Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Domain-constrained knowledge representation: A modal framework
arXiv:2604.01770v1 Announce Type: new Abstract: Knowledge graphs store large numbers of relations efficiently, but they remain weak at representing a quieter difficulty: the meaning of a concept often shifts with the domain in which it is used. A triple such as Apple, instance-of, Company may be acceptable in one setting while being misleading or unusable in another. In most current systems, domain information is attached as metadata, qualifiers, or graph-level organization. These mechanisms he
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cs.AI, q-bio.NC updates on arXiv.org
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GPA: Learning GUI Process Automation from Demonstrations
arXiv:2604.01676v1 Announce Type: cross Abstract: GUI Process Automation (GPA) is a lightweight but general vision-based Robotic Process Automation (RPA), which enables fast and stable process replay with only a single demo. Addressing the fragility of traditional RPA and the non-deterministic risks of current vision language model-based GUI agents, GPA introduces three core benefits: (1) Robustness via Sequential Monte Carlo-based localization to handle rescaling and detection uncertainty; (2)
GPA: Learning GUI Process Automation from Demonstrations
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cs.AI, q-bio.NC updates on arXiv.org
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LiveMathematicianBench: A Live Benchmark for Mathematician-Level Reasoning with Proof Sketches
arXiv:2604.01754v1 Announce Type: cross Abstract: Mathematical reasoning is a hallmark of human intelligence, and whether large language models (LLMs) can meaningfully perform it remains a central question in artificial intelligence and cognitive science. As LLMs are increasingly integrated into scientific workflows, rigorous evaluation of their mathematical capabilities becomes a practical necessity. Existing benchmarks are limited by synthetic settings and data contamination. We present LiveM
LiveMathematicianBench: A Live Benchmark for Mathematician-Level Reasoning with Proof Sketches
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cs.AI, q-bio.NC updates on arXiv.org
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HAFixAgent: History-Aware Program Repair Agent
arXiv:2511.01047v3 Announce Type: replace-cross Abstract: Automated program repair (APR) has recently shifted toward large language models and agent-based systems, yet most systems rely on local snapshot context, overlooking repository history. Prior work shows that repository history helps repair single-line bugs, since the last commit touching the buggy line is often the bug-introducing one. In this paper, we investigate whether repository history can also improve agentic APR systems at scale
HAFixAgent: History-Aware Program Repair Agent
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cs.AI, q-bio.NC updates on arXiv.org
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Think, Act, Build: An Agentic Framework with Vision Language Models for Zero-Shot 3D Visual Grounding
arXiv:2604.00528v2 Announce Type: replace-cross Abstract: 3D Visual Grounding (3D-VG) aims to localize objects in 3D scenes via natural language descriptions. While recent advancements leveraging Vision-Language Models (VLMs) have explored zero-shot possibilities, they typically suffer from a static workflow relying on preprocessed 3D point clouds, essentially degrading grounding into proposal matching. To bypass this reliance, our core motivation is to decouple the task: leveraging 2D VLMs to
Think, Act, Build: An Agentic Framework with Vision Language Models for Zero-Shot 3D Visual Grounding
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Nature Cancer
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PRET is a few-shot system for pan-cancer recognition without example training
Nature Cancer, Published online: 03 April 2026; doi:10.1038/s43018-026-01141-2Li et al. present PRET, a few-shot system for pan-cancer detection not requiring model fine-tuning, validated it in multicenter datasets and found that it outperformed existing approaches across tasks and pathologists in lymph node metastasis detection.
