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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 mirrors how human experts author skills: by holistically analyzing broad execution experience before distilling it into a single, comprehensive guide. Instead of reacting sequentially to individual trajectories, Trace2Skill dispatches a parallel fleet of sub-agents to analyze a diverse pool of executions. It extracts trajectory-specific lessons and hierarchically consolidates them into a unified, conflict-free skill directory via inductive reasoning. Trace2Skill supports both deepening existing human-written skills and creating new ones from scratch. Experiments in challenging domains, such as spreadsheet, VisionQA and math reasoning, show that Trace2Skill significantly improves upon strong baselines, including Anthropic's official xlsx skills. Crucially, this trajectory-grounded evolution does not merely memorize task instances or model-specific quirks: evolved skills transfer across LLM scales and generalize to OOD settings. For example, skills evolved by Qwen3.5-35B on its own trajectories improved a Qwen3.5-122B agent by up to 57.65 absolute percentage points on WikiTableQuestions. Ultimately, our results demonstrate that complex agent experience can be packaged into highly transferable, declarative skills -- requiring no parameter updates, no external retrieval modules, and utilizing open-source models as small as 35B parameters.
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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/s41420-026-03014-0

Doxorubicin promotes the production of inflammatory cytokines in tumor-associated macrophages through activating lactate dehydrogenase A
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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.

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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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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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 Science Database of the People Mental Health survey conducted between March 2013 and December 2022 by the National Population Health Data Center of the National Research Institute for Family Planning. Through stratified sampling, 20,893 adolescents were recruited from 16 Chinese provinces. After excluding samples with missing relevant variables, 10,664 (55.89%; aged 16-17.9 y; n=5826, 54.63% women) adolescents were included in the final analysis. STB was the outcome variable, with NLE and IA as mediators, all assessed via a questionnaire that was uniformly administered by trained investigators in school settings. The Pearson χ test was used to analyze the association between SA and STB. Using a combination of multiple linear regression and bootstrap testing, the study constructed a chain mediation model to explore how SA influences STB in adolescents through NLE and IA. Results: The scores for SA, NLE, IA, and STB were 1.330 (SD 1.714), 51.960 (SD 23.822), 34.88 (SD 13.852), and 0.690 (SD 1.396), respectively. Multiple linear regression analysis indicated SA was associated with NLE (β=2.382, 95% CI 2.112‐2.653;
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Spatial Omics in Gastrointestinal Oncology: Recent Advances, Therapeutic Insights, and Clinical Translation

J Cancer. 2026 Jan 30;17(3):515-523. doi: 10.7150/jca.127381. eCollection 2026.

ABSTRACT

Gastrointestinal (GI) cancers remain a leading cause of cancer-related morbidity and mortality worldwide, largely due to their molecular heterogeneity, complex tumor microenvironment (TME), and variable treatment responses. In recent years, the emergence of spatially resolved omics technologies-encompassing spatial transcriptomics, proteomics, metabolomics, and epigenomics-has revolutionized the ability to interrogate tumor architecture with unprecedented resolution. These methods enable precise mapping of cellular and molecular interactions within intact tissue contexts, thereby uncovering spatially defined niches that influence tumor progression, immune evasion, and therapeutic resistance. In GI malignancies such as colorectal, gastric, and esophageal cancers, spatial omics have provided critical insights into cancer-stromal-immune crosstalk, identified predictive biomarkers for immunotherapy and targeted agents, and guided the development of novel therapeutic strategies. This review synthesizes the latest advances in spatial omics applied to GI oncology over the past five years, with an emphasis on their integration into early diagnosis, treatment stratification, and real-time monitoring of therapeutic efficacy. We also discuss current challenges, including standardization, data integration, and clinical validation, as well as future directions for incorporating spatial profiling into routine oncology practice. By bridging the gap between bench discoveries and bedside applications, spatial omics hold transformative potential for achieving truly personalized treatment in gastrointestinal cancers.

