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BLM$_1$: A Boundless Large Model for Cross-Space, Cross-Task, and Cross-Embodiment Learning

arXiv:2510.24161v1 Announce Type: new Abstract: Multimodal large language models (MLLMs) have advanced vision-language reasoning and are increasingly deployed in embodied agents. However, significant limitations remain: MLLMs generalize poorly across digital-physical spaces and embodiments; vision-language-action models (VLAs) produce low-level actions yet lack robust high-level embodied reasoning; and most embodied large language models (ELLMs) are constrained to digital-space with poor generalization to the physical world. Thus, unified models that operate seamlessly across digital and physical spaces while generalizing across embodiments and tasks remain absent. We introduce the \textbf{Boundless Large Model (BLM$_1$)}, a multimodal spatial foundation model that preserves instruction following and reasoning, incorporates embodied knowledge, and supports robust cross-embodiment control. BLM$_1$ integrates three key capabilities -- \textit{cross-space transfer, cross-task learning, and cross-embodiment generalization} -- via a two-stage training paradigm. Stage I injects embodied knowledge into the MLLM through curated digital corpora while maintaining language competence. Stage II trains a policy module through an intent-bridging interface that extracts high-level semantics from the MLLM to guide control, without fine-tuning the MLLM backbone. This process is supported by a self-collected cross-embodiment demonstration suite spanning four robot embodiments and six progressively challenging tasks. Evaluations across digital and physical benchmarks show that a single BLM$_1$ instance outperforms four model families -- MLLMs, ELLMs, VLAs, and GMLMs -- achieving $\sim\!\textbf{6%}$ gains in digital tasks and $\sim\!\textbf{3%}$ in physical tasks.
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From Cross-Task Examples to In-Task Prompts: A Graph-Based Pseudo-Labeling Framework for In-context Learning

arXiv:2510.24528v1 Announce Type: new Abstract: The capability of in-context learning (ICL) enables large language models (LLMs) to perform novel tasks without parameter updates by conditioning on a few input-output examples. However, collecting high-quality examples for new or challenging tasks can be costly and labor-intensive. In this work, we propose a cost-efficient two-stage pipeline that reduces reliance on LLMs for data labeling. Our approach first leverages readily available cross-task examples to prompt an LLM and pseudo-label a small set of target task instances. We then introduce a graph-based label propagation method that spreads label information to the remaining target examples without additional LLM queries. The resulting fully pseudo-labeled dataset is used to construct in-task demonstrations for ICL. This pipeline combines the flexibility of cross-task supervision with the scalability of LLM-free propagation. Experiments across five tasks demonstrate that our method achieves strong performance while lowering labeling costs.
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Generative AI for Healthcare: Fundamentals, Challenges, and Perspectives

arXiv:2510.24551v1 Announce Type: new Abstract: Generative Artificial Intelligence (GenAI) is taking the world by storm. It promises transformative opportunities for advancing and disrupting existing practices, including healthcare. From large language models (LLMs) for clinical note synthesis and conversational assistance to multimodal systems that integrate medical imaging, electronic health records, and genomic data for decision support, GenAI is transforming the practice of medicine and the delivery of healthcare, such as diagnosis and personalized treatments, with great potential in reducing the cognitive burden on clinicians, thereby improving overall healthcare delivery. However, GenAI deployment in healthcare requires an in-depth understanding of healthcare tasks and what can and cannot be achieved. In this paper, we propose a data-centric paradigm in the design and deployment of GenAI systems for healthcare. Specifically, we reposition the data life cycle by making the medical data ecosystem as the foundational substrate for generative healthcare systems. This ecosystem is designed to sustainably support the integration, representation, and retrieval of diverse medical data and knowledge. With effective and efficient data processing pipelines, such as semantic vector search and contextual querying, it enables GenAI-powered operations for upstream model components and downstream clinical applications. Ultimately, it not only supplies foundation models with high-quality, multimodal data for large-scale pretraining and domain-specific fine-tuning, but also serves as a knowledge retrieval backend to support task-specific inference via the agentic layer. The ecosystem enables the deployment of GenAI for high-quality and effective healthcare delivery.
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Genotype-Phenotype Integration through Machine Learning and Personalized Gene Regulatory Networks for Cancer Metastasis Prediction