PRET is a few-shot system for pan-cancer recognition without example training
Nature Cancer, Published online: 03 April 2026; doi:10.1038/s43018-026-01141-2
Li et al. present PRET, a few-shot system for pan-cancer detection not requiring model fine-tuning, validated it in multicenter datasets and found that it outperformed existing approaches across tasks and pathologists in lymph node metastasis detection.-
Cell
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Functional RNA splitting drove the evolutionary emergence of type V CRISPR-Cas systems from transposons
(Cell 188, 6283–6300.e1–e10; October 30, 2025)
Functional RNA splitting drove the evolutionary emergence of type V CRISPR-Cas systems from transposons
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cs.AI, q-bio.NC updates on arXiv.org
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Tracking vs. Deciding: The Dual-Capability Bottleneck in Searchless Chess Transformers
arXiv:2603.29761v1 Announce Type: new Abstract: A human-like chess engine should mimic the style, errors, and consistency of a strong human player rather than maximize playing strength. We show that training from move sequences alone forces a model to learn two capabilities: state tracking, which reconstructs the board from move history, and decision quality, which selects good moves from that reconstructed state. These impose contradictory data requirements: low-rated games provide the diversi
Tracking vs. Deciding: The Dual-Capability Bottleneck in Searchless Chess Transformers
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cs.AI, q-bio.NC updates on arXiv.org
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IMPASTO: Integrating Model-Based Planning with Learned Dynamics Models for Robotic Oil Painting Reproduction
arXiv:2603.29315v1 Announce Type: cross Abstract: Robotic reproduction of oil paintings using soft brushes and pigments requires force-sensitive control of deformable tools, prediction of brushstroke effects, and multi-step stroke planning, often without human step-by-step demonstrations or faithful simulators. Given only a sequence of target oil painting images, can a robot infer and execute the stroke trajectories, forces, and colors needed to reproduce it? We present IMPASTO, a robotic oil-p
IMPASTO: Integrating Model-Based Planning with Learned Dynamics Models for Robotic Oil Painting Reproduction
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cs.AI, q-bio.NC updates on arXiv.org
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MacTok: Robust Continuous Tokenization for Image Generation
arXiv:2603.29634v1 Announce Type: cross Abstract: Continuous image tokenizers enable efficient visual generation, and those based on variational frameworks can learn smooth, structured latent representations through KL regularization. Yet this often leads to posterior collapse when using fewer tokens, where the encoder fails to encode informative features into the compressed latent space. To address this, we introduce \textbf{MacTok}, a \textbf{M}asked \textbf{A}ugmenting 1D \textbf{C}ontinuous
MacTok: Robust Continuous Tokenization for Image Generation
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cs.AI, q-bio.NC updates on arXiv.org
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Trace2Skill: Distill Trajectory-Local Lessons into Transferable Agent Skills
arXiv:2603.25158v3 Announce Type: replace Abstract: Equipping Large Language Model (LLM) agents with domain-specific skills is critical for tackling complex tasks. Yet, manual authoring creates a severe scalability bottleneck. Conversely, automated skill generation often yields fragile or fragmented results because it either relies on shallow parametric knowledge or sequentially overfits to non-generalizable trajectory-local lessons. To overcome this, we introduce Trace2Skill, a framework that
Trace2Skill: Distill Trajectory-Local Lessons into Transferable Agent Skills
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cs.AI, q-bio.NC updates on arXiv.org
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Incorporating LLM Embeddings for Variation Across the Human Genome
arXiv:2509.20702v2 Announce Type: replace-cross Abstract: Recent advances in large language model (LLM) embeddings have enabled powerful representations for biological data, but most applications to date focus on gene-level information. We present one of the first systematic frameworks to generate genetic variant-level embeddings across the entire human genome. Using curated annotations from FAVOR, ClinVar, and the GWAS Catalog, we construct functional text descriptions for 8.9 billion possible
Incorporating LLM Embeddings for Variation Across the Human Genome
