Artificial intelligence has advanced rapidly in biomedicine through large-scale multimodal data integration, enabling increasingly accurate prediction of clinical outcomes and patient stratification. These systems, however, remain fundamentally observational: they learn statistical associations from historical data and operate within previously observed biological and clinical states, limiting their ability to generalize to novel therapies or unobserved interventions. We argue that AI in biomedicine is undergoing a structural transition. As biomedical decision-making increasingly depends on reasoning about intervention rather than extrapolation from past observations, predictive architectures become structurally insufficient. Systems that learn from historical data cannot, by construction, represent how biological systems evolve under perturbation, and therefore cannot reliably support decision-making in the presence of novel interventions. We introduce a conceptual framework distinguishing observational and interventional intelligence and define disease-level models as systems that explicitly represent the state, dynamics, and intervention response of biological processes. These m
Magnetotactic bacteria synthesize linear chains of magnetite nanoparticles within their bodies, which allow the bacteria to navigate the Earth's magnetic field in search of the best habitat. Biogenic magnetite particles, called magnetosomes, are very promising for use in biomedicine. Magnetosome chains have also been found in ancient fossils and sediments. The study of magnetofossils provides valuable information about the Earth's biological past. The presence of biogenic magnetite in ancient rock samples can be detected by measuring ferromagnetic resonance spectra, first-order magnetization reversal curves, or quasi-static hysteresis loops. Theoretical analyses of these experiments generally assume that magnetosomes are spherical nanoparticles, although the shape of some types of magnetosomes is close to spheroidal one. In this work, simple formulas for describing the magneto-dipole interaction of oriented spheroids are obtained and quasi-static hysteresis loops of randomly oriented magnetosome chain assembly consisting of elongated spheroids are calculated.
Measurements of microscale surface patterns are essential for process and quality control in industries across semiconductors, micro-machining, and biomedicines. However, the development of miniaturized and intelligent profiling systems remains a longstanding challenge, primarily due to the complexity and bulkiness of existing benchtop systems required to scan large-area samples. A real-time, in-situ, and fast detection alternative is therefore highly desirable for predicting surface topography on the fly. In this paper, we present an ultracompact geometric profiler based on photonic integrated circuits, which directly encodes the optical reflectance of the sample and decodes it with a neural network. This platform is free of complex interferometric configurations and avoids time-consuming nonlinear fitting algorithms. We show that a silicon programmable circuit can generate pseudo-random kernels to project input data into higher dimensions, enabling efficient feature extraction via a lightweight one-dimensional convolutional neural network. Our device is capable of high-fidelity, fast-scanning-rate thickness identification for both smoothly varying samples and intricate 3D printed
Neuromorphic engineering has matured over the past four decades and is currently experiencing explosive growth with the potential to transform biomedical engineering and neurotechnologies. Participants at the Neuromorphic Principles in Biomedicine and Healthcare (NPBH) Workshop (October 2024) -- representing a broad cross-section of the community, including early-career and established scholars, engineers, scientists, clinicians, industry, and funders -- convened to discuss the state of the field, current and future challenges, and strategies for advancing neuromorphic research and development for biomedical applications. Publicly approved recordings with transcripts (https://2024.neuro-med.org/program/session-video-and-transcripts) and slides (https://2024.neuro-med.org/program/session-slides) can be found at the workshop website.
Generative AI has had a profound impact on biomedicine and health, both in professional work and in education. Based on large language models (LLMs), generative AI has been found to perform as well as humans in simulated situations taking medical board exams, answering clinical questions, solving clinical cases, applying clinical reasoning, and summarizing information. Generative AI is also being used widely in education, performing well in academic courses and their assessments. This review summarizes the successes of LLMs and highlights some of their challenges in the context of education, most notably aspects that may undermines the acquisition of knowledge and skills for professional work. It then provides recommendations for best practices overcoming shortcomings for LLM use in education. Although there are challenges for use of generative AI in education, all students and faculty, in biomedicine and health and beyond, must have understanding and be competent in its use.
