arXiv:2511.15061v1 Announce Type: new Abstract: Genomic question answering often requires complex reasoning and integration across diverse biomedical sources. GeneGPT addressed this challenge by combining domain-specific APIs with OpenAI's code-davinci-002 large language model to enable natural language interaction with genomic databases. However, its reliance on a proprietary model limits scalability, increases operational costs, and raises concerns about data privacy and generalization. In this work, we revisit and reproduce GeneGPT in a pilot study using open source models, including Llama 3.1, Qwen2.5, and Qwen2.5 Coder, within a monolithic architecture; this allows us to identify the limitations of this approach. Building on this foundation, we then develop OpenBioLLM, a modular multi-agent framework that extends GeneGPT by introducing agent specialization for tool routing, query generation, and response validation. This enables coordinated reasoning and role-based task execution. OpenBioLLM matches or outperforms GeneGPT on over 90% of the benchmark tasks, achieving average scores of 0.849 on Gene-Turing and 0.830 on GeneHop, while using smaller open-source models without additional fine-tuning or tool-specific pretraining. OpenBioLLM's modular multi-agent design reduces latency by 40-50% across benchmark tasks, significantly improving efficiency without compromising model capability. The results of our comprehensive evaluation highlight the potential of open-source multi-agent systems for genomic question answering. Code and resources are available at https://github.com/ielab/OpenBioLLM.

arXiv:2511.15534v1 Announce Type: new Abstract: There is growing interest in using AI agents for scientific research, yet fundamental questions remain about their capabilities as scientists and reviewers. To explore these questions, we organized Agents4Science, the first conference in which AI agents serve as both primary authors and reviewers, with humans as co-authors and co-reviewers. Here, we discuss the key learnings from the conference and their implications for human-AI collaboration in science.

arXiv:2511.11743v2 Announce Type: replace-cross Abstract: Deploying deep neural networks on resource-constrained devices faces two critical challenges: maintaining accuracy under aggressive quantization while ensuring predictable inference latency. We present a curiosity-driven quantized Mixture-of-Experts framework that addresses both through Bayesian epistemic uncertainty-based routing across heterogeneous experts (BitNet ternary, 1-16 bit BitLinear, post-training quantization). Evaluated on audio classification benchmarks (ESC-50, Quinn, UrbanSound8K), our 4-bit quantization maintains 99.9 percent of 16-bit accuracy (0.858 vs 0.859 F1) with 4x compression and 41 percent energy savings versus 8-bit. Crucially, curiosity-driven routing reduces MoE latency variance by 82 percent (p = 0.008, Levene's test) from 230 ms to 29 ms standard deviation, enabling stable inference for battery-constrained devices. Statistical analysis confirms 4-bit/8-bit achieve practical equivalence with full precision (p > 0.05), while MoE architectures introduce 11 percent latency overhead (p

Nature Cancer, Published online: 19 November 2025; doi:10.1038/s43018-025-01060-8

Gao et al. present SMMILe, a multiple-instance learning-based tool that leverages whole-slide images for accurate spatial quantification without compromising on classification performance, and show it outperforms state-of-the-art methods.

Nature Biotechnology, Published online: 19 November 2025; doi:10.1038/s41587-025-02929-w

Need for a shared language and minimum information standards for bioprocess development

