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

Disentangling Hallucinations: Orthogonal Semantic Projection for Robust Interpretability

As Vision-Language Models are increasingly deployed in safety-critical applications, the trustworthiness of their explanations becomes crucial. Explainable AI (XAI) methods for Vision-Language Models often suffer from semantic hallucination, where attribution maps highlight prominent image regions even when prompted with incorrect text descriptions (e.g., highlighting a dog when prompted ``cat''). Although this problem is widespread, a formal mathematical analysis of XAI methods and CLIP embeddings is largely missing in the literature. We demonstrate that this phenomenon is not specific to a single architecture but is a fundamental consequence of Linear Semantic Leakage in high-dimensional embedding spaces. We propose a unified theoretical framework, Linear Semantic Attribution (LSA), which generalizes across discriminative methods. We introduce OSP, a geometric intervention that utilizes the residual property of OMP to disentangle unique semantic signals from shared concepts. We prove theoretically and demonstrate empirically that OSP minimizes hallucination by orthogonalizing the query vector against distractor concepts, rendering the attribution model blind to shared features while preserving fidelity for correct prompts. Our code is available at: https://github.com/emirhanbilgic/Orthogonal-Semantic-Projection

02.
arXiv (CS.AI) 2026-06-19

QMFOL: Benchmarking Large Language Model Reasoning via Quantifiable Monadic First-Order Logic Test Case Generation

arXiv:2606.20227v1 Announce Type: new Abstract: Large Language Models (LLMs) have made significant progress in reasoning, particularly in deductive reasoning, which is crucial for high-stakes decision-making. As models improve, evaluation benchmarks should evolve to keep pace. However, existing benchmarks lack fine-grained control over logical complexity and struggle to balance semantic diversity with logical consistency. To address these issues, we propose QMFOL, an automated framework for generating monadic first-order logic reasoning tasks with quantifiable and controllable complexity. It constructs formal logical structures using conjunction and disjunction patterns, enabling precise control over reasoning depth, width, label types, and distractors. These structures are then translated into natural language via LLMs, with logical consistency ensured through round-trip verification using an external prover. Based on our framework, we build QMFOLBench, a benchmark comprising 2880 instances with 960 configurations across diverse logical and semantic dimensions. Evaluations on six large reasoning models (LRMs) and two LLMs show that performance degrades and computational overhead increases with rising logical complexity. Models perform better on True-labeled tasks than on False or Unknown ones, and exhibit sensitivity to semantic variation. Overall, QMFOL offers a scalable and reliable approach for constructing deductive reasoning benchmarks with controllable complexity, enabling more precise evaluation of reasoning capabilities in modern language models.

03.
bioRxiv (Bioinfo) 2026-06-11

DModE: An end-to-end framework for Differential Modification and Expression Analysis of Nanopore direct RNA sequencing data

Summary: Nanopore direct RNA sequencing (DRS) enables simultaneous quantification of transcript abundance and RNA modifications from native RNA molecules, providing a unique opportunity to study transcriptional and epitranscriptomic regulation within a single experiment. However, comprehensive analysis of DRS data remains challenging, as existing workflows typically focus on individual processing steps and often require manual integration of multiple software packages for expression analysis, modification detection, statistical testing, and visualization. Furthermore, integrated differential expression and differential RNA modification analysis at both gene and isoform resolution remains poorly supported by current workflows. Here, we present DModE (Differential Modification and Expression Analysis), an end-to-end framework for integrated analysis of Nanopore DRS data. DModE combines an Epi2ME-compatible Nextflow preprocessing workflow with a dedicated Python package for downstream statistical analysis, visualization, and reporting. The framework supports differential gene and isoform expression analysis, differential RNA modification analysis at genome and transcript level, metagene profiling, exploratory epitranscriptomic analyses, and integrated assessment of relationships between expression and modification dynamics. Results are automatically summarized in interactive HTML reports, facilitating reproducible and accessible data interpretation. By integrating transcriptomic and epitranscriptomic analyses within a single framework, DModE substantially simplifies comprehensive DRS data analysis and lowers the barrier for studying RNA modification biology using Nanopore sequencing.