arXiv:2510.23620v1 Announce Type: cross Abstract: Metastasis is the leading cause of cancer-related mortality, yet most predictive models rely on shallow architectures and neglect patient-specific regulatory mechanisms. Here, we integrate classical machine learning and deep learning to predict metastatic potential across multiple cancer types. Gene expression profiles from the Cancer Cell Line Encyclopedia were combined with a transcription factor-target prior from DoRothEA, focusing on nine metastasis-associated regulators. After selecting differential genes using the Kruskal-Wallis test, ElasticNet, Random Forest, and XGBoost models were trained for benchmarking. Personalized gene regulatory networks were then constructed using PANDA and LIONESS and analyzed through a graph attention neural network (GATv2) to learn topological and expression-based representations. While XGBoost achieved the highest AUROC (0.7051), the GNN captured non-linear regulatory dependencies at the patient level. These results demonstrate that combining traditional machine learning with graph-based deep learning enables a scalable and interpretable framework for metastasis risk prediction in precision oncology.
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Integrating Genomics into Multimodal EHR Foundation Models

arXiv:2510.23639v1 Announce Type: cross Abstract: This paper introduces an innovative Electronic Health Record (EHR) foundation model that integrates Polygenic Risk Scores (PRS) as a foundational data modality, moving beyond traditional EHR-only approaches to build more holistic health profiles. Leveraging the extensive and diverse data from the All of Us (AoU) Research Program, this multimodal framework aims to learn complex relationships between clinical data and genetic predispositions. The methodology extends advancements in generative AI to the EHR foundation model space, enhancing predictive capabilities and interpretability. Evaluation on AoU data demonstrates the model's predictive value for the onset of various conditions, particularly Type 2 Diabetes (T2D), and illustrates the interplay between PRS and EHR data. The work also explores transfer learning for custom classification tasks, showcasing the architecture's versatility and efficiency. This approach is pivotal for unlocking new insights into disease prediction, proactive health management, risk stratification, and personalized treatment strategies, laying the groundwork for more personalized, equitable, and actionable real-world evidence generation in healthcare.
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Quanvolutional Neural Networks for Pneumonia Detection: An Efficient Quantum-Assisted Feature Extraction Paradigm

arXiv:2510.23660v1 Announce Type: cross Abstract: Pneumonia poses a significant global health challenge, demanding accurate and timely diagnosis. While deep learning, particularly Convolutional Neural Networks (CNNs), has shown promise in medical image analysis for pneumonia detection, CNNs often suffer from high computational costs, limitations in feature representation, and challenges in generalizing from smaller datasets. To address these limitations, we explore the application of Quanvolutional Neural Networks (QNNs), leveraging quantum computing for enhanced feature extraction. This paper introduces a novel hybrid quantum-classical model for pneumonia detection using the PneumoniaMNIST dataset. Our approach utilizes a quanvolutional layer with a parameterized quantum circuit (PQC) to process 2x2 image patches, employing rotational Y-gates for data encoding and entangling layers to generate non-classical feature representations. These quantum-extracted features are then fed into a classical neural network for classification. Experimental results demonstrate that the proposed QNN achieves a higher validation accuracy of 83.33 percent compared to a comparable classical CNN which achieves 73.33 percent. This enhanced convergence and sample efficiency highlight the potential of QNNs for medical image analysis, particularly in scenarios with limited labeled data. This research lays the foundation for integrating quantum computing into deep-learning-driven medical diagnostic systems, offering a computationally efficient alternative to traditional approaches.
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Closing Gaps: An Imputation Analysis of ICU Vital Signs

arXiv:2510.24217v1 Announce Type: cross Abstract: As more Intensive Care Unit (ICU) data becomes available, the interest in developing clinical prediction models to improve healthcare protocols increases. However, the lack of data quality still hinders clinical prediction using Machine Learning (ML). Many vital sign measurements, such as heart rate, contain sizeable missing segments, leaving gaps in the data that could negatively impact prediction performance. Previous works have introduced numerous time-series imputation techniques. Nevertheless, more comprehensive work is needed to compare a representative set of methods for imputing ICU vital signs and determine the best practice. In reality, ad-hoc imputation techniques that could decrease prediction accuracy, like zero imputation, are still used. In this work, we compare established imputation techniques to guide researchers in improving the performance of clinical prediction models by selecting the most accurate imputation technique. We introduce an extensible and reusable benchmark with currently 15 imputation and 4 amputation methods, created for benchmarking on major ICU datasets. We hope to provide a comparative basis and facilitate further ML development to bring more models into clinical practice.
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Dynamic Monitoring of Recurrent Ovarian Cancer Using Serial ctDNA: A Real-World Case Series

Curr Oncol. 2025 Oct 21;32(10):585. doi: 10.3390/curroncol32100585.