PMID:41869445 | PMC:PMC13003551 | DOI:10.7150/jca.127381

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Assembly of helper NLR resistosome clusters upon activation of a coiled-coil NLR

Nature, Published online: 11 March 2026; doi:10.1038/s41586-026-10215-1

SUMM2, a coiled-coil NLR, promotes the assembly of higher-order resistosome clusters to initiate cell death in plants.
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Task learning increases information redundancy of neural responses in macaque visual cortex

arXiv:2603.07369v1 Announce Type: new Abstract: How does the brain optimize sensory information for decision-making in new tasks? One hypothesis suggests learning reduces redundancy in neural representations to improve efficiency, while another, based on Bayesian inference, predicts learning increases redundancy by distributing information across neurons. We tested these hypotheses by tracking population responses in macaque cortical area V4 as monkeys learned visual discrimination tasks. We found strong support for the Bayesian predictions: task learning increased redundancy in neural responses over weeks of training and within single trials. This redundancy did not reduce information but instead increased the information carried by individual neurons. These insights suggest sensory processing in the brain reflects a generative rather than discriminative inference process.
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Merlin: A Computed Tomography Vision-Language Foundation Model and Dataset

arXiv:2406.06512v2 Announce Type: replace-cross Abstract: The large volume of abdominal computed tomography (CT) scans coupled with the shortage of radiologists have intensified the need for automated medical image analysis tools. Previous state-of-the-art approaches for automated analysis leverage vision-language models (VLMs) that jointly model images and radiology reports. However, current medical VLMs are generally limited to 2D images and short reports. Here to overcome these shortcomings for abdominal CT interpretation, we introduce Merlin, a 3D VLM that learns from volumetric CT scans, electronic health record data and radiology reports. This approach is enabled by a multistage pretraining framework that does not require additional manual annotations. We trained Merlin using a high-quality clinical dataset of paired CT scans (>6 million images from 15,331 CT scans), diagnosis codes (>1.8 million codes) and radiology reports (>6 million tokens). We comprehensively evaluated Merlin on 6 task types and 752 individual tasks that covered diagnostic, prognostic and quality-related tasks. The non-adapted (off-the-shelf) tasks included zero-shot classification of findings (30 findings), phenotype classification (692 phenotypes) and zero-shot cross-modal retrieval (image-to-findings and image-to-impression). The model-adapted tasks included 5-year chronic disease prediction (6 diseases), radiology report generation and 3D semantic segmentation (20 organs). We validated Merlin at scale, with internal testing on 5,137 CT scans and external testing on 44,098 CT scans from 3 independent sites and 2 public datasets. The results demonstrated high generalization across institutions and anatomies. Merlin outperformed 2D VLMs, CT foundation models and off-the-shelf radiology models. We also release our trained models, code, and dataset, available at: https://github.com/StanfordMIMI/Merlin.
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Towards Personalized Deep Research: Benchmarks and Evaluations

arXiv:2509.25106v3 Announce Type: replace-cross Abstract: Deep Research Agents (DRAs) can autonomously conduct complex investigations and generate comprehensive reports, demonstrating strong real-world potential. However, existing evaluations mostly rely on close-ended benchmarks, while open-ended deep research benchmarks remain scarce and typically neglect personalized scenarios. To bridge this gap, we introduce Personalized Deep Research Bench (PDR-Bench), the first benchmark for evaluating personalization in DRAs. It pairs 50 diverse research tasks across 10 domains with 25 authentic user profiles that combine structured persona attributes with dynamic real-world contexts, yielding 250 realistic user-task queries. To assess system performance, we propose the PQR Evaluation Framework, which jointly measures Personalization Alignment, Content Quality, and Factual Reliability. Our experiments on a range of systems highlight current capabilities and limitations in handling personalized deep research. This work establishes a rigorous foundation for developing and evaluating the next generation of truly personalized AI research assistants.
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Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles

arXiv:2603.02406v1 Announce Type: cross Abstract: Generative models have recently advanced $\textit{de novo}$ protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce $\textbf{RigidSSL}$ ($\textit{Rigidity-Aware Self-Supervised Learning}$), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43\% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8\% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling. The code is available at: https://github.com/ZhanghanNi/RigidSSL.git.
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Skywork-Reward-V2: Scaling Preference Data Curation via Human-AI Synergy