04.
arXiv (CS.AI) 2026-06-12

Fusion Learning from Dynamic Functional Connectivity: Combining the Amplitude and Phase of fMRI Signals to Identify Brain Disorders

arXiv:2603.24603v2 Announce Type: replace-cross Abstract: Dynamic functional connectivity (dFC) derived from resting-state functional magnetic resonance imaging (fMRI) has been extensively utilized in brain science research. The sliding window correlation (SWC) method is a widely used approach for constructing dFC by computing correlation coefficients between amplitude time series of signals from pairs of brain regions. In this study, we propose an integrated approach that incorporates both amplitude and phase information of fMRI signals to improve the detection of brain disorders. Specifically, we introduce a multi-scale fusion learning framework, namely MSFL, which leverages two complementary dFC features derived from SWC and phase synchronization (PS). Here, SWC captures amplitude correlations, while PS measures phase coherence within dFC. We evaluated the efficacy of MSFL in classifying autism spectrum disorder and major depressive disorder using two publicly available datasets: ABIDE I and REST-meta-MDD, respectively. The results indicate that MSFL significantly outperforms existing comparative models. Moreover, we performed model explanation analysis using the SHAP framework, which showed that both types of dFC features from SWC and PS contribute to detecting brain disorders.

05.
bioRxiv (Bioinfo) 2026-06-10

APOSM: Pairwise preference learning improves generative small-molecule design

Small-molecule lead refinement is constrained by the cost of synthesizing and assaying candidates, making the surrogate models that prioritize compounds for experimental testing central to the design process. The reliability of such surrogates is limited by the noise and sparsity of screening measurements. We show that training the surrogate on pairwise comparisons between candidate molecules, rather than on absolute predicted scores, yields a substantially more reliable signal for active candidate selection in this regime. We develop APOSM, an active-learning algorithm that combines a fragment-based generator, a pairwise message-passing graph neural network surrogate, and probabilistic ranking inside a batched acquisition loop. On the Practical Molecular Optimization benchmark and a GPCR ligand rediscovery task, APOSM improves target attainment and sampling efficiency over unguided fragment-based optimization, the Graph-GA genetic algorithm, and a pointwise-regression ablation, with the largest gains on tasks where absolute scores are hardest to calibrate.

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

The Pragmatic Persona: Discovering LLM Persona through Bridging Inference

Large Language Models (LLMs) reveal inherent and distinctive personas through dialogue. However, most existing persona discovery approaches rely on surface-level lexical or stylistic cues, treating dialogue as a flat sequence of tokens and failing to capture the deeper discourse-level structures that sustain persona consistency. To address this limitation, we propose a novel analytical framework that interprets LLM dialogue through bridging inference – implicit conceptual relations that connect utterances via shared world knowledge and discourse coherence. By modeling these relations as structured knowledge graphs, our approach captures latent semantic links that govern how LLMs organize meaning across turns, enabling persona discovery at the level of discourse coherence rather than surface realizations. Experimental results across multiple reasoning backbones and target LLMs, ranging from small-scale models to 80B-parameter systems, demonstrate that bridging-inference graphs yield significantly stronger semantic coherence and more stable persona identification than frequency or style-based baselines. These results show that persona traits are consistently encoded in the structural organization of discourse rather than isolated lexical patterns. This work presents a systematic framework for probing, extracting, and visualizing latent LLM personas through the lens of Cognitive Discourse Theory, bridging computational linguistics, cognitive semantics, and persona reasoning in large language models. Codes are available at https://github.com/JiSoo-Yang/Persona_Bridging.git