arXiv:2511.14256v1 Announce Type: new Abstract: Knowledge graph reasoning (KGR) is the task of inferring new knowledge by performing logical deductions on knowledge graphs. Recently, large language models (LLMs) have demonstrated remarkable performance in complex reasoning tasks. Despite promising success, current LLM-based KGR methods still face two critical limitations. First, existing methods often extract reasoning paths indiscriminately, without assessing their different importance, which may introduce irrelevant noise that misleads LLMs. Second, while many methods leverage LLMs to dynamically explore potential reasoning paths, they require high retrieval demands and frequent LLM calls. To address these limitations, we propose PathMind, a novel framework designed to enhance faithful and interpretable reasoning by selectively guiding LLMs with important reasoning paths. Specifically, PathMind follows a "Retrieve-Prioritize-Reason" paradigm. First, it retrieves a query subgraph from KG through the retrieval module. Next, it introduces a path prioritization mechanism that identifies important reasoning paths using a semantic-aware path priority function, which simultaneously considers the accumulative cost and the estimated future cost for reaching the target. Finally, PathMind generates accurate and logically consistent responses via a dual-phase training strategy, including task-specific instruction tuning and path-wise preference alignment. Extensive experiments on benchmark datasets demonstrate that PathMind consistently outperforms competitive baselines, particularly on complex reasoning tasks with fewer input tokens, by identifying essential reasoning paths.

arXiv:2407.04055v2 Announce Type: replace-cross Abstract: The prediction modeling of drug-target interactions is crucial to drug discovery and design, which has seen rapid advancements owing to deep learning technologies. Recently developed methods, such as those based on graph neural networks (GNNs) and Transformers, demonstrate exceptional performance across various datasets by effectively extracting structural information. However, the benchmarking of these novel methods often varies significantly in terms of hyperparameter settings and datasets, which limits algorithmic progress. In view of these, we conducted a comprehensive survey and benchmark for drug-target interaction modeling from a structural perspective via integrating tens of explicit (i.e., GNN-based) and implicit (i.e., Transformer-based) structure learning algorithms. We conducted a macroscopical comparison between these two classes of encoding strategies as well as the different featurization techniques that inform molecules' chemical and physical properties. We then carry out the microscopical comparison between all the integrated models across the six datasets via comprehensively benchmarking their effectiveness and efficiency. To ensure fairness, we investigate model performance under individually optimized configuration. Remarkably, the summarized insights from the benchmark studies lead to the design of model combos. We demonstrate that our combos can achieve new state-of-the-art performance on various datasets associated with cost-effective memory and computation.

The Ryder Cup is an almost-century-old tournament pitting Europe against the United States in an elite showcase of golf skill and strategy. At the 2025 event, nearly a quarter of a million spectators gathered to watch three days of fierce competition on the fairways.

From a technology and logistics perspective, pulling off an event of this scale is no easy feat. The Ryder Cup’s infrastructure must accommodate the tens of thousands of network users who flood the venue (this year, at Bethpage Black in Farmingdale, New York) every day.

To manage this IT complexity, Ryder Cup engaged technology partner HPE to create a central hub for its operations. The solution centered around a platform where tournament staff could access data visualization supporting operational decision-making. This dashboard, which leveraged a high-performance network and private-cloud environment, aggregated and distilled insights from diverse real-time data feeds.

It was a glimpse into what AI-ready networking looks like at scale—a real-world stress test with implications for everything from event management to enterprise operations. While models and data readiness get the lion’s share of boardroom attention and media hype, networking is a critical third leg of successful AI implementation, explains Jon Green, CTO of HPE Networking. “Disconnected AI doesn’t get you very much; you need a way to get data into it and out of it for both training and inference,” he says.

As businesses move toward distributed, real-time AI applications, tomorrow’s networks will need to parse even more massive volumes of information at ever more lightning-fast speeds. What played out on the greens at Bethpage Black represents a lesson being learned across industries: Inference-ready networks are a make-or-break factor for turning AI’s promise into real-world performance.

Making a network AI inference-ready

More than half of organizations are still struggling to operationalize their data pipelines. In a recent HPE cross-industry survey of 1,775  IT leaders, 45% said they could run real-time data pushes and pulls for innovation. It’s a noticeable change over last year’s numbers (just 7% reported having such capabilities in 2024), but there’s still work to be done to connect data collection with real-time decision-making.