arXiv:2507.01352v3 Announce Type: replace-cross Abstract: Despite the critical role of reward models (RMs) in Reinforcement Learning from Human Feedback (RLHF), current state-of-the-art open RMs perform poorly on most existing evaluation benchmarks, failing to capture nuanced human preferences. We hypothesize that this brittleness stems primarily from limitations in preference datasets, which are often narrowly scoped, synthetically labeled, or lack rigorous quality control. To address these challenges, we present SynPref-40M, a large-scale preference dataset comprising 40 million preference pairs. To enable data curation at scale, we design a human-AI synergistic two-stage pipeline that leverages the complementary strengths of human annotation quality and AI scalability. In this pipeline, humans provide verified annotations, while LLMs perform automatic curation based on human guidance. Training on this preference mixture, we introduce Skywork-Reward-V2, a suite of eight reward models ranging from 0.6B to 8B parameters, trained on a carefully curated subset of 26 million preference pairs from SynPref-40M. We demonstrate that Skywork-Reward-V2 is versatile across a wide range of capabilities, including alignment with human preferences, objective correctness, safety, resistance to stylistic biases, and best-of-N scaling. These reward models achieve state-of-the-art performance across seven major reward model benchmarks, outperform generative reward models, and demonstrate strong downstream performance. Ablation studies confirm that effectiveness stems not only from data scale but also from high-quality curation. The Skywork-Reward-V2 series represents substantial progress in open reward models, demonstrating how human-AI curation synergy can unlock significantly higher data quality.
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ScaleDoc: Scaling LLM-based Predicates over Large Document Collections

arXiv:2509.12610v2 Announce Type: replace-cross Abstract: Predicates are foundational components in data analysis systems. However, modern workloads increasingly involve unstructured documents, which demands semantic understanding, beyond traditional value-based predicates. Given enormous documents and ad-hoc queries, while Large Language Models (LLMs) demonstrate powerful zero-shot capabilities, their high inference cost leads to unacceptable overhead. Therefore, we introduce \textsc{ScaleDoc}, a novel system that addresses this by decoupling predicate execution into an offline representation phase and an optimized online filtering phase. In the offline phase, \textsc{ScaleDoc} leverages a LLM to generate semantic representations for each document. Online, for each query, it trains a lightweight proxy model on these representations to filter the majority of documents, forwarding only the ambiguous cases to the LLM for final decision. Furthermore, \textsc{ScaleDoc} proposes two core innovations to achieve significant efficiency: (1) a contrastive-learning-based framework that trains the proxy model to generate reliable predicating decision scores; (2) an adaptive cascade mechanism that determines the effective filtering policy while meeting specific accuracy targets. Our evaluations across three datasets demonstrate that \textsc{ScaleDoc} achieves over a 2$\times$ end-to-end speedup and reduces expensive LLM invocations by up to 85\%, making large-scale semantic analysis practical and efficient.
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AgentCAT: An LLM Agent for Extracting and Analyzing Catalytic Reaction Data from Chemical Engineering Literature

arXiv:2602.18479v1 Announce Type: cross Abstract: This paper presents a large language model (LLM) agent named AgentCAT, which extracts and analyzes catalytic reaction data from chemical engineering papers, %and supports natural language based interactive analysis of the extracted data. AgentCAT serves as an alternative to overcome the long-standing data bottleneck in chemical engineering field, and its natural language based interactive data analysis functionality is friendly to the community. AgentCAT also presents a formal abstraction and challenge analysis of the catalytic reaction data extraction task in an artificial intelligence-friendly manner. This abstraction would help the artificial intelligence community understand this problem and in turn would attract more attention to address it. Technically, the complex catalytic process leads to complicated dependency structure in catalytic reaction data with respect to elementary reaction steps, molecular behaviors, measurement evidence, etc. This dependency structure makes it challenging to guarantee the correctness and completeness of data extraction, as well as representing them for analysis. AgentCAT addresses this challenge and it makes four folds of technical contributions: (1) a schema-governed extraction pipeline with progressive schema evolution, enabling robust data extraction from chemical engineering papers; (2) a dependency-aware reaction-network knowledge graph that links catalysts/active sites, synthesis-derived descriptors, mechanistic claims with evidence, and macroscopic outcomes, preserving process coupling and traceability; (3) a general querying module that supports natural-language exploration and visualization over the constructed graph for cross-paper analysis; (4) an evaluation on $\sim$800 peer-reviewed chemical engineering publications demonstrating the effectiveness of AgentCAT.
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EIDOS: Latent-Space Predictive Learning for Time Series Foundation Models