ABSTRACT

Recurrent ovarian cancer (OC) is challenging to detect early using current methods like CA-125 and imaging. Circulating tumor DNA (ctDNA) may improve disease monitoring. Here, we assess the real-world clinical utility of serial ctDNA analyses in patients with recurrent OC. We analyzed serial plasma samples (N = 23) from six patients with recurrent OC using a tumor-informed next-generation sequencing assay targeting 68 cancer-related genes developed at the University of Washington. ctDNA variant allele frequencies (VAFs) were correlated with CA-125 levels, radiographic findings, and clinical outcomes. ctDNA levels generally reflected clinical status, accurately mirroring disease progression and therapeutic response. In one patient, rising ctDNA preceded clinical recurrence by four months, despite normal CA-125 and imaging, highlighting its potential advantage. Conversely, some patients exhibited clinical progression with undetectable ctDNA, indicating limitations in assay sensitivity, biological factors, or metastatic sites (e.g., brain metastases). ctDNA and CA-125 showed complementary value in most cases, suggesting potential combined use in clinical monitoring. Our findings demonstrate that ctDNA is a promising biomarker to complement existing monitoring approaches for recurrent OC. In some cases, capable of predicting relapse and treatment response ahead of current clinical indicators. However, identified discordances underscore technical and biological challenges that warrant further investigation. Larger prospective studies are necessary to refine ctDNA's clinical utility and integration into personalized OC care.

PMID:41149505 | PMC:PMC12563156 | DOI:10.3390/curroncol32100585

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Tongyi DeepResearch Technical Report

arXiv:2510.24701v1 Announce Type: cross Abstract: We present Tongyi DeepResearch, an agentic large language model, which is specifically designed for long-horizon, deep information-seeking research tasks. To incentivize autonomous deep research agency, Tongyi DeepResearch is developed through an end-to-end training framework that combines agentic mid-training and agentic post-training, enabling scalable reasoning and information seeking across complex tasks. We design a highly scalable data synthesis pipeline that is fully automatic, without relying on costly human annotation, and empowers all training stages. By constructing customized environments for each stage, our system enables stable and consistent interactions throughout. Tongyi DeepResearch, featuring 30.5 billion total parameters, with only 3.3 billion activated per token, achieves state-of-the-art performance across a range of agentic deep research benchmarks, including Humanity's Last Exam, BrowseComp, BrowseComp-ZH, WebWalkerQA, xbench-DeepSearch, FRAMES and xbench-DeepSearch-2510. We open-source the model, framework, and complete solutions to empower the community.
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Agent Data Protocol: Unifying Datasets for Diverse, Effective Fine-tuning of LLM Agents

arXiv:2510.24702v1 Announce Type: cross Abstract: Public research results on large-scale supervised finetuning of AI agents remain relatively rare, since the collection of agent training data presents unique challenges. In this work, we argue that the bottleneck is not a lack of underlying data sources, but that a large variety of data is fragmented across heterogeneous formats, tools, and interfaces. To this end, we introduce the agent data protocol (ADP), a light-weight representation language that serves as an "interlingua" between agent datasets in diverse formats and unified agent training pipelines downstream. The design of ADP is expressive enough to capture a large variety of tasks, including API/tool use, browsing, coding, software engineering, and general agentic workflows, while remaining simple to parse and train on without engineering at a per-dataset level. In experiments, we unified a broad collection of 13 existing agent training datasets into ADP format, and converted the standardized ADP data into training-ready formats for multiple agent frameworks. We performed SFT on these data, and demonstrated an average performance gain of ~20% over corresponding base models, and delivers state-of-the-art or near-SOTA performance on standard coding, browsing, tool use, and research benchmarks, without domain-specific tuning. All code and data are released publicly, in the hope that ADP could help lower the barrier to standardized, scalable, and reproducible agent training.
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The Confidence Paradox: Can LLM Know When It's Wrong