The network may hold the key to further narrowing that gap. Part of the solution will likely come down to infrastructure design. While traditional enterprise networks are engineered to handle the predictable flow of business applications—email, browsers, file sharing, etc.—they’re not designed to field the dynamic, high-volume data movement required by AI workloads. Inferencing in particular depends on shuttling vast datasets between multiple GPUs with supercomputer-like precision.

“There’s an ability to play fast and loose with a standard, off-the-shelf enterprise network,” says Green. “Few will notice if an email platform is half a second slower than it might’ve been. But with AI transaction processing, the entire job is gated by the last calculation taking place. So it becomes really noticeable if you’ve got any loss or congestion.”

Networks built for AI, therefore, must operate with a different set of performance characteristics, including ultra-low latency, lossless throughput, specialized equipment, and adaptability at scale. One of these differences is AI’s distributed nature, which affects the seamless flow of data.

The Ryder Cup was a vivid demonstration of this new class of networking in action. During the event, a Connected Intelligence Center was put in place to ingest data from ticket scans, weather reports, GPS-tracked golf carts, concession and merchandise sales, spectator and consumer queues, and network performance. Additionally, 67 AI-enabled cameras were positioned throughout the course. Inputs were analyzed through an operational intelligence dashboard and provided staff with an instantaneous view of activity across the grounds.

“The tournament is really complex from a networking perspective, because you have many big open areas that aren’t uniformly packed with people,” explains Green. “People tend to follow the action. So in certain areas, it’s really dense with lots of people and devices, while other areas are completely empty.”

To handle that variability, engineers built out a two-tiered architecture. Across the sprawling venue, more than 650 WiFi 6E access points, 170 network switches, and 25 user experience sensors worked together to maintain continuous connectivity and feed a private cloud AI cluster for live analytics. The front-end layer connected cameras, sensors, and access points to capture live video and movement data, while a back-end layer—located within a temporary on-site data center—linked GPUs and servers in a high-speed, low-latency configuration that effectively served as the system’s brain. Together, the setup enabled both rapid on-the-ground responses and data collection that could inform future operational planning. “AI models also were available to the team which could process video of the shots taken and help determine, from the footage, which ones were the most interesting,” says Green.

Physical AI and the return of on-prem intelligence

If time is of the essence for event management, it’s even more critical in contexts where safety is on the line—for instance a self-driving car making a split-second decision to accelerate or brake.

In planning for the rise of physical AI, where applications move off screens and onto factory floors and city streets, a growing number of enterprises are rethinking their architectures. Instead of sending the data to centralized clouds for inference, some are deploying edge-based AI clusters that process information closer to where it is generated. Data-intensive training may still occur in the cloud, but inferencing happens on-site.

This hybrid approach is fueling a wave of operational repatriation, as workloads once relegated to the cloud return to on-premises infrastructure for enhanced speed, security, sovereignty, and cost reasons. “We’ve had an out-migration of IT into the cloud in recent years, but physical AI is one of the use cases that we believe will bring a lot of that back on-prem,” predicts Green, giving the example of an AI-infused factory floor, where a round-trip of sensor data to the cloud would be too slow to safely control automated machinery. “By the time processing happens in the cloud, the machine has already moved,” he explains.

There’s data to back up Green’s projection: research from Enterprise Research Group shows that 84% of respondents are reevaluating application deployment strategies due to the growth of AI. Market forecasts also reflect this shift. According to IDC, the AI market for infrastructure is expected to reach $758 billion by 2029.

AI for networking and the future of self-driving infrastructure

The relationship between networking and AI is circular: Modern networks make AI at scale possible, but AI is also helping make networks smarter and more capable.

“Networks are some of the most data-rich systems in any organization,” says Green. “That makes them a perfect use case for AI. We can analyze millions of configuration states across thousands of customer environments and learn what actually improves performance or stability.”

At HPE for example, which has one of the largest network telemetry repositories in the world, AI models analyze anonymized data collected from billions of connected devices to identify trends and refine behavior over time. The platform processes more than a trillion telemetry points each day, which means it can continuously learn from real-world conditions.