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

The Value Axis: Language Models Encode Whether They're on the Right Track

We investigate whether language models internally track the value of their current trajectory, defined as the likelihood that their ongoing strategy will achieve their goals. Using synthetic, in-context reinforcement learning data, we construct a "value" axis for Qwen3-8B. We find that activations along this axis distinguish between high vs. low verbalized confidence, rollouts without and with backtracking, and correct vs. corrupted code. Steering towards high value causally suppresses self-correction and reduces explanatory verbosity, while steering towards low value induces backtracking and exploration. We demonstrate that direct preference optimization (DPO) can increase the internal value of rewarded behaviors (e.g. use a certain word), causing the model to act more confidently after exhibiting them. Finally, we apply the value axis to study in-the-wild settings. For example, we find that Qwen assigns low value to politically sensitive chat queries after post-training and that supervised fine-tuning increases internal confidence within the training domain. Our results suggest that language models linearly encode an estimate of expected goal success that modulates their confidence in pursuing a direction.

08.
arXiv (CS.CV) 2026-06-18

Low-Rank Tensor Completion Based on Fractional Regularization with Ky Fan p-k Norm

This paper addresses low-rank tensor completion (LRTC) by proposing a novel nonconvex surrogate, namely the ratio of the tensor nuclear norm to the tensor Ky Fan p-k norm (TNPK), to accurately approximate the tensor tubal rank. The TNPK possesses appealing properties, including scale invariance, parameter flexibility, and the existence of closed-form solutions under specific choices of p and k. With specific parameter settings of p and k, it reduces to the ratio of the tensor nuclear norm to the tensor Ky Fan k norm (TNK) or the ratio of the tensor nuclear norm to the tensor Frobenius norm (TNF). We construct a LRTC model and, under the tensor null space property (NSP), prove that low-rank tensors are local minimizers of the proposed model. Moreover, we derive the proximal operator of the Ky Fan p-k inverse-norm and further develop an efficient alternating direction method of multipliers (ADMM) algorithm with guaranteed subsequential convergence under mild conditions. Extensive experiments on synthetic and real-world datasets validate the superior performance of our method against state-of-the-art competitors.

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

What's Old is New Again: Classical Dimensionality Reduction for Efficient Saliency-Guided Biometric Attack Detection

Saliency-guided training is a paradigm in visual recognition that encourages models to focus on the most relevant image regions during learning. While its application in biometric presentation attack detection (PAD) has shown strong benefits in robustness and generalization, adoption is often limited by the high cost, domain specificity, and limited scalability of existing saliency acquisition methods, such as human annotations over a limited dataset. We present a novel, cost-efficient, and highly-scalable approach to saliency acquisition using maps inspired by classical dimensionality reduction techniques: PCA and LDA. Our proposed methods generate saliency maps directly from raw training data, requiring no human annotation nor domain knowledge. We contextualize the effectiveness of these saliency sources in three saliency-explored domains (iris PAD, synthetic face detection, fingerprint PAD) and demonstrate its scalability in two saliency-novel domains (fingerprint vein PAD and ID card PAD). Across all domains tested, models trained using dimensionality reduction-sourced saliency maps exceed baseline and sometimes SOTA saliency methods without any resource investment or domain-specific tooling. Our findings overcome an important yet unaddressed barrier to saliency-guided training for biometric attack detection and beyond.

10.
arXiv (CS.AI) 2026-06-15

A Two-Stage Statistical Framework for Evaluating Associative Interference in Large Language Models

