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:2411.05034v2 Announce Type: replace-cross Abstract: Embeddings have become a cornerstone in the functionality of large language models (LLMs) due to their ability to transform text data into rich, dense numerical representations that capture semantic and syntactic properties. These embedding vector databases serve as the long-term memory of LLMs, enabling efficient handling of a wide range of natural language processing tasks. However, the surge in popularity of embedding vector databases in LLMs has been accompanied by significant concerns about privacy leakage. Embedding vector databases are particularly vulnerable to embedding inversion attacks, where adversaries can exploit the embeddings to reverse-engineer and extract sensitive information from the original text data. Existing defense mechanisms have shown limitations, often struggling to balance security with the performance of downstream tasks. To address these challenges, we introduce Eguard, a novel defense mechanism designed to mitigate embedding inversion attacks. Eguard employs a transformer-based projection network and text mutual information optimization to safeguard embeddings while preserving the utility of LLMs. Our approach significantly reduces privacy risks, protecting over 95% of tokens from inversion while maintaining high performance across downstream tasks consistent with original embeddings.

arXiv:2509.07928v2 Announce Type: replace-cross Abstract: As local AI grows in popularity, there is a critical gap between the benchmark performance of object detectors and their practical viability on consumer-grade hardware. While models like YOLOv10s promise real-time speeds, these metrics are typically achieved on high-power, desktop-class GPUs. This paper reveals that on resource-constrained systems, such as laptops with RTX 4060 GPUs, performance is not compute-bound but is instead dominated by system-level bottlenecks, as illustrated by a simple bottleneck test. To overcome this hardware-level constraint, we introduce a Two-Pass Adaptive Inference algorithm, a model-independent approach that requires no architectural changes. This study mainly focuses on adaptive inference strategies and undertakes a comparative analysis of architectural early-exit and resolution-adaptive routing, highlighting their respective trade-offs within a unified evaluation framework. The system uses a fast, low-resolution pass and only escalates to a high-resolution model pass when detection confidence is low. On a 5000-image COCO dataset, our method achieves a 1.85x speedup over a PyTorch Early-Exit baseline, with a modest mAP loss of 5.51%. This work provides a practical and reproducible blueprint for deploying high-performance, real-time AI on consumer-grade devices by shifting the focus from pure model optimization to hardware-aware inference strategies that maximize throughput.

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

In many parts of the United States, patients have gotten used to living without primary care. Nearly 75 million people in the United States live in an area with a shortage of these critical providers, leading to long wait times — if a patient can find primary care at all. 

The scale of the access problem, “it’s like red alert — red, red, red alert level — and it’s been like that for a while,” said physician Rajesh Patel, vice president of digital patient experience at Mass General Brigham.

The situation is only getting worse: By 2037, the nation will be short 87,000 primary care physicians, according to federal estimates. 

Clinical artificial intelligence company K Health thinks it has part of the solution. Over the last two years, it has partnered with five large health systems — Cedars-Sinai, Mayo Clinic, Hackensack Meridian Health, Hartford HealthCare, and Mass General Brigham — to launch round-the-clock virtual primary care platforms enabled by its AI. Today, it announced another partnership with Northwell Health, New York’s largest health system, which began rolling out its platform in October. 

Continue to STAT+ to read the full story…

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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.

Wikipedia's guide to “Signs of AI writing” is a great resource for learning to spot LLM-generated prose.

Nature, Published online: 19 November 2025; doi:10.1038/d41586-025-03770-6

Synthetic RNA molecules can program cells to ignore DNA mutations that interfere with protein production.

Nature, Published online: 19 November 2025; doi:10.1038/d41586-025-03714-0

Ethicists say AI-powered advances will threaten the privacy and autonomy of people who use neurotechnology.

Nature, Published online: 19 November 2025; doi:10.1038/d41586-025-03587-3

Genome editing has been used to generate a type of transfer RNA that overcomes the harmful effects of ‘nonsense’ gene variants — a possible remedy for a range of diseases.

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

Nature Biotechnology, Published online: 19 November 2025; doi:10.1038/s41587-025-02933-0

Biopharma’s reawakened interest in cardiovascular diseases spans new targets and modalities, with more convenient formulations to boost access and adherence.

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:2511.14445v1 Announce Type: cross Abstract: We present Tell Me, a mental well-being system that leverages advances in large language models to provide accessible, context-aware support for users and researchers. The system integrates three components: (i) a retrieval-augmented generation (RAG) assistant for personalized, knowledge-grounded dialogue; (ii) a synthetic client-therapist dialogue generator conditioned on client profiles to facilitate research on therapeutic language and data augmentation; and (iii) a Well-being AI crew, implemented with CrewAI, that produces weekly self-care plans and guided meditation audio. The system is designed as a reflective space for emotional processing rather than a substitute for professional therapy. It illustrates how conversational assistants can lower barriers to support, complement existing care, and broaden access to mental health resources. To address the shortage of confidential therapeutic data, we introduce synthetic client-therapist dialogue generation conditioned on client profiles. Finally, the planner demonstrates an innovative agentic workflow for dynamically adaptive, personalized self-care, bridging the limitations of static well-being tools. We describe the architecture, demonstrate its functionalities, and report evaluation of the RAG assistant in curated well-being scenarios using both automatic LLM-based judgments and a human-user study. This work highlights opportunities for interdisciplinary collaboration between NLP researchers and mental health professionals to advance responsible innovation in human-AI interaction for well-being.

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.

Oncogenesis, Published online: 18 November 2025; doi:10.1038/s41389-025-00585-y

Sphingosine 1-phosphate signalling in cancer stem cells

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.