The concept broadly known as AIOps (or AI-driven IT operations) is changing how enterprise networks are managed across industries. Today, AI surfaces insights as recommendations that administrators can choose to apply with a single click. Tomorrow, those same systems might automatically test and deploy low-risk changes themselves.

That long-term vision, Green notes, is referred to as a “self-driving network”—one that handles the repetitive, error-prone tasks that have historically plagued IT teams. “AI isn’t coming for the network engineer’s job, but it will eliminate the tedious stuff that slows them down,” he says. “You’ll be able to say, ‘Please go configure 130 switches to solve this issue,’ and the system will handle it. When a port gets stuck or someone plugs a connector in the wrong direction, AI can detect it—and in many cases, fix it automatically.”

Digital initiatives now depend on how effectively information moves. Whether coordinating a live event or streamlining a supply chain, the performance of the network increasingly defines the performance of the business. Building that foundation today will separate those who pilot from those who scale AI.

For more, register to watch MIT Technology Review’s EmTech AI Salon, featuring HPE.

This content was produced by Insights, the custom content arm of MIT Technology Review. It was not written by MIT Technology Review’s editorial staff. It was researched, designed, and written by human writers, editors, analysts, and illustrators. This includes the writing of surveys and collection of data for surveys. AI tools that may have been used were limited to secondary production processes that passed thorough human review.

arXiv:2506.09095v4 Announce Type: replace-cross Abstract: Foundation models (FMs) are changing the way medical images are analyzed by learning from large collections of unlabeled data. Instead of relying on manually annotated examples, FMs are pre-trained to learn general-purpose visual features that can later be adapted to specific clinical tasks with little additional supervision. In this review, we examine how FMs are being developed and applied in pathology, radiology, and ophthalmology, drawing on evidence from over 150 studies. We explain the core components of FM pipelines, including model architectures, self-supervised learning methods, and strategies for downstream adaptation. We also review how FMs are being used in each imaging domain and compare design choices across applications. Finally, we discuss key challenges and open questions to guide future research.

npj Digital Medicine, Published online: 18 November 2025; doi:10.1038/s41746-025-02042-x

Large language models driven neural architecture search for universal and lightweight disease diagnosis on histopathology slide images

arXiv:2511.11597v1 Announce Type: new Abstract: Evaluating how Large Language Models (LLMs) handle complex, specialized knowledge remains a critical challenge. We address this through the lens of climate change by introducing CLINB, a benchmark that assesses models on open-ended, grounded, multimodal question answering tasks with clear requirements for knowledge quality and evidential support. CLINB relies on a dataset of real users' questions and evaluation rubrics curated by leading climate scientists. We implement and validate a model-based evaluation process and evaluate several frontier models. Our findings reveal a critical dichotomy. Frontier models demonstrate remarkable knowledge synthesis capabilities, often exhibiting PhD-level understanding and presentation quality. They outperform "hybrid" answers curated by domain experts assisted by weaker models. However, this performance is countered by failures in grounding. The quality of evidence varies, with substantial hallucination rates for references and images. We argue that bridging this gap between knowledge synthesis and verifiable attribution is essential for the deployment of AI in scientific workflows and that reliable, interpretable benchmarks like CLINB are needed to progress towards building trustworthy AI systems.