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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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Heracles: Bridging Precise Tracking and Generative Synthesis for General Humanoid Control
arXiv:2603.27756v2 Announce Type: replace-cross Abstract: Achieving general-purpose humanoid control requires a delicate balance between the precise execution of commanded motions and the flexible, anthropomorphic adaptability needed to recover from unpredictable environmental perturbations. Current general controllers predominantly formulate motion control as a rigid reference-tracking problem. While effective in nominal conditions, these trackers often exhibit brittle, non-anthropomorphic fai
Heracles: Bridging Precise Tracking and Generative Synthesis for General Humanoid Control
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Oncogene - Issue - nature.com science feeds
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Targeting FTO shows therapeutic potential in esophageal squamous cell carcinoma by modulating microRNA biogenesis
Oncogene, Published online: 01 April 2026; doi:10.1038/s41388-026-03754-4Targeting FTO shows therapeutic potential in esophageal squamous cell carcinoma by modulating microRNA biogenesis
Targeting FTO shows therapeutic potential in esophageal squamous cell carcinoma by modulating microRNA biogenesis
Oncogene, Published online: 01 April 2026; doi:10.1038/s41388-026-03754-4
Targeting FTO shows therapeutic potential in esophageal squamous cell carcinoma by modulating microRNA biogenesis-
Cell Death Discovery nature.com science feeds
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Doxorubicin promotes the production of inflammatory cytokines in tumor-associated macrophages through activating lactate dehydrogenase A
Cell Death Discovery, Published online: 31 March 2026; doi:10.1038/s41420-026-03014-0Doxorubicin promotes the production of inflammatory cytokines in tumor-associated macrophages through activating lactate dehydrogenase A
Doxorubicin promotes the production of inflammatory cytokines in tumor-associated macrophages through activating lactate dehydrogenase A
Cell Death Discovery, Published online: 31 March 2026; doi:10.1038/s41420-026-03014-0
Doxorubicin promotes the production of inflammatory cytokines in tumor-associated macrophages through activating lactate dehydrogenase A-
Omics in Gastric
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Multi-omics analysis reveals AR as a potential prognostic factor and immune-related therapeutic target in gastric cancer
Biochem Biophys Rep. 2026 Mar 16;46:102537. doi: 10.1016/j.bbrep.2026.102537. eCollection 2026 Jun.ABSTRACTBACKGROUND: Although studies have shown that the androgen receptor (AR) is associated with tumor progression and malignant regulation, its role in the tumor immune microenvironment and predictive value for prognosis and immunotherapy response in various cancer types have not been systematically analyzed.METHODS: In this paper, multi-omics techniques was used to analyze AR comprehensively.RE
Multi-omics analysis reveals AR as a potential prognostic factor and immune-related therapeutic target in gastric cancer
Biochem Biophys Rep. 2026 Mar 16;46:102537. doi: 10.1016/j.bbrep.2026.102537. eCollection 2026 Jun.
ABSTRACT
BACKGROUND: Although studies have shown that the androgen receptor (AR) is associated with tumor progression and malignant regulation, its role in the tumor immune microenvironment and predictive value for prognosis and immunotherapy response in various cancer types have not been systematically analyzed.
METHODS: In this paper, multi-omics techniques was used to analyze AR comprehensively.
RESULTS: A comprehensive pan-cancer analysis revealed that the AR was expressed in a variety of tumors, especially as a risk factor for poor prognosis in gastric cancer. In addition, gene set enrichment analysis showed that the AR promotes cell proliferation and tumor cell invasion and regulates anti-tumor response. Immune score, immune cell infiltration, and anticancer immune cycle analysis showed that high AR levels were correlated with low infiltration of CD4+ T cells and NKT cells, high infiltration of Th2 cells and MDSCs, negatively correlated with antigen-presenting molecules, and positively correlated with various immune-negative regulatory molecules. Single-cell sequencing highlighted the heterogeneous expression of ARs in different cell types, particularly in epithelial cells, where high AR levels were associated with the enhanced activity of tumor-promoting pathways.
CONCLUSIONS: In conclusion, this study highlights the potential of the AR as a novel biomarker for gastric cancer prognosis and immunotherapy efficacy, expanding its applicability in the development of new antitumor drugs.