arXiv:2606.14117v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly evaluated for bias using adaptations of human psychological paradigms, yet methodological limitations-particularly the conflation of refusal behavior with task performance-have hindered clear interpretation. Here, we adapt the Implicit Association Test (IAT) to a controlled, forced-choice framework and introduce a two-stage modeling approach that separates response compliance from task-consistent classification. Across three contemporary LLMs (Claude Sonnet-4, Gemini 2.5 Pro, and GPT-5), we evaluate associative interference, defined as reduced task-consistency in incongruent relative to congruent conditions. While compliance with the structured response format was uniformly high, interference effects varied substantially across models and domains. Claude Sonnet-4 exhibited strong interference in the Gender–Career domain (DeltaP = 0.086, 95% CrI [0.026, 0.173]) and smaller but credible effects in Gender–Science. Gemini 2.5 Pro showed attenuated interference, and GPT-5 exhibited minimal or no detectable interference across domains. These findings demonstrate that IAT-style associative asymmetries are not a universal property of LLMs, but instead depend on model-specific characteristics. By isolating interference from compliance and modeling item-level variability, this study provides a principled framework for evaluating structured response patterns in LLMs. The results highlight the importance of model-specific assessment and suggest that associative interference can be substantially mitigated in modern systems.

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

Beyond Classification: A Cough Regression Benchmark for Respiratory Acoustic Foundation Models

arXiv:2606.15436v1 Announce Type: cross Abstract: Respiratory acoustic foundation models (FMs) excel at cough classification, yet their ability to predict continuous health quantities from cough audio remains largely unexplored, despite the clinical value of passive age, BMI, and disease probability estimation in settings where physical measurements are unavailable. We introduce the multi-model, multi-target cough regression benchmark evaluating five FMs (OPERA-CT, OPERA-CE, OPERA-GT, HeAR, M2D+Resp) across six targets on three datasets under subject-disjoint protocols, comparing linear, MLP-small, and full MLP regression heads. MLP-small beats the mean-predictor baseline on all tasks and linear probing in 23 of 30 model x task cases, with full MLP overfitting on small clinical data but recovering on larger sets, revealing a dataset size x head-capacity trade-off. HeAR leads within-dataset age regression on Coswara (9.12 yr MAE); its CIDRZ result is excluded from headline claims owing to possible HeAR-CIDRZ pretraining overlap. OPERA-GT is favored over OPERA-CT on age in all three datasets, with the CIDRZ margin within seed variance, extending a generative-pretraining advantage from breath to cough. HeAR and M2D+Resp reach near-full performance at N = 50 samples while OPERA models require N = 400. Cross-dataset transfer is strongly asymmetric as large diverse data generalises to small clinical populations (CoughVID to CIDRZ: -0.17 yr) but not vice versa (CIDRZ to Coswara: +2.43 yr, +26.6%).

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

Diffusion-Refined Segmentation and Vision-Language Interpretation for Pediatric Brain Tumor MRI

Accurate pediatric brain tumor segmentation remains challenging due to limited annotated data, heterogeneous imaging phenotypes, diffuse tumor boundaries, and class imbalance across tumor subregions. Here, we present a two-stage deep learning framework for improving multi-modal pediatric brain MRI segmentation and clinical interpretation. First, we evaluate 3D Res U-Net and Swin-UNETR baselines on BraTS-PEDs MRI scans, using four co-registered modalities to predict tumor core, whole tumor, and enhancing tumor regions. Second, we introduce diffusion-based refinement models conditioned on coarse Swin-UNETR predictions, including a 3D DDPM refiner and MedSegDiff. Conditioning substantially improves diffusion stability and performance, particularly for enhancing tumor boundary segmentation. Conditioned MedSegDiff achieves the strongest boundary agreement with the lowest HD95. Finally, predicted tumor volumes and representative segmentation overlays are integrated with a multimodal language model to generate structured radiology-style reports. Together, our results suggest that coarse-to-refined diffusion segmentation can improve pediatric tumor boundary delineation and support end-to-end interpretable AI-assisted neuro-oncology workflows.

