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cs.AI, q-bio.NC updates on arXiv.org
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EchoDistill:Alignment Noisy-to-Clean Self-Distillation for Robust Audio LLMs
arXiv:2605.23954v1 Announce Type: cross Abstract: Audio Large Language Models (ALLMs) are highly vulnerable to real-world noise, which often induces severe semantic drift and hallucinations. Existing robustness methods primarily rely on waveform-level acoustic enhancement, answer-level supervision, or the internal suppression of noise representations. To address these issues, we propose echodistill, an alignment-based noisy-to-clean self-distillation framework. Echodistill leverages a frozen cl
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cs.AI, q-bio.NC updates on arXiv.org
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PathMem: Toward Cognition-Aligned Memory Transformation for Pathology MLLMs
arXiv:2603.09943v2 Announce Type: replace Abstract: Computational pathology demands both visual pattern recognition and dynamic integration of structured domain knowledge, including taxonomy, grading criteria, and clinical evidence. In practice, diagnostic reasoning requires linking morphological evidence with formal diagnostic and grading criteria. Although multimodal large language models (MLLMs) demonstrate strong vision language reasoning capabilities, they lack explicit mechanisms for stru
PathMem: Toward Cognition-Aligned Memory Transformation for Pathology MLLMs
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cs.AI, q-bio.NC updates on arXiv.org
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Krause Synchronization Transformers
arXiv:2602.11534v4 Announce Type: replace-cross Abstract: Self-attention in Transformers relies on globally normalized softmax weights, causing all tokens to compete for influence at every layer. When composed across depth, this interaction pattern induces strong synchronization dynamics that favor convergence toward a dominant mode, a behavior associated with representation collapse and attention sink phenomena. We introduce Krause Attention, a principled attention mechanism inspired by bounde
Krause Synchronization Transformers
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Omics in Hepatocellular
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Multi-omics integration identifies ribosome biogenesis-active macrophage subpopulation and its key gene GNL2 in driving liver hepatocellular carcinoma progression and mechanisms
Cancer Cell Int. 2026 May 14. doi: 10.1186/s12935-026-04330-2. Online ahead of print.ABSTRACTBACKGROUND: Liver hepatocellular carcinoma (LIHC) is a common malignancy, yet the core genes driving its progression and potential therapeutic targets remain insufficiently explored. Ribosome biogenesis (RB) is a critical biological process linked to various cancers; however, its systematic role in LIHC remains unclear.METHODS: This study integrated LIHC single-cell RNA-Seq, bulk RNA-Seq, and spatial tra
Multi-omics integration identifies ribosome biogenesis-active macrophage subpopulation and its key gene GNL2 in driving liver hepatocellular carcinoma progression and mechanisms
Cancer Cell Int. 2026 May 14. doi: 10.1186/s12935-026-04330-2. Online ahead of print.
ABSTRACT
BACKGROUND: Liver hepatocellular carcinoma (LIHC) is a common malignancy, yet the core genes driving its progression and potential therapeutic targets remain insufficiently explored. Ribosome biogenesis (RB) is a critical biological process linked to various cancers; however, its systematic role in LIHC remains unclear.
METHODS: This study integrated LIHC single-cell RNA-Seq, bulk RNA-Seq, and spatial transcriptomic data with ribosome biogenesis-related gene sets to construct a single-cell atlas of LIHC. Weighted Gene Co-expression Network Analysis (WGCNA) was employed to characterize myeloid cell subsets. Furthermore, an LIHC prognostic risk model based on RB-related genes was developed using 117 machine-learning algorithm combinations. Key findings were subsequently corroborated through experimental validation and clinical sample analysis.
RESULTS: We identified a distinct macrophage subpopulation with high ribosome biogenesis activity, termed ribosome biogenesis-active macrophages (RAMs). These cells exhibited strong communication with inflammatory macrophages, potentially mediated by MIF-related receptor-ligand interactions. We further constructed an 8-gene prognostic model (PA2G4, GNL2, PWP1, DDX49, NOC4L, GDI2, CST7, and RCL1), which showed good predictive performance. Drug sensitivity analysis suggested that the high-risk group may be more responsive to several agents, including docetaxel. Among these genes, GNL2 was selected for further investigation. Elevated GNL2 expression was associated with increased stemness features in myeloid cells. Molecular docking analysis identified several candidate compounds with potential binding affinity to GNL2. Functionally, GNL2 knockdown in macrophages reduced TGF-β and TNF-α expression and was associated with decreased proliferation, migration, and invasion of LIHC cells.