PMID:41890218 | PMC:PMC13014673 | DOI:10.1016/j.bbrep.2026.102537
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Omics in Hepatocellular
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SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data
Biology (Basel). 2026 Mar 19;15(6):492. doi: 10.3390/biology15060492.ABSTRACTBACKGROUND: Tumor neoantigens are key targets for personalized vaccines and T-cell therapies, yet most pipelines focus on neoantigens derived from SNV/small indel and often yield a limited number of high-quality candidates. SVs are prevalent in tumors and can generate novel chimeric sequences and neopeptides, making them a promising additional source of neoantigens. However, SV-derived neoantigen prediction remains chal
SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data
Biology (Basel). 2026 Mar 19;15(6):492. doi: 10.3390/biology15060492.
ABSTRACT
BACKGROUND: Tumor neoantigens are key targets for personalized vaccines and T-cell therapies, yet most pipelines focus on neoantigens derived from SNV/small indel and often yield a limited number of high-quality candidates. SVs are prevalent in tumors and can generate novel chimeric sequences and neopeptides, making them a promising additional source of neoantigens. However, SV-derived neoantigen prediction remains challenging due to breakpoint uncertainty, isoform-dependent coding inference, and limited integration of multi-dimensional evidence and reproducibility.
METHODS: We developed SVNeoPP (Structural Variant Neoantigen Prediction and Prioritization), an end-to-end workflow for SV-derived neoantigen analysis. SVNeoPP takes WGS and RNA-seq as inputs, performs SV calling and annotation, and reconstructs altered transcripts and coding sequences in a traceable, isoform-aware manner to generate candidate peptides. Candidates are prescreened by integrating antigen-processing features with HLA binding prediction, and then hierarchically filtered and prioritized based on transcript expression, LC-MS/MS proteomics evidence, immunogenicity predictions, and sequence similarity to experimentally validated neoantigen databases. SVNeoPP is implemented in Snakemake to enable modular extension, checkpoint-based restarts, and end-to-end reproducibility.
RESULTS: Using a hepatocellular carcinoma (HCC) multi-omics dataset as a proof of concept, we demonstrated the performance of SVNeoPP and obtained a high-priority shortlist of candidate peptides. Compared with other methods, SVNeoPP substantially expanded the candidate search space for SV-derived neoantigens and showed more favorable distributions of antigen-processing and HLA binding features.
CONCLUSIONS: SVNeoPP provides a reusable, traceable, and interpretable multi-dimensional evidence-driven framework for SV-derived neoantigens. As a complementary module to SNV/small-indel pipelines, it broadens the neoantigen candidate repertoire and generates ranked candidates with interpretable evidence to facilitate downstream prioritization and decision-making.
PMID:41892252 | PMC:PMC13024079 | DOI:10.3390/biology15060492
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Journal of Medical Internet Research
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Suicidal Thoughts and Behaviors Among Chinese Adolescents in Relation to Negative Life Events, Internet Addiction, and Sexual Abuse: Cross-Sectional Study
Background: Increasing suicidal thoughts and behaviors (STB) among adolescents raise social concerns and have a well-recognized association with sexual abuse (SA). However, research regarding the mechanisms explaining the association between SA and STB remains limited. Objective: This study aims to examine the chained mediating effects of negative life events (NLE) and internet addiction (IA) between SA and STB among adolescents in China. Methods: This cross-sectional study used data from the Sc
Suicidal Thoughts and Behaviors Among Chinese Adolescents in Relation to Negative Life Events, Internet Addiction, and Sexual Abuse: Cross-Sectional Study
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cs.AI, q-bio.NC updates on arXiv.org
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UniFluids: Unified Neural Operator Learning with Conditional Flow-matching
arXiv:2603.22309v1 Announce Type: cross Abstract: Partial differential equation (PDE) simulation holds extensive significance in scientific research. Currently, the integration of deep neural networks to learn solution operators of PDEs has introduced great potential. In this paper, we present UniFluids, a conditional flow-matching framework that harnesses the scalability of diffusion Transformer to unify learning of solution operators across diverse PDEs with varying dimensionality and physica