13.
medRxiv (Medicine) 2026-06-15

Non-invasive intracranial pressure waveform reconstruction with deep learning

Purpose: Continuous intracranial pressure (ICP) monitoring requires invasive instrumentation, reaching only a narrow subset of critically ill patients. We tested whether deep learning models trained on routinely acquired extracranial signals can reconstruct continuous ICP waveforms at clinically relevant accuracy in an independent external cohort. Methods: In adults admitted to the ICU at a single quaternary health system, five deep learning architectures were trained on high-frequency arterial blood pressure (ABP), photoplethysmography (PPG), and electrocardiography (ECG) waveforms, using invasive (intraparenchymal) ICP as ground truth. Two fusion strategies (early and late) and three training objectives (waveform-morphology, baseline robust regression, and weighted robust regression) were evaluated. Models were externally validated on the held-out MIMIC-III Waveform Database. Performance was assessed by mean absolute error (MAE) and waveform similarity by Pearson correlation (r). Results: We analyzed data from 158 critically ill adults (~5,322 hours) across two quaternary health systems (Johns Hopkins Hospital, Baltimore; Beth Israel Deaconess Medical Center, Boston). Validation MAE ranged from 4.276 mmHg [95% CI 4.269, 4.283] (gated recurrent, late fusion) to 4.946 mmHg [95% CI 4.938, 4.956] (attention-based, early fusion), with Pearson r ranging from 0.599 [95% CI 0.599, 0.600] to 0.722 [95% CI 0.722, 0.723]. The multiscale encoder-decoder model demonstrated the most favorable MAE-correlation tradeoff. Conclusion: This is the first demonstration that continuous ICP waveform reconstruction from bedside signals generalizes across institutions at clinically relevant accuracy, establishing a foundation for non-invasive ICP monitoring and motivating validation across broader populations and ICP ranges.

14.
Nature (Science) 2026-06-10

Whole-genome duplication shaped cell-type evolution in the vertebrate brain

Authors:

The complex brains of vertebrates have more cell types than those of their closest relatives. Whole-genome duplications (WGDs) occurred during early vertebrate evolution1, but it is unclear whether the duplicated genes (ohnologues) facilitated cell-type evolution. Here using brain single-cell transcriptomes from five chordates—human2, mouse3, lizard4, lamprey5 and amphioxus—we report that many cell-type families with conserved core transcription factors in vertebrates do not show one-to-one homology with amphioxus. Moreover, ohnologues, particularly those from the first WGD, were more important than small-scale duplication paralogues for vertebrate cell-type evolution. To explore whether ohnologues are mechanistically important for this process, we predicted ancestral cell-type states and compared them to amphioxus and experimentally investigated macroglia. The findings indicate that ohnologues had a role in early vertebrate cell-type diversification. Moreover, by examining paralogue expression across cell types and species, we show that expression changes were mainly driven by dosage selection and subfunctionalization. We also link ohnologues to cellular diversity at different anatomical and cell-type scales. Our findings demonstrate the importance of WGDs for the evolution of early vertebrate brain complexity and highlight that the resultant ohnologues continued to capacitate cell-type evolution long after they were formed. Analyses of brain single-cell transcriptomes from human, mouse, lizard, lamprey and amphioxus reveal that duplicated genes (ohnologues) played a pivotal part in early vertebrate cell-type diversification.

15.
arXiv (CS.CV) 2026-06-16

Faithful Action-unit Causal Reasoning for Counterfactually Faithful Emotion Explanations