Recent development in Retrieval-Augmented Large Language Models (LLMs) have shown great promise in biomedical applications. How ever, a critical gap persists in reliably evaluating their curation ability the process by which models select and integrate relevant references while filtering out noise. To address this, we introduce the benchmark for Curation of Retrieval-Augmented LLMs in Biomedicine (CRAB), the first multilingual benchmark tailored for evaluating the biomedical curation of retrieval-augmented LLMs, available in English, French, German and Chinese. By incorporating a novel citation-based evaluation metric, CRAB quantifies the curation performance of retrieval-augmented LLMs in biomedicine. Experimental results reveal significant discrepancies in the curation performance of mainstream LLMs, underscoring the urgent need to improve it in the domain of biomedicine. Our dataset is available at https://huggingface.co/datasets/zhm0/CRAB.
Foundation models, including language models, e.g., GPT, and vision models, e.g., CLIP, have significantly advanced numerous biomedical tasks. Despite these advancements, the high inference latency and the "overthinking" issues in model inference impair the efficiency and effectiveness of foundation models, thus limiting their application in real-time clinical settings. To address these challenges, we proposed EPEE (Entropy- and Patience-based Early Exiting), a novel hybrid strategy designed to improve the inference efficiency of foundation models. The core idea was to leverage the strengths of entropy-based and patience-based early exiting methods to overcome their respective weaknesses. To evaluate EPEE, we conducted experiments on three core biomedical tasks-classification, relation extraction, and event extraction-using four foundation models (BERT, ALBERT, GPT-2, and ViT) across twelve datasets, including clinical notes and medical images. The results showed that EPEE significantly reduced inference time while maintaining or improving accuracy, demonstrating its adaptability to diverse datasets and tasks. EPEE addressed critical barriers to deploying foundation models in healt
Quantum dots (QDs) have emerged as promising nanomaterials with unique optical and physical properties, making them highly attractive for various applications in biomedicine. This review provides a comprehensive overview of the types, modes of synthesis, characterization, applications, and recent advances of QDs in the field of biomedicine, with a primary focus on bioimaging, drug delivery, and biosensors. The unique properties of QDs, such as tunable emission spectra, long-term photostability, high quantum yield, and targeted drug delivery, hold tremendous promise for advancing diagnostics, therapeutics, and imaging techniques in biomedical research. However, several significant hurdles remain before their full potential in the biomedical field, like bioaccumulation, toxicity, and short-term stability. Addressing these hurdles is essential to effectively incorporate QDs into clinical use and enhance their influence on healthcare outcomes. Furthermore, the review conducts a critical analysis of potential QD toxicity and explores recent progress in strategies and methods to mitigate these adverse effects, such as surface modification, surface coatings, and encapsulation. By thorough
Large Language Models (LLMs) show promise in biomedicine but lack true causal understanding, relying instead on correlations. This paper envisions causal LLM agents that integrate multimodal data (text, images, genomics, etc.) and perform intervention-based reasoning to infer cause-and-effect. Addressing this requires overcoming key challenges: designing safe, controllable agentic frameworks; developing rigorous benchmarks for causal evaluation; integrating heterogeneous data sources; and synergistically combining LLMs with structured knowledge (KGs) and formal causal inference tools. Such agents could unlock transformative opportunities, including accelerating drug discovery through automated hypothesis generation and simulation, enabling personalized medicine through patient-specific causal models. This research agenda aims to foster interdisciplinary efforts, bridging causal concepts and foundation models to develop reliable AI partners for biomedical progress.
Traditional Chinese Medicine diagnosis and treatment principles, established through centuries of trial-and-error clinical practice, directly maps patient-specific symptom patterns to personalised herbal therapies. These empirical holistic mapping principles offer valuable strategies to address remaining challenges of reductionism methodologies in modern biomedicine. However, the lack of a quantitative framework and molecular-level evidence has limited their interpretability and reliability. Here, we present an AI framework trained on ancient and classical TCM formula records to quantify the symptom pattern-herbal therapy mappings. Interestingly, we find that empirical TCM diagnosis and treatment are consistent with the encoding-decoding processes in the AI model. This enables us to construct an interpretable TCM embedding space (TCM-ES) using the model's quantitative representation of TCM principles. Validated through broad and extensive TCM patient data, the TCM-ES offers universal quantification of the TCM practice and therapeutic efficacy. We further map biomedical entities into the TCM-ES through correspondence alignment. We find that the principal directions of the TCM-ES are
Large language models (LLMs) in biomedicine face a fundamental conflict between static parameter knowledge and the dynamic nature of clinical evidence. Retrieval-Augmented Generation (RAG) addresses this by grounding generation in external data, yet it introduces new complexities in latency and architecture. This survey synthesizes the biomedical RAG landscape (2020-2025), classifying systems into naive, advanced, and modular paradigms. Beyond a technological taxonomy, we formalize the biomedical RAG trilemma, identifying the inherent trade-offs between reasoning depth, inference latency, and data privacy that constrain current clinical deployment. We analyze how recent agentic workflows enhance diagnostic reasoning but risk prohibitive latency, and how privacy constraints dictate the choice between powerful cloud-based models and local deployment. Finally, we outline the alignment gap in multimodal RAG and propose future directions for self-correcting, verifiable clinical agents.
