should infer the hidden structure shared across those tasks and use it to improve future decisions. This cross-task experiential learning capability is pivotal in domains such as personalization and interactive assistance, but existing training/evaluation frameworks do not provide shared, controllable latent structures and cannot measure whether or why agents improve. We introduce LatentGym: a controllable suite in which each environment is organized around a ground-truth latent variable governing the structure across tasks. Our construction yields metrics that separate exploration (whether the agent's actions gather information about the latent) from exploitation (whether the agent uses what it has gathered). We demonstrate our suite on empirical studies addressing three questions: how and why frontier models fail to adapt across related tasks; whether post-training on related task sequences improves general cross-task adaptation, and where those gains come from; and how design choices such as inter-task feedback shape training dynamics and generalization. Together, these results establish a controlled foundation for studying how LLM agents learn from experience across tasks, and for designing agents that adapt more reliably in sequential, personalized, and interactive settings.