Multimodal models can name the action units (AUs) behind a facial emotion, but their AU->emotion rationales are typically plausible rather than faithful: nothing forces the AUs a model invokes to be the AUs that actually drive its prediction. We cast AU->emotion reasoning as a counterfactual-consistency problem between the rationale, the label, and a structural AU->emotion causal graph G, and propose FACR, which grounds the reasoner in an independently induced, polarity-aware G and trains a counterfactual-faithfulness objective: a do-intervention on an AU that G marks causal for a class must move the prediction, while one it marks irrelevant must leave it unchanged. Faithfulness is thereby both trainable and measurable through a matching interventional metric, which we evaluate against a known causal structure, the PSPI pain-AU composition, as no existing affective-reasoning benchmark allows. We are explicit that this metric tests fidelity to the supplied structure rather than its rediscovery: it asks whether the trained reasoner invokes the AUs the structure marks causal, on held-out subjects and a second dataset. Under subject-independent evaluation on UNBC-PAIN, the objective raises the agreement between the invoked AUs and the PSPI composition from a no-objective baseline of 0.08 to 0.57, at a small detection cost; an unfaithfulness control attributes the gain to the objective. On a cross-dataset emotion transfer, the objective likewise raises fidelity to G on a seven-class task (0.50 to 0.84). Finally, we attach a language verbalizer and extend the audit to the generated text: biasing each action unit's emission by its latent activation makes the rationale faithful by construction, so that ablating an AU removes it from the explanation, a property that transfers to a second language-model backbone, whereas a freely generated rationale is unfaithful.

16.
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.

17.
Science (Express) 2026-04-23

Structural N- and O-glycans revealed by high-resolution cryo-EM analysis of tubular mastigonemes | Science

Authors: Unknown Author

The chemical complexity and non-templated biosynthesis of glycans have posed significant challenges for establishing sequence-structure relationships. Here we report cryo-EM structures of tubular mastigonemes from a golden alga species, Ochromonas danica , in which a large number of N- and O-glycans are resolved at 1.8-2.2 Å resolution. Beyond high-mannose and complex N-glycans, we identify a non-canonical N-glycan on the Ala- Asn -Asp (A N D) motif. The surface spikes comprise dense O-glycans coating PSXX tetrapeptide repeats, with two glycans linked on trihydroxylated proline and one on serine per repeat. In addition to various types of sugars and their covalent modifiers, water molecules (>10% of resolved volume) and cations are clearly resolved and mediate the structural assembly. Our study establishes a framework for investigating glycan folding in high-order biological assemblies.

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

RODS: Reward-Driven Online Data Synthesis for Multi-Turn Tool-Use Agents

arXiv:2606.19047v1 Announce Type: new Abstract: Multi-turn tool-use RL is bottlenecked by the rapid depletion of informative samples in static datasets. We observe that the gradient signal in GRPO concentrates on tasks with the highest rollout reward variance, a consequence of the Popoviciu upper bound. Consequently, samples near the agent's capability boundary – where successes and failures are roughly balanced – contribute disproportionately large policy gradients. As training progresses, this boundary continuously shifts, which gradually depletes the pool of informative samples in a static dataset. We propose RODS (Reward-driven Online Data Synthesis) to resolve this depletion. RODS closes the loop between RL training and data generation by repurposing the progress reward variance as a practical, zero-cost boundary detector that requires no extra inference beyond the rollouts already computed for training. It continuously identifies such boundary samples, synthesizes new multi-turn variants matching their structural complexity (e.g., API topology and dependency depth) via a skill-aligned resampling pipeline, and manages a dynamic replay buffer that co-evolves with the policy. Starting from 400 human seeds and maintaining an active training pool of ~800 samples, RODS achieves comparable performance to a 17K-sample offline pipeline while requiring roughly 20x fewer trajectories, and improves over fixed-data RL and environment augmentation in our controlled setting.

19.
arXiv (CS.AI) 2026-06-16

PISA: A Pragmatic Psych-Inspired Unified Memory System for Enhanced AI Agency

arXiv:2510.15966v2 Announce Type: replace Abstract: Memory systems are fundamental to AI agents, yet existing work often lacks adaptability to diverse tasks and overlooks the constructive and task-oriented role of AI agent memory. Drawing from Piaget's theory of cognitive development, we propose PISA, a pragmatic, psych-inspired unified memory system that addresses these limitations by treating memory as a constructive and adaptive process. To enable continuous learning and adaptability, PISA introduces a trimodal adaptation mechanism (i.e., schema updation, schema evolution, and schema creation) that preserves coherent organization while supporting flexible memory updates. Building on these schema-grounded structures, we further design a hybrid memory access architecture that seamlessly integrates symbolic reasoning with neural retrieval, significantly improving retrieval accuracy and efficiency. Our empirical evaluation, conducted on the existing LOCOMO benchmark and our newly proposed AggQA benchmark for data analysis tasks, confirms that PISA sets a new state-of-the-art by significantly enhancing adaptability and long-term knowledge retention.