CONCLUSION: We identified a highly active ribosome biogenesis-macrophage subpopulation (RAM), and constructed a robust risk model to aid in the diagnosis, prognosis, and treatment of LIHC. GNL2 is associated with increased expression of TGF-β and TNF-α and may contribute to LIHC progression.
PMID:42135716 | DOI:10.1186/s12935-026-04330-2
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cs.AI, q-bio.NC updates on arXiv.org
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SecureVibeBench: Evaluating Secure Coding Capabilities of Code Agents with Realistic Vulnerability Scenarios
arXiv:2509.22097v2 Announce Type: replace-cross Abstract: Large language model-powered code agents are rapidly transforming software engineering, yet the security risks of their generated code have become a critical concern. Existing benchmarks have provided valuable insights, but they fail to capture scenarios in which vulnerabilities are actually introduced by human developers, making fair comparisons between humans and agents infeasible. We therefore introduce SecureVibeBench, a benchmark of
SecureVibeBench: Evaluating Secure Coding Capabilities of Code Agents with Realistic Vulnerability Scenarios
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cs.AI, q-bio.NC updates on arXiv.org
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MCP Security Bench (MSB): Benchmarking Attacks Against Model Context Protocol in LLM Agents
arXiv:2510.15994v2 Announce Type: replace-cross Abstract: The Model Context Protocol (MCP) standardizes how large language model (LLM) agents discover, describe, and call external tools. While MCP unlocks broad interoperability, it also enlarges the attack surface by making tools first-class, composable objects with natural-language metadata, and standardized I/O. We present MSB (MCP Security Benchmark), the first end-to-end evaluation suite that systematically measures how well LLM agents resi
MCP Security Bench (MSB): Benchmarking Attacks Against Model Context Protocol in LLM Agents
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Omics in Hepatocellular
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ESM1 drives cancer angiogenesis and bevacizumab resistance via trioleate synthesis
Neoplasia. 2026 May;75:101298. doi: 10.1016/j.neo.2026.101298. Epub 2026 Mar 20.ABSTRACTBACKGROUND: Hepatocellular carcinoma (HCC) exhibits high recurrence rates and limited therapeutic options. Endothelial cell-specific molecule 1 (ESM1) and angiopoietin-like 4 (ANGPTL4) are implicated in tumor progression, yet their synergistic role in HCC lipid metabolism and angiogenesis remains unexplored.METHODS: We integrated multi-omics approaches, including RNA sequencing, metabolomics, and immunoprecip
ESM1 drives cancer angiogenesis and bevacizumab resistance via trioleate synthesis
Neoplasia. 2026 May;75:101298. doi: 10.1016/j.neo.2026.101298. Epub 2026 Mar 20.
ABSTRACT
BACKGROUND: Hepatocellular carcinoma (HCC) exhibits high recurrence rates and limited therapeutic options. Endothelial cell-specific molecule 1 (ESM1) and angiopoietin-like 4 (ANGPTL4) are implicated in tumor progression, yet their synergistic role in HCC lipid metabolism and angiogenesis remains unexplored.
METHODS: We integrated multi-omics approaches, including RNA sequencing, metabolomics, and immunoprecipitation-mass spectrometry, in HCC cell lines and patient-derived xenograft models. Key experiments involved Co-IP, Western blotting, tube formation assays, and clinical tissue microarray analysis to validate the ESM1-ANGPTL4-FASN-trioleate axis.
RESULTS: ESM1 and ANGPTL4 formed a positive feedback loop, stabilizing fatty acid synthase (FASN) to promote trioleate synthesis. Trioleate activated the NF-κB/IL-17 pathway in HCC cells and upregulated CD99 in endothelial cells, driving angiogenesis. In vivo, ESM1/ANGPTL4 knockdown suppressed tumor growth, which was rescued by trioleate supplementation. Clinical data revealed elevated ESM1/ANGPTL4 expression in bevacizumab-resistant HCC, correlating with poor prognosis.