arXiv:2602.14024v1 Announce Type: cross Abstract: Most time series foundation models are pretrained by directly predicting future observations, which often yields weakly structured latent representations that capture surface noise rather than coherent and predictable temporal dynamics. In this work, we introduce EIDOS, a foundation model family that shifts pretraining from future value prediction to latent-space predictive learning. We train a causal Transformer to predict the evolution of latent representations, encouraging the emergence of structured and temporally coherent latent states. To ensure stable targets for latent-space learning, we design a lightweight aggregation branch to construct target representations. EIDOS is optimized via a joint objective that integrates latent-space alignment, observational grounding to anchor representations to the input signal, and direct forecasting supervision. On the GIFT-Eval benchmark, EIDOS mitigates structural fragmentation in the representation space and achieves state-of-the-art performance. These results demonstrate that constraining models to learn predictable latent dynamics is a principled step toward more robust and reliable time series foundation models.
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OmniVideoBench: Towards Audio-Visual Understanding Evaluation for Omni MLLMs

arXiv:2510.10689v2 Announce Type: replace Abstract: Recent advances in multimodal large language models (MLLMs) have demonstrated substantial potential in video understanding. However, existing benchmarks fail to comprehensively evaluate synergistic reasoning capabilities across audio and visual modalities, often neglecting either one of the modalities or integrating them in a logically inconsistent manner. To bridge this gap, we introduce OmniVideoBench, a large-scale and rigorously designed benchmark dedicated to assessing synergistic audio-visual understanding, with a strong emphasis on modality complementarity and logical consistency. Specifically, OmniVideoBench comprises 1000 high-quality question-answer(QA) pairs, each annotated with step-by-step reasoning traces, derived from 628 diverse videos ranging from several seconds to 30 minutes, and manually verified to guarantee complete correctness and uniqueness. Moreover, OmniVideoBench encompasses 13 carefully designed question types, covering temporal reasoning, spatial localization, counting, causal inference, summarization, and beyond, thereby capturing the essential challenges of video understanding. Evaluation of multiple MLLMs on OmniVideoBench reveals a pronounced gap between model performance and human reasoning, with open-source models lagging significantly behind their closed-source counterparts, underscoring the inherent difficulty of genuine audio-visual reasoning. We will release OmniVideoBench to foster the development of MLLMs with stronger and more generalizable reasoning capabilities.
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Vision-Based Early Fault Diagnosis and Self-Recovery for Strawberry Harvesting Robots

arXiv:2601.02085v2 Announce Type: replace-cross Abstract: Strawberry harvesting robots faced persistent challenges such as low integration of visual perception, fruit-gripper misalignment, empty grasping/misgrasp, and strawberry slippage from the gripper due to insufficient gripping force, all of which compromised harvesting stability and efficiency in orchard environments. To overcome these issues, this paper proposed a visual fault diagnosis and self-recovery framework that integrated multi-task perception with corrective control strategies. At the core of this framework was SRR-Net, an end-to-end multi-task perception model that simultaneously performed strawberry detection, segmentation, and ripeness estimation, thereby unifying visual perception with fault diagnosis.Based on this integrated perception, a relative error compensation method based on the simultaneous target-gripper detection was designed to address positional misalignment, correcting deviations when error exceeded the tolerance threshold.To mitigate empty grasping/misgrasp and fruit-slippage faults, an early abort strategy was implemented. A micro-optical camera embedded in the end-effector provided real-time visual feedback, enabling grasp classification during the deflating stage and strawberry slip prediction during snap-off through MobileNet V3-Small classifier and a time-series LSTM classifier. Experiments demonstrated that SRR-Net maintained high perception accuracy. For detection, it achieved a precision of 0.895 and recall of 0.813 on strawberries, and 0.972/0.958 on hands. In segmentation, it yielded a precision of 0.887 and recall of 0.747 for strawberries, and 0.974/0.947 for hands. For ripeness estimation, SRR-Net attained a mean absolute error of 0.035, while simultaneously supporting multi-task perception and sustaining a competitive inference speed of 163.35 FPS.
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