arXiv:2506.23464v2 Announce Type: replace Abstract: Document Visual Question Answering (DocVQA) models often produce overconfident or ethically misaligned responses, especially under uncertainty. Existing models like LayoutLMv3, UDOP, and DONUT focus on accuracy but lack ethical calibration. We propose HonestVQA, a model-agnostic, self-supervised framework that aligns model confidence with correctness using weighted loss and contrastive learning. We introduce two new metrics Honesty Score (H-Score) and Ethical Confidence Index (ECI)-to evaluate ethical alignment. HonestVQA improves accuracy and F1 by up to 4.3% across SpDocVQA, InfographicsVQA, and SROIE datasets, while reducing overconfidence. It also generalizes well across domains, achieving 78.9% accuracy and 76.1% F1-score.
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The Role of Omentin in Gastrointestinal Cancer: Diagnostic, Prognostic, and Therapeutic Perspectives

Metabolites. 2025 Sep 30;15(10):649. doi: 10.3390/metabo15100649.

ABSTRACT

Background/Objectives: Omentin, also known as intelectin-1, is a secreted adipokine with anti-inflammatory, insulin-sensitizing, and immune-modulatory functions, primarily expressed in visceral adipose tissue. While omentin has been associated with favorable metabolic outcomes, its role in cancer pathogenesis appears context-dependent and remains poorly understood. This review investigates the biological functions, expression patterns, and clinical relevance of omentin across gastrointestinal malignancies. Methods: A comprehensive review of the literature was conducted using PubMed, Scopus, and Web of Science up to August 2025 to evaluate the role of omentin in gastrointestinal cancers. Both preclinical and clinical studies evaluating omentin, its analogues and omentin-enhancing agents in gastric, colorectal, hepatic, pancreatic, and esophageal cancers were included. Results: Omentin exhibits anti-proliferative, anti-inflammatory, and anti-angiogenic effects within the tumor microenvironment in several GI malignancies. However, evidence also indicates a dual role. High intratumoral omentin expression correlates with improved prognosis in colorectal, gastric, and hepatic cancers; in contrast, elevated circulating levels-particularly in colorectal and pancreatic cancers-have been paradoxically associated with increased cancer risk and poor outcomes. Mechanistically, omentin modulates PI3K/Akt, NF-κB, AMPK, and oxidative stress pathways, and interacts with TMEM207. However, most available studies are small-scale and heterogeneous, with methodological inconsistencies and limited multi-omics integration, leaving major knowledge gaps. Conclusions: This review highlights omentin's distinct systemic and local roles across GI cancers, underscoring its translational implications. Omentin emerges as a promising but context-dependent biomarker and therapeutic target, with future research needed to address heterogeneity, standardize assays, and validate its clinical utility in large-scale prospective studies.

PMID:41149627 | PMC:PMC12566161 | DOI:10.3390/metabo15100649

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A Comprehensive Survey on Reinforcement Learning-based Agentic Search: Foundations, Roles, Optimizations, Evaluations, and Applications

arXiv:2510.16724v2 Announce Type: replace Abstract: The advent of large language models (LLMs) has transformed information access and reasoning through open-ended natural language interaction. However, LLMs remain limited by static knowledge, factual hallucinations, and the inability to retrieve real-time or domain-specific information. Retrieval-Augmented Generation (RAG) mitigates these issues by grounding model outputs in external evidence, but traditional RAG pipelines are often single turn and heuristic, lacking adaptive control over retrieval and reasoning. Recent advances in agentic search address these limitations by enabling LLMs to plan, retrieve, and reflect through multi-step interaction with search environments. Within this paradigm, reinforcement learning (RL) offers a powerful mechanism for adaptive and self-improving search behavior. This survey provides the first comprehensive overview of \emph{RL-based agentic search}, organizing the emerging field along three complementary dimensions: (i) What RL is for (functional roles), (ii) How RL is used (optimization strategies), and (iii) Where RL is applied (scope of optimization). We summarize representative methods, evaluation protocols, and applications, and discuss open challenges and future directions toward building reliable and scalable RL driven agentic search systems. We hope this survey will inspire future research on the integration of RL and agentic search. Our repository is available at https://github.com/ventr1c/Awesome-RL-based-Agentic-Search-Papers.
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Understanding AI Trustworthiness: A Scoping Review of AIES & FAccT Articles

