Artificial intelligence systems are increasingly deployed in biomedical research. However, current evaluation frameworks may inadequately assess their effectiveness as research collaborators. This rapid review examines benchmarking practices for AI systems in preclinical biomedical research. Three major databases and two preprint servers were searched from January 1, 2018 to October 31, 2025, identifying 14 benchmarks that assess AI capabilities in literature understanding, experimental design, and hypothesis generation. The results revealed that all current benchmarks assess isolated component capabilities, including data analysis quality, hypothesis validity, and experimental protocol design. However, authentic research collaboration requires integrated workflows spanning multiple sessions, with contextual memory, adaptive dialogue, and constraint propagation. This gap implies that systems excelling on component benchmarks may fail as practical research co-pilots. A process-oriented evaluation framework is proposed that addresses four critical dimensions absent from current benchmarks: dialogue quality, workflow orchestration, session continuity, and researcher experience. These dimensions are essential for evaluating AI systems as research co-pilots rather than as isolated task executors.

Pre-trained audio models excel at detecting acoustic patterns in auscultation sounds but often fail to grasp their clinical significance, limiting their use and performance in diagnostic tasks. To bridge this gap, we introduce AcuLa (Audio-Clinical Understanding via Language Alignment), a lightweight post-training framework that instills semantic understanding into any audio encoder by aligning it with a medical language model, which acts as a "semantic teacher." To enable alignment at scale, we construct a large-scale dataset by leveraging off-the-shelf large language models to translate the rich, structured metadata accompanying existing audio recordings into coherent clinical reports. Our alignment strategy combines a representation-level contrastive objective with a self-supervised modeling, ensuring that the model learns clinical semantics while preserving fine-grained temporal cues. AcuLa achieves state-of-the-art results across 18 diverse cardio-respiratory tasks from 10 different datasets, improving the mean AUROC on classification benchmarks from 0.68 to 0.79 and, on the most challenging COVID-19 cough detection task, boosting the AUROC from 0.55 to 0.89. Our work demonstrates that this audio-language alignment transforms purely acoustic models into clinically-aware diagnostic tools, establishing a novel paradigm for enhancing physiological understanding in audio-based health monitoring.

Expanding the linguistic diversity of instruct large language models (LLMs) is crucial for global accessibility but is often hindered by the reliance on costly specialized target language labeled data and catastrophic forgetting during adaptation. We tackle this challenge under a realistic, low-resource constraint: adapting instruct LLMs using only unlabeled target language data. We introduce Source-Shielded Updates (SSU), a selective parameter update strategy that proactively preserves source knowledge. Using a small set of source data and a parameter importance scoring method, SSU identifies parameters critical to maintaining source abilities. It then applies a column-wise freezing strategy to protect these parameters before adaptation. Experiments across five typologically diverse languages and 7B and 13B models demonstrate that SSU successfully mitigates catastrophic forgetting. It reduces performance degradation on monolingual source tasks to just 3.4% (7B) and 2.8% (13B) on average, a stark contrast to the 20.3% and 22.3% from full fine-tuning. SSU also achieves target-language performance highly competitive with full fine-tuning, outperforming it on all benchmarks for 7B models and the majority for 13B models.

Generative AI systems may pose serious risks to individuals vulnerable to eating disorders. Existing safeguards tend to overlook subtle but clinically significant cues, leaving many risks unaddressed. To better understand the nature of these risks, we conducted semi-structured interviews with 15 clinicians, researchers, and advocates with expertise in eating disorders. Using abductive qualitative analysis, we developed an expert-guided taxonomy of generative AI risks across seven categories: (1) providing generalized health advice; (2) encouraging disordered behaviors; (3) supporting symptom concealment; (4) creating thinspiration; (5) reinforcing negative self-beliefs; (6) promoting excessive focus on the body; and (7) perpetuating narrow views about eating disorders. Our results demonstrate how certain user interactions with generative AI systems intersect with clinical features of eating disorders in ways that may intensify risk. We discuss implications of our work, including approaches for risk assessment, safeguard design, and participatory evaluation practices with domain experts.

Large Language Models (LLMs) exhibit remarkable capabilities but remain vulnerable to adversarial manipulations such as jailbreaking, where crafted prompts bypass safety mechanisms. Understanding the causal factors behind such vulnerabilities is essential for building reliable defenses. In this work, we introduce a unified causality analysis framework that systematically supports all levels of causal investigation in LLMs, ranging from token-level, neuron-level, and layer-level interventions to representation-level analysis. The framework enables consistent experimentation and comparison across diverse causality-based attack and defense methods. Accompanying this implementation, we provide the first comprehensive survey of causality-driven jailbreak studies and empirically evaluate the framework on multiple open-weight models and safety-critical benchmarks including jailbreaks, hallucination detection, backdoor identification, and fairness evaluation. Our results reveal that: (1) targeted interventions on causally critical components can reliably modify safety behavior; (2) safety-related mechanisms are highly localized (i.e., concentrated in early-to-middle layers with only 1--2\% of neurons exhibiting causal influence); and (3) causal features extracted from our framework achieve over 95\% detection accuracy across multiple threat types. By bridging theoretical causality analysis and practical model safety, our framework establishes a reproducible foundation for research on causality-based attacks, interpretability, and robust attack detection and mitigation in LLMs. Code is available at https://github.com/Amadeuszhao/SOK_Casuality.