Foundation models, first introduced in 2021, refer to large-scale pretrained models (e.g., large language models (LLMs) and vision-language models (VLMs)) that learn from extensive unlabeled datasets through unsupervised methods, enabling them to excel in diverse downstream tasks. These models, like GPT, can be adapted to various applications such as question answering and visual understanding, outperforming task-specific AI models and earning their name due to broad applicability across fields. The development of biomedical foundation models marks a significant milestone in the use of artificial intelligence (AI) to understand complex biological phenomena and advance medical research and practice. This survey explores the potential of foundation models in diverse domains within biomedical fields, including computational biology, drug discovery and development, clinical informatics, medical imaging, and public health. The purpose of this survey is to inspire ongoing research in the application of foundation models to health science.
Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations. Retrieval-augmented generation provided a solution for these models to update knowledge and enhance their performance. In contrast to previous retrieval-augmented LMs, which utilize specialized cross-attention mechanisms to help LLM encode retrieved text, BiomedRAG adopts a simpler approach by directly inputting the retrieved chunk-based documents into the LLM. This straightforward design is easily applicable to existing retrieval and language models, effectively bypassing noise information in retrieved documents, particularly in noise-intensive tasks. Moreover, we demonstrate the potential for utilizing the LLM to supervise the retrieval model in the biomedical domain, enabling it to retrieve the document that assists the LM in improving its predictions. Our experiments reveal that with the tuned scorer,\textsc{ BiomedRAG} attains superior performance across 5 biomedical NLP tasks, encompassing information extraction (triple extraction, relation e
Artificial intelligence (AI) systems have the potential to revolutionize clinical practices, including improving diagnostic accuracy and surgical decision-making, while also reducing costs and manpower. However, it is important to recognize that these systems may perpetuate social inequities or demonstrate biases, such as those based on race or gender. Such biases can occur before, during, or after the development of AI models, making it critical to understand and address potential biases to enable the accurate and reliable application of AI models in clinical settings. To mitigate bias concerns during model development, we surveyed recent publications on different debiasing methods in the fields of biomedical natural language processing (NLP) or computer vision (CV). Then we discussed the methods that have been applied in the biomedical domain to address bias. We performed our literature search on PubMed, ACM digital library, and IEEE Xplore of relevant articles published between January 2018 and December 2023 using multiple combinations of keywords. We then filtered the result of 10,041 articles automatically with loose constraints, and manually inspected the abstracts of the rem
Biomedical literature is a rapidly expanding field of science and technology. Classification of biomedical texts is an essential part of biomedicine research, especially in the field of biology. This work proposes the fine-tuned DistilBERT, a methodology-specific, pre-trained generative classification language model for mining biomedicine texts. The model has proven its effectiveness in linguistic understanding capabilities and has reduced the size of BERT models by 40\% but by 60\% faster. The main objective of this project is to improve the model and assess the performance of the model compared to the non-fine-tuned model. We used DistilBert as a support model and pre-trained on a corpus of 32,000 abstracts and complete text articles; our results were impressive and surpassed those of traditional literature classification methods by using RNN or LSTM. Our aim is to integrate this highly specialised and specific model into different research industries.