arXiv:2510.21293v2 Announce Type: replace Abstract: Background: Trustworthy AI serves as a foundational pillar for two major AI ethics conferences: AIES and FAccT. However, current research often adopts techno-centric approaches, focusing primarily on technical attributes such as reliability, robustness, and fairness, while overlooking the sociotechnical dimensions critical to understanding AI trustworthiness in real-world contexts. Objectives: This scoping review aims to examine how the AIES and FAccT communities conceptualize, measure, and validate AI trustworthiness, identifying major gaps and opportunities for advancing a holistic understanding of trustworthy AI systems. Methods: We conduct a scoping review of AIES and FAccT conference proceedings to date, systematically analyzing how trustworthiness is defined, operationalized, and applied across different research domains. Our analysis focuses on conceptualization approaches, measurement methods, verification and validation techniques, application areas, and underlying values. Results: While significant progress has been made in defining technical attributes such as transparency, accountability, and robustness, our findings reveal critical gaps. Current research often predominantly emphasizes technical precision at the expense of social and ethical considerations. The sociotechnical nature of AI systems remains less explored and trustworthiness emerges as a contested concept shaped by those with the power to define it. Conclusions: An interdisciplinary approach combining technical rigor with social, cultural, and institutional considerations is essential for advancing trustworthy AI. We propose actionable measures for the AI ethics community to adopt holistic frameworks that genuinely address the complex interplay between AI systems and society, ultimately promoting responsible technological development that benefits all stakeholders.
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Multi-Agent Evolve: LLM Self-Improve through Co-evolution

arXiv:2510.23595v2 Announce Type: replace Abstract: Reinforcement Learning (RL) has demonstrated significant potential in enhancing the reasoning capabilities of large language models (LLMs). However, the success of RL for LLMs heavily relies on human-curated datasets and verifiable rewards, which limit their scalability and generality. Recent Self-Play RL methods, inspired by the success of the paradigm in games and Go, aim to enhance LLM reasoning capabilities without human-annotated data. However, their methods primarily depend on a grounded environment for feedback (e.g., a Python interpreter or a game engine); extending them to general domains remains challenging. To address these challenges, we propose Multi-Agent Evolve (MAE), a framework that enables LLMs to self-evolve in solving diverse tasks, including mathematics, reasoning, and general knowledge Q&A. The core design of MAE is based on a triplet of interacting agents (Proposer, Solver, Judge) that are instantiated from a single LLM, and applies reinforcement learning to optimize their behaviors. The Proposer generates questions, the Solver attempts solutions, and the Judge evaluates both while co-evolving. Experiments on Qwen2.5-3B-Instruct demonstrate that MAE achieves an average improvement of 4.54% on multiple benchmarks. These results highlight MAE as a scalable, data-efficient method for enhancing the general reasoning abilities of LLMs with minimal reliance on human-curated supervision.
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Learned, Lagged, LLM-splained: LLM Responses to End User Security Questions

arXiv:2411.14571v2 Announce Type: replace-cross Abstract: Answering end user security questions is challenging. While large language models (LLMs) like GPT, LLAMA, and Gemini are far from error-free, they have shown promise in answering a variety of questions outside of security. We studied LLM performance in the area of end user security by qualitatively evaluating 3 popular LLMs on 900 systematically collected end user security questions. While LLMs demonstrate broad generalist ``knowledge'' of end user security information, there are patterns of errors and limitations across LLMs consisting of stale and inaccurate answers, and indirect or unresponsive communication styles, all of which impacts the quality of information received. Based on these patterns, we suggest directions for model improvement and recommend user strategies for interacting with LLMs when seeking assistance with security.
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Multimodal 3D Genome Pre-training

arXiv:2504.09060v2 Announce Type: replace-cross Abstract: Deep learning techniques have driven significant progress in various analytical tasks within 3D genomics in computational biology. However, a holistic understanding of 3D genomics knowledge remains underexplored. Here, we propose MIX-HIC, the first multimodal foundation model of 3D genome that integrates both 3D genome structure and epigenomic tracks, which obtains unified and comprehensive semantics. For accurate heterogeneous semantic fusion, we design the cross-modal interaction and mapping blocks for robust unified representation, yielding the accurate aggregation of 3D genome knowledge. Besides, we introduce the first large-scale dataset comprising over 1 million pairwise samples of Hi-C contact maps and epigenomic tracks for high-quality pre-training, enabling the exploration of functional implications in 3D genomics. Extensive experiments show that MIX-HIC can significantly surpass existing state-of-the-art methods in diverse downstream tasks. This work provides a valuable resource for advancing 3D genomics research.
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Robustness is Important: Limitations of LLMs for Data Fitting