arXiv:2511.11899v1 Announce Type: new Abstract: Fine-grained analysis of intraoperative behavior and its impact on patient outcomes remain a longstanding challenge. We present Frame-to-Outcome (F2O), an end-to-end system that translates tissue dissection videos into gesture sequences and uncovers patterns associated with postoperative outcomes. Leveraging transformer-based spatial and temporal modeling and frame-wise classification, F2O robustly detects consecutive short (~2 seconds) gestures in the nerve-sparing step of robot-assisted radical prostatectomy (AUC: 0.80 frame-level; 0.81 video-level). F2O-derived features (gesture frequency, duration, and transitions) predicted postoperative outcomes with accuracy comparable to human annotations (0.79 vs. 0.75; overlapping 95% CI). Across 25 shared features, effect size directions were concordant with small differences (~ 0.07), and strong correlation (r = 0.96, p

arXiv:2511.12306v1 Announce Type: new Abstract: As large language model (LLM) agents increasingly undertake digital work, reliable frameworks are needed to evaluate their real-world competence, adaptability, and capacity for human collaboration. Existing benchmarks remain largely static, synthetic, or domain-limited, providing limited insight into how agents perform in dynamic, economically meaningful environments. We introduce UpBench, a dynamically evolving benchmark grounded in real jobs drawn from the global Upwork labor marketplace. Each task corresponds to a verified client transaction, anchoring evaluation in genuine work activity and financial outcomes. UpBench employs a rubric-based evaluation framework, in which expert freelancers decompose each job into detailed, verifiable acceptance criteria and assess AI submissions with per-criterion feedback. This structure enables fine-grained analysis of model strengths, weaknesses, and instruction-following fidelity beyond binary pass/fail metrics. Human expertise is integrated throughout the data pipeline (from job curation and rubric construction to evaluation) ensuring fidelity to real professional standards and supporting research on human-AI collaboration. By regularly refreshing tasks to reflect the evolving nature of online work, UpBench provides a scalable, human-centered foundation for evaluating agentic systems in authentic labor-market contexts, offering a path toward a collaborative framework, where AI amplifies human capability through partnership rather than replacement.

arXiv:2511.12378v1 Announce Type: new Abstract: Autonomous agents operating in sequential decision-making tasks under uncertainty can benefit from external action suggestions, which provide valuable guidance but inherently vary in reliability. Existing methods for incorporating such advice typically assume static and known suggester quality parameters, limiting practical deployment. We introduce a framework that dynamically learns and adapts to varying suggester reliability in partially observable environments. First, we integrate suggester quality directly into the agent's belief representation, enabling agents to infer and adjust their reliance on suggestions through Bayesian inference over suggester types. Second, we introduce an explicit ``ask'' action allowing agents to strategically request suggestions at critical moments, balancing informational gains against acquisition costs. Experimental evaluation demonstrates robust performance across varying suggester qualities, adaptation to changing reliability, and strategic management of suggestion requests. This work provides a foundation for adaptive human-agent collaboration by addressing suggestion uncertainty in uncertain environments.

arXiv:2511.12439v1 Announce Type: new Abstract: Online health resources and large language models (LLMs) are increasingly used as a first point of contact for medical decision-making, yet their reliability in healthcare remains limited by low accuracy, lack of transparency, and susceptibility to unverified information. We introduce a proof-of-concept conversational self-triage system that guides LLMs with 100 clinically validated flowcharts from the American Medical Association, providing a structured and auditable framework for patient decision support. The system leverages a multi-agent framework consisting of a retrieval agent, a decision agent, and a chat agent to identify the most relevant flowchart, interpret patient responses, and deliver personalized, patient-friendly recommendations, respectively. Performance was evaluated at scale using synthetic datasets of simulated conversations. The system achieved 95.29% top-3 accuracy in flowchart retrieval (N=2,000) and 99.10% accuracy in flowchart navigation across varied conversational styles and conditions (N=37,200). By combining the flexibility of free-text interaction with the rigor of standardized clinical protocols, this approach demonstrates the feasibility of transparent, accurate, and generalizable AI-assisted self-triage, with potential to support informed patient decision-making while improving healthcare resource utilization.