In recent years, Multimodal Large Language Models (MLLM) have achieved notable advancements, demonstrating the feasibility of developing an intelligent biomedical assistant. However, current biomedical MLLMs predominantly focus on image-level understanding and restrict interactions to textual commands, thus limiting their capability boundaries and the flexibility of usage. In this paper, we introduce a novel end-to-end multimodal large language model for the biomedical domain, named MedPLIB, which possesses pixel-level understanding. Excitingly, it supports visual question answering (VQA), arbitrary pixel-level prompts (points, bounding boxes, and free-form shapes), and pixel-level grounding. We propose a novel Mixture-of-Experts (MoE) multi-stage training strategy, which divides MoE into separate training phases for a visual-language expert model and a pixel-grounding expert model, followed by fine-tuning using MoE. This strategy effectively coordinates multitask learning while maintaining the computational cost at inference equivalent to that of a single expert model. To advance the research of biomedical MLLMs, we introduce the Medical Complex Vision Question Answering Dataset (
Automated lay summarisation (LS) aims to simplify complex technical documents into a more accessible format to non-experts. Existing approaches using pre-trained language models, possibly augmented with external background knowledge, tend to struggle with effective simplification and explanation. Moreover, automated methods that can effectively assess the `layness' of generated summaries are lacking. Recently, large language models (LLMs) have demonstrated a remarkable capacity for text simplification, background information generation, and text evaluation. This has motivated our systematic exploration into using LLMs to generate and evaluate lay summaries of biomedical articles. We propose a novel \textit{Explain-then-Summarise} LS framework, which leverages LLMs to generate high-quality background knowledge to improve supervised LS. We also evaluate the performance of LLMs for zero-shot LS and propose two novel LLM-based LS evaluation metrics, which assess layness from multiple perspectives. Finally, we conduct a human assessment of generated lay summaries. Our experiments reveal that LLM-generated background information can support improved supervised LS. Furthermore, our novel
With the rapid development of multimodal large language models (MLLMs), especially their capabilities in visual chat through refer and ground functionalities, their significance is increasingly recognized. However, the biomedical field currently exhibits a substantial gap in this area, primarily due to the absence of a dedicated refer and ground dataset for biomedical images. To address this challenge, we devised the Med-GRIT-270k dataset. It comprises 270k question-and-answer pairs and spans eight distinct medical imaging modalities. Most importantly, it is the first dedicated to the biomedical domain and integrating refer and ground conversations. The key idea is to sample large-scale biomedical image-mask pairs from medical segmentation datasets and generate instruction datasets from text using chatGPT. Additionally, we introduce a Refer-and-Ground Multimodal Large Language Model for Biomedicine (BiRD) by using this dataset and multi-task instruction learning. Extensive experiments have corroborated the efficacy of the Med-GRIT-270k dataset and the multi-modal, fine-grained interactive capabilities of the BiRD model. This holds significant reference value for the exploration and
Large Language Models (LLMs) demonstrate remarkable versatility in various NLP tasks but encounter distinct challenges in biomedical due to the complexities of language and data scarcity. This paper investigates LLMs application in the biomedical domain by exploring strategies to enhance their performance for the NER task. Our study reveals the importance of meticulously designed prompts in the biomedical. Strategic selection of in-context examples yields a marked improvement, offering ~15-20\% increase in F1 score across all benchmark datasets for biomedical few-shot NER. Additionally, our results indicate that integrating external biomedical knowledge via prompting strategies can enhance the proficiency of general-purpose LLMs to meet the specialized needs of biomedical NER. Leveraging a medical knowledge base, our proposed method, DiRAG, inspired by Retrieval-Augmented Generation (RAG), can boost the zero-shot F1 score of LLMs for biomedical NER. Code is released at \url{https://github.com/masoud-monajati/LLM_Bio_NER}
Multi-modal learning has significantly advanced generative AI, especially in vision-language modeling. Innovations like GPT-4V and open-source projects such as LLaVA have enabled robust conversational agents capable of zero-shot task completions. However, applying these technologies in the biomedical field presents unique challenges. Recent initiatives like LLaVA-Med have started to adapt instruction-tuning for biomedical contexts using large datasets such as PMC-15M. Our research offers three key contributions: (i) we present a new instruct dataset enriched with medical image-text pairs from Claude3-Opus and LLaMA3 70B, (ii) we propose a novel image encoding strategy using hierarchical representations to improve fine-grained biomedical visual comprehension, and (iii) we develop the Llama3-Med model, which achieves state-of-the-art zero-shot performance on biomedical visual question answering benchmarks, with an average performance improvement of over 10% compared to previous methods. These advancements provide more accurate and reliable tools for medical professionals, bridging gaps in current multi-modal conversational assistants and promoting further innovations in medical AI.