arXiv:2508.19563v3 Announce Type: replace-cross Abstract: Large Language Models (LLMs) are being applied in a wide array of settings, well beyond the typical language-oriented use cases. In particular, LLMs are increasingly used as a plug-and-play method for fitting data and generating predictions. Prior work has shown that LLMs, via in-context learning or supervised fine-tuning, can perform competitively with many tabular supervised learning techniques in terms of predictive performance. However, we identify a critical vulnerability of using LLMs for data fitting -- making changes to data representation that are completely irrelevant to the underlying learning task can drastically alter LLMs' predictions on the same data. For example, simply changing variable names can sway the size of prediction error by as much as 82% in certain settings. Such prediction sensitivity with respect to task-irrelevant variations manifests under both in-context learning and supervised fine-tuning, for both close-weight and open-weight general-purpose LLMs. Moreover, by examining the attention scores of an open-weight LLM, we discover a non-uniform attention pattern: training examples and variable names/values which happen to occupy certain positions in the prompt receive more attention when output tokens are generated, even though different positions are expected to receive roughly the same attention. This partially explains the sensitivity in the presence of task-irrelevant variations. We also consider a state-of-the-art tabular foundation model (TabPFN) trained specifically for data fitting. Despite being explicitly designed to achieve prediction robustness, TabPFN is still not immune to task-irrelevant variations. Overall, despite LLMs' impressive predictive capabilities, currently they lack even the basic level of robustness to be used as a principled data-fitting tool.
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Energy-Efficient Domain-Specific Artificial Intelligence Models and Agents: Pathways and Paradigms

arXiv:2510.22052v1 Announce Type: new Abstract: The field of artificial intelligence (AI) has taken a tight hold on broad aspects of society, industry, business, and governance in ways that dictate the prosperity and might of the world's economies. The AI market size is projected to grow from 189 billion USD in 2023 to 4.8 trillion USD by 2033. Currently, AI is dominated by large language models that exhibit linguistic and visual intelligence. However, training these models requires a massive amount of data scraped from the web as well as large amounts of energy (50--60 GWh to train GPT-4). Despite these costs, these models often hallucinate, a characteristic that prevents them from being deployed in critical application domains. In contrast, the human brain consumes only 20~W of power. What is needed is the next level of AI evolution in which lightweight domain-specific multimodal models with higher levels of intelligence can reason, plan, and make decisions in dynamic environments with real-time data and prior knowledge, while learning continuously and evolving in ways that enhance future decision-making capability. This will define the next wave of AI, progressing from today's large models, trained with vast amounts of data, to nimble energy-efficient domain-specific agents that can reason and think in a world full of uncertainty. To support such agents, hardware will need to be reimagined to allow energy efficiencies greater than 1000x over the state of the art. Such a vision of future AI systems is developed in this work.
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Embracing Trustworthy Brain-Agent Collaboration as Paradigm Extension for Intelligent Assistive Technologies

arXiv:2510.22095v1 Announce Type: new Abstract: Brain-Computer Interfaces (BCIs) offer a direct communication pathway between the human brain and external devices, holding significant promise for individuals with severe neurological impairments. However, their widespread adoption is hindered by critical limitations, such as low information transfer rates and extensive user-specific calibration. To overcome these challenges, recent research has explored the integration of Large Language Models (LLMs), extending the focus from simple command decoding to understanding complex cognitive states. Despite these advancements, deploying agentic AI faces technical hurdles and ethical concerns. Due to the lack of comprehensive discussion on this emerging direction, this position paper argues that the field is poised for a paradigm extension from BCI to Brain-Agent Collaboration (BAC). We emphasize reframing agents as active and collaborative partners for intelligent assistance rather than passive brain signal data processors, demanding a focus on ethical data handling, model reliability, and a robust human-agent collaboration framework to ensure these systems are safe, trustworthy, and effective.
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