CONCLUSIONS: The ESM1-ANGPTL4-FASN-trioleate axis orchestrates metabolic reprogramming and endothelial activation, representing a promising therapeutic target. Future studies should explore combination therapies targeting this axis and overcoming bevacizumab resistance in HCC.
PMID:41864037 | PMC:PMC13019581 | DOI:10.1016/j.neo.2026.101298
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cs.AI, q-bio.NC updates on arXiv.org
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Diagnosing Retrieval Bias Under Multiple In-Context Knowledge Updates in Large Language Models
arXiv:2603.12271v1 Announce Type: cross Abstract: LLMs are widely used in knowledge-intensive tasks where the same fact may be revised multiple times within context. Unlike prior work focusing on one-shot updates or single conflicts, multi-update scenarios contain multiple historically valid versions that compete at retrieval, yet remain underexplored. This challenge resembles the AB-AC interference paradigm in cognitive psychology: when the same cue A is successively associated with B and C, t
Diagnosing Retrieval Bias Under Multiple In-Context Knowledge Updates in Large Language Models
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cs.AI, q-bio.NC updates on arXiv.org
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daVinci-Env: Open SWE Environment Synthesis at Scale
arXiv:2603.13023v1 Announce Type: cross Abstract: Training capable software engineering (SWE) agents demands large-scale, executable, and verifiable environments that provide dynamic feedback loops for iterative code editing, test execution, and solution refinement. However, existing open-source datasets remain limited in scale and repository diversity, while industrial solutions are opaque with unreleased infrastructure, creating a prohibitive barrier for most academic research groups. We pres
daVinci-Env: Open SWE Environment Synthesis at Scale
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cs.AI, q-bio.NC updates on arXiv.org
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Better Eyes, Better Thoughts: Why Vision Chain-of-Thought Fails in Medicine
arXiv:2603.06665v1 Announce Type: cross Abstract: Large vision-language models (VLMs) often benefit from chain-of-thought (CoT) prompting in general domains, yet its efficacy in medical vision-language tasks remains underexplored. We report a counter-intuitive trend: on medical visual question answering, CoT frequently underperforms direct answering (DirA) across general-purpose and medical-specific models. We attribute this to a \emph{medical perception bottleneck}: subtle, domain-specific cue
Better Eyes, Better Thoughts: Why Vision Chain-of-Thought Fails in Medicine
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cs.AI, q-bio.NC updates on arXiv.org
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Reallocating Attention Across Layers to Reduce Multimodal Hallucination
arXiv:2510.10285v3 Announce Type: replace Abstract: Multimodal large reasoning models (MLRMs) often suffer from hallucinations that stem not only from insufficient visual grounding but also from imbalanced allocation between perception and reasoning processes. Building upon recent interpretability findings suggesting a staged division of attention across layers, we analyze how this functional misalignment leads to two complementary failure modes: perceptual bias in shallow layers and reasoning
Reallocating Attention Across Layers to Reduce Multimodal Hallucination
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cs.AI, q-bio.NC updates on arXiv.org
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Chimera: Neuro-Symbolic Attention Primitives for Trustworthy Dataplane Intelligence
arXiv:2602.12851v2 Announce Type: replace-cross Abstract: Deploying expressive learning models directly on programmable dataplanes promises line-rate, low-latency traffic analysis but remains hindered by strict hardware constraints and the need for predictable, auditable behavior. Chimera introduces a principled framework that maps attention-oriented neural computations and symbolic constraints onto dataplane primitives, enabling trustworthy inference within the match-action pipeline. Chimera c
Chimera: Neuro-Symbolic Attention Primitives for Trustworthy Dataplane Intelligence
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cs.AI, q-bio.NC updates on arXiv.org
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CoFL: Continuous Flow Fields for Language-Conditioned Navigation
arXiv:2603.02854v1 Announce Type: cross Abstract: Language-conditioned navigation pipelines often rely on brittle modular components or costly action-sequence generation. To address these limitations, we present CoFL, an end-to-end policy that directly maps a bird's-eye view (BEV) observation and a language instruction to a continuous flow field for navigation. Instead of predicting discrete action tokens or sampling action chunks via iterative denoising, CoFL outputs instantaneous velocities t