Large Language Models (LLMs) have become a key topic in AI and NLP, transforming sectors like healthcare, finance, education, and marketing by improving customer service, automating tasks, providing insights, improving diagnostics, and personalizing learning experiences. Information extraction from clinical records is a crucial task in digital healthcare. Although traditional NLP techniques have been used for this in the past, they often fall short due to the complexity, variability of clinical language, and high inner semantics in the free clinical text. Recently, Large Language Models (LLMs) have become a powerful tool for better understanding and generating human-like text, making them highly effective in this area. In this paper, we explore the ability of open-source multilingual LLMs to understand EHRs (Electronic Health Records) in Italian and help extract information from them in real-time. Our detailed experimental campaign on comorbidity extraction from EHR reveals that some LLMs struggle in zero-shot, on-premises settings, and others show significant variation in performance, struggling to generalize across various diseases when compared to native pattern matching and manual annotations.

Agentic AI systems, software agents with autonomy, decision-making ability, and adaptability, are increasingly used to execute complex tasks on behalf of organisations. Most such systems rely on Large Language Models (LLMs), whose broad semantic capabilities enable powerful language processing but lack explicit, institution-specific grounding. In enterprises, data rarely comes with an inspectable semantic layer, and constructing one typically requires labour-intensive "data archaeology": cleaning, modelling, and curating knowledge into ontologies, taxonomies, and other formal structures. At the same time, explainability methods such as saliency maps expose an "interpretability gap": they highlight what the model attends to but not why, leaving decision processes opaque. In this preprint, we present a case study, developed by Kaiasm and Avantra AI through their work with The Turing Way Practitioners Hub, a forum developed under the InnovateUK BridgeAI program. This study presents a collaborative human-AI approach to building an inspectable semantic layer for Agentic AI. AI agents first propose candidate knowledge structures from diverse data sources; domain experts then validate, correct, and extend these structures, with their feedback used to improve subsequent models. Authors show how this process captures tacit institutional knowledge, improves response quality and efficiency, and mitigates institutional amnesia. We argue for a shift from post-hoc explanation to justifiable Agentic AI, where decisions are grounded in explicit, inspectable evidence and reasoning accessible to both experts and non-specialists.

Discovering the neural mechanisms underpinning cognition is one of the grand challenges of neuroscience. However, previous approaches for building models of RNN dynamics that explain behaviour required iterative refinement of architectures and/or optimisation objectives, resulting in a piecemeal, and mostly heuristic, human-in-the-loop process. Here, we offer an alternative approach that automates the discovery of viable RNN mechanisms by explicitly training RNNs to reproduce behaviour, including the same characteristic errors and suboptimalities, that humans and animals produce in a cognitive task. Achieving this required two main innovations. First, as the amount of behavioural data that can be collected in experiments is often too limited to train RNNs, we use a non-parametric generative model of behavioural responses to produce surrogate data for training RNNs. Second, to capture all relevant statistical aspects of the data, we developed a novel diffusion model-based approach for training RNNs. To showcase the potential of our approach, we chose a visual working memory task as our test-bed, as behaviour in this task is well known to produce response distributions that are patently multimodal (due to swap errors). The resulting network dynamics correctly qualitative features of macaque neural data. Importantly, these results were not possible to obtain with more traditional approaches, i.e., when only a limited set of behavioural signatures (rather than the full richness of behavioural response distributions) were fitted, or when RNNs were trained for task optimality (instead of reproducing behaviour). Our approach also yields novel predictions about the mechanism of swap errors, which can be readily tested in experiments. These results suggest that fitting RNNs to rich patterns of behaviour provides a powerful way to automatically discover mechanisms of important cognitive functions.

We introduce SIMA 2, a generalist embodied agent that understands and acts in a wide variety of 3D virtual worlds. Built upon a Gemini foundation model, SIMA 2 represents a significant step toward active, goal-directed interaction within an embodied environment. Unlike prior work (e.g., SIMA 1) limited to simple language commands, SIMA 2 acts as an interactive partner, capable of reasoning about high-level goals, conversing with the user, and handling complex instructions given through language and images. Across a diverse portfolio of games, SIMA 2 substantially closes the gap with human performance and demonstrates robust generalization to previously unseen environments, all while retaining the base model's core reasoning capabilities. Furthermore, we demonstrate a capacity for open-ended self-improvement: by leveraging Gemini to generate tasks and provide rewards, SIMA 2 can autonomously learn new skills from scratch in a new environment. This work validates a path toward creating versatile and continuously learning agents for both virtual and, eventually, physical worlds.

AI agent-based systems are becoming increasingly integral to modern software architectures, enabling autonomous decision-making, dynamic task execution, and multimodal interactions through large language models (LLMs). However, these systems introduce novel and evolving security challenges, including prompt injection attacks, context poisoning, model manipulation, and opaque agent-to-agent communication, that are not effectively captured by traditional threat modeling frameworks. In this paper, we introduce ASTRIDE, an automated threat modeling platform purpose-built for AI agent-based systems. ASTRIDE extends the classical STRIDE framework by introducing a new threat category, A for AI Agent-Specific Attacks, which encompasses emerging vulnerabilities such as prompt injection, unsafe tool invocation, and reasoning subversion, unique to agent-based applications. To automate threat modeling, ASTRIDE combines a consortium of fine-tuned vision-language models (VLMs) with the OpenAI-gpt-oss reasoning LLM to perform end-to-end analysis directly from visual agent architecture diagrams, such as data flow diagrams(DFDs). LLM agents orchestrate the end-to-end threat modeling automation process by coordinating interactions between the VLM consortium and the reasoning LLM. Our evaluations demonstrate that ASTRIDE provides accurate, scalable, and explainable threat modeling for next-generation intelligent systems. To the best of our knowledge, ASTRIDE is the first framework to both extend STRIDE with AI-specific threats and integrate fine-tuned VLMs with a reasoning LLM to fully automate diagram-driven threat modeling in AI agent-based applications.