20.
medRxiv (Medicine) 2026-06-15

ICD-10 Code Ambiguity Obscures Treatment-Eligible Adults with Spinal Muscular Atrophy: A Single-Center Chart Review and Patient Outreach Study

Background. Three disease-modifying therapies (DMTs) for spinal muscular atrophy (SMA) have been approved since 2016, yet many adults remain untreated. Identifying them depends on ICD-10 codes that capture SMA but do not reliably distinguish it from other related conditions. We examined, in one U.S. health system, both patients' engagement with therapy and the accuracy of the codes used to find them. Methods. We conducted a retrospective chart review of adults in an academic health system identified by SMA-associated ICD-10 codes, with manual adjudication of diagnosis and DMT status. Confirmed SMA-positive, DMT-naive patients were invited to a structured telephone interview on treatment awareness and barriers. Results. Of 60 charts, 22 (36.7%; 95% CI 25.6-49.3%) were appropriately coded for SMA or a related disorder; only 16 (26.7%) had molecularly confirmed SMA. The other 38 (63.3%) were miscoded, spanning spinal and bulbar muscular atrophy, asymptomatic carriers, prenatal screening, and conditions unrelated to SMA. Ten of the 16 confirmed patients (62.5%) were DMT-naive; one was interviewed, one declined, and eight could not be reached. The non-response is itself a finding: the patients least visible to administrative data are the hardest to reach. Conclusions. ICD-10 ambiguity is a barrier to treatment access in adult SMA, as is loss to follow-up. We make two recommendations: continuous documentation-coding alignment that uses natural language processing to verify the genetic precondition, and type-specific SMA codes (subcodes for Types 0-4) anchored on molecular SMN1 confirmation. Together these would support cohort identification, outreach, and evidence generation without adding to clinician burden.

21.
bioRxiv (Bioinfo) 2026-06-19

Accurate detection of tumor clonality and ongoing expansion mode from genomic data

Recent evidence shows that despite considerable effort, currently available algorithms for estimating intra-tumor heterogeneity (ITH) remain limited. We developed DECODE (Deciphering Cancer Origin from DNA Evolution), a novel mutation clustering method that incorporates the impact of sample-specific sequencing coverage and mutation calling biases. On synthetic data, DECODE outperformed existing methods across multiple clonality metrics and accurately detected and characterized the neutral tail in the site frequency spectrum (SFS), which encodes the tumor's ongoing expansion mode. In acute myeloid leukemia, accounting for the neutral tail enabled DECODE to yield more parsimonious clonal decompositions that align more closely with known subclonal dynamics that drive relapse. Applied to data from The Cancer Genome Atlas, DECODE not only detected a neutral SFS tail in most samples across tumor types but also uncovered a clinically meaningful link between ITH and survival in low-grade glioma. By jointly inferring clonality and expansion mode, DECODE provides two complementary and prognostically relevant readouts of tumor evolution from single tumor genomic samples.

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

Discovering Lattice Reduction Strategies via Self-Play

arXiv:2606.15301v1 Announce Type: cross Abstract: The Lenstra-Lenstra-Lovász (LLL) algorithm is a seminal contribution to computer science used for lattice basis reduction, yet its polynomial-time outputs produce bases that are far from optimal as the dimension grows. We show that deep reinforcement learning can discover strictly superior, generalizable reduction strategies by interacting with the primitive action space of LLL. We formulate lattice reduction as a single-player Markov Decision Process (MDP) and train a deep residual network using an AlphaZero-style self-play pipeline augmented with adaptive-horizon MCTS (Monte Carlo Tree Search), which couples multi-step network predictions with an entropy-gated expansion mechanism. The resulting policy, DeltaStar, is trained exclusively on small $8$-dimensional $q$-ary lattices and requires fewer primitive row operations than LLL. Crucially, it generalizes zero-shot to unseen moduli and higher dimensions up to $n=32$ without retraining.