arXiv:2511.13137v1 Announce Type: new Abstract: Task decomposition has shown promise in complex cooperative multi-agent reinforcement learning (MARL) tasks, which enables efficient hierarchical learning for long-horizon tasks in dynamic and uncertain environments. However, learning dynamic task decomposition from scratch generally requires a large number of training samples, especially exploring the large joint action space under partial observability. In this paper, we present the Conditional Diffusion Model for Dynamic Task Decomposition (C$\text{D}^\text{3}$T), a novel two-level hierarchical MARL framework designed to automatically infer subtask and coordination patterns. The high-level policy learns subtask representation to generate a subtask selection strategy based on subtask effects. To capture the effects of subtasks on the environment, C$\text{D}^\text{3}$T predicts the next observation and reward using a conditional diffusion model. At the low level, agents collaboratively learn and share specialized skills within their assigned subtasks. Moreover, the learned subtask representation is also used as additional semantic information in a multi-head attention mixing network to enhance value decomposition and provide an efficient reasoning bridge between individual and joint value functions. Experimental results on various benchmarks demonstrate that C$\text{D}^\text{3}$T achieves better performance than existing baselines.

arXiv:2511.13290v1 Announce Type: new Abstract: Humans display significant uncertainty when confronted with moral dilemmas, yet the extent of such uncertainty in machines and AI agents remains underexplored. Recent studies have confirmed the overly confident tendencies of machine-generated responses, particularly in large language models (LLMs). As these systems are increasingly embedded in ethical decision-making scenarios, it is important to understand their moral reasoning and the inherent uncertainties in building reliable AI systems. This work examines how uncertainty influences moral decisions in the classical trolley problem, analyzing responses from 32 open-source models and 9 distinct moral dimensions. We first find that variance in model confidence is greater across models than within moral dimensions, suggesting that moral uncertainty is predominantly shaped by model architecture and training method. To quantify uncertainty, we measure binary entropy as a linear combination of total entropy, conditional entropy, and mutual information. To examine its effects, we introduce stochasticity into models via "dropout" at inference time. Our findings show that our mechanism increases total entropy, mainly through a rise in mutual information, while conditional entropy remains largely unchanged. Moreover, this mechanism significantly improves human-LLM moral alignment, with correlations in mutual information and alignment score shifts. Our results highlight the potential to better align model-generated decisions and human preferences by deliberately modulating uncertainty and reducing LLMs' confidence in morally complex scenarios.

arXiv:2511.13293v1 Announce Type: new Abstract: Accurate healthcare prediction is critical for improving patient outcomes and reducing operational costs. Bolstered by growing reasoning capabilities, large language models (LLMs) offer a promising path to enhance healthcare predictions by drawing on their rich parametric knowledge. However, LLMs are prone to factual inaccuracies due to limitations in the reliability and coverage of their embedded knowledge. While retrieval-augmented generation (RAG) frameworks, such as GraphRAG and its variants, have been proposed to mitigate these issues by incorporating external knowledge, they face two key challenges in the healthcare scenario: (1) identifying the clinical necessity to activate the retrieval mechanism, and (2) achieving synergy between the retriever and the generator to craft contextually appropriate retrievals. To address these challenges, we propose GHAR, a \underline{g}enerative \underline{h}ierarchical \underline{a}gentic \underline{R}AG framework that simultaneously resolves when to retrieve and how to optimize the collaboration between submodules in healthcare. Specifically, for the first challenge, we design a dual-agent architecture comprising Agent-Top and Agent-Low. Agent-Top acts as the primary physician, iteratively deciding whether to rely on parametric knowledge or to initiate retrieval, while Agent-Low acts as the consulting service, summarising all task-relevant knowledge once retrieval was triggered. To tackle the second challenge, we innovatively unify the optimization of both agents within a formal Markov Decision Process, designing diverse rewards to align their shared goal of accurate prediction while preserving their distinct roles. Extensive experiments on three benchmark datasets across three popular tasks demonstrate our superiority over state-of-the-art baselines, highlighting the potential of hierarchical agentic RAG in advancing healthcare systems.