23.
arXiv (quant-ph) 2026-06-12

Interference of critical dynamics associated with zero modes

arXiv:2606.13200v1 Announce Type: new Abstract: We study the interference of critical dynamics associated with zero modes (ICDZM) in the generalized Creutz ladders using closed quench paths that pass through two critical points successively. By reading out the final zero-mode transfer probability, we find rich ICDZM interference patterns dependent on the quench path. In particular, when the closed path links two topologically nontrivial phases, the ICDZM pattern may either vanish or exhibit period doubling. Within the framework of WKB analysis, this phenomenon is well clarified by the interference phase accumulated in the quench procedure. We also demonstrate that the zero-mode transfer probability can be detected by the deviation of the boundary particle number from its initial fractional value, which arises from the blending of bulk modes in the critical dynamics. As an edge defect, the zero-mode transfer probability captures both the ICDZM oscillation and the known anomalous defect production in a non-closed quench path. These results identify ICDZM and the corresponding edge defect as probes for critical dynamics associated with topological zero modes.

24.
arXiv (CS.CL) 2026-06-15

Large Language Model Agents Are Not Always Faithful Self-Evolvers

Self-evolving large language model (LLM) agents continually improve by accumulating and reusing past experience, yet it remains unclear whether they faithfully rely on that experience to guide their behavior. We present the first systematic investigation of experience faithfulness, the causal dependence of an agent's decisions on the experience it is given, in self-evolving LLM agents. Using controlled causal interventions on both raw and condensed forms of experience, we comprehensively evaluate four representative frameworks across 13 LLM backbones and 9 environments. Our analysis uncovers a striking asymmetry: while agents consistently depend on raw experience, they often disregard or misinterpret condensed experience, even when it is the only experience provided. This gap persists across single- and multi-agent configurations and across backbone scales. We trace its underlying causes to three factors: the semantic limitations of condensed content, internal processing biases that suppress experience, and task regimes where pretrained priors already suffice. These findings challenge prevailing assumptions about self-evolving methods and underscore the need for more faithful and reliable approaches to experience integration.

25.
arXiv (CS.LG) 2026-06-18

Lifecycle-Aware Dynamic Analysis for Secure ML Model Execution

arXiv:2606.19023v1 Announce Type: cross Abstract: The growing reliance on pre-trained Machine Learning (ML) models has introduced new attack surfaces. Recent vulnerabilities demonstrate that malicious behavior can be embedded within model artifacts, often bypassing existing defenses. Current model-scanning solutions primarily rely on static, format-specific rules or known attack signatures, which limit their ability to generalize across frameworks and to detect novel exploitation paths. In contrast, we propose a solution that focuses on the effects an attack has on the host system executing the model and builds on foundational intuitions about ML model execution. In particular, we observe that ML models operate within well-defined lifecycle phases and that, within each phase, interactions with the host system are highly structured and predictable. We translate these intuitions into Moat, a dynamic lifecycle-aware approach for securing ML model execution, and instantiate this design in Re-Moat, our reference implementation. We evaluate Re-Moat across multiple ML frameworks using 77,974 real-world model artifacts from the Hugging Face Hub, 31 Proofs-of-Concept (PoCs) from CVEs, and 334 models from a state-of-the-art dataset, and compare it against state-of-the-art model-scanning solutions. Our results show that our approach detects all evaluated attack classes while maintaining a close-to-zero false-positive rate, validating our intuitions and motivating dynamic analysis for securing ML model execution.