Large language models (LLMs) are rapidly transforming various domains, including biomedicine and healthcare, and demonstrate remarkable potential from scientific research to new drug discovery. Graph-based retrieval-augmented generation (RAG) systems, as a useful application of LLMs, can improve contextual reasoning through structured entity and relationship identification from long-context knowledge, e.g. biomedical literature. Even though many advantages over naive RAGs, most of graph-based RAGs are computationally intensive, which limits their application to large-scale dataset. To address this issue, we introduce fastbmRAG, an fast graph-based RAG optimized for biomedical literature. Utilizing well organized structure of biomedical papers, fastbmRAG divides the construction of knowledge graph into two stages, first drafting graphs using abstracts; and second, refining them using main texts guided by vector-based entity linking, which minimizes redundancy and computational load. Our evaluations demonstrate that fastbmRAG is over 10x faster than existing graph-RAG tools and achieve superior coverage and accuracy to input knowledge. FastbmRAG provides a fast solution for quickly understanding, summarizing, and answering questions about biomedical literature on a large scale. FastbmRAG is public available in https://github.com/menggf/fastbmRAG.

Abstract--Endometriosis is a common women's condition exhibiting a manifold visual appearance in various body-internal locations. Having such properties makes its identification very difficult and error-prone, at least for laymen and non-specialized medical practitioners. In an attempt to provide assistance to gynecologic physicians treating endometriosis, this demo paper describes a system that is trained to segment one frequently occurring visual appearance of endometriosis, namely dark endometrial implants. The system is capable of analyzing la-paroscopic surgery videos, annotating identified implant regions with multi-colored overlays and displaying a detection summary for improved video browsing. Endoscopic surgical procedures are well established particularly in gynecology.

The grinding trial-and-error process that precedes world-changing scientific discoveries doesn't really lend itself to dramatization. Instead of our heroes chasing bad guys down dark alleys, the exciting story action involves them standing in front of a blackboard or gazing into a microscope. So dramatic tension is injected by financial or political forces threatening to derail a project of urgent importance (Oppenheimer); the scientists fighting for credibility in the face of belonging to a marginalized group (Hidden Figures, The Imitation Game, any biopic of a female scientist); or the old reliable of the main scientist being a difficult, maverick genius (Oppenheimer again). Joy: The Birth of IVF, Ben Taylor's new film out now on Netflix, about the arduous path to develop a viable technique for fertilizing human eggs outside the body and implanting them in the womb, aka in vitro fertilization, hits many of these notes. There's the irascible pioneer, here played by Bill Nighy at his most crotchety but sympathetic as gynecologist Patrick Steptoe, who introduced laparoscopy to the U.K. He's teamed with the driven visionary--physiologist Robert Edwards, played by James Norton, who, like Jude Law, is always required to conceal his innate gorgeousness under an unbecoming wig or glasses to convince as an ordinary guy.

Screening questionnaires are used in medicine as a diagnostic aid. Creating them is a long and expensive process, which could potentially be improved through analysis of social media posts related to symptoms and behaviors prior to diagnosis. Here we show a preliminary investigation into the feasibility of generating screening questionnaires for a given medical condition from social media postings. The method first identifies a cohort of relevant users through their posts in dedicated patient groups and a control group of users who reported similar symptoms but did not report being diagnosed with the condition of interest. Posts made prior to diagnosis are used to generate decision rules to differentiate between the different groups, by clustering symptoms mentioned by these users and training a decision tree to differentiate between the two groups. We validate the generated rules by correlating them with scores given by medical doctors to matching hypothetical cases. We demonstrate the proposed method by creating questionnaires for three conditions (endometriosis, lupus, and gout) using the data of several hundreds of users from Reddit. These questionnaires were then validated by medical doctors. The average Pearson's correlation between the latter's scores and the decision rules were 0.58 (endometriosis), 0.40 (lupus) and 0.27 (gout). Our results suggest that the process of questionnaire generation can be, at least partly, automated. These questionnaires are advantageous in that they are based on real-world experience but are currently lacking in their ability to capture the context, duration, and timing of symptoms.

Machine learning has emerged as a powerful tool for scientific discovery, enabling researchers to extract meaningful insights from complex datasets. For instance, it has facilitated the identification of disease-predictive genes from gene expression data, significantly advancing healthcare. However, the traditional process for analyzing such datasets demands substantial human effort and expertise for the data selection, processing, and analysis. To address this challenge, we introduce a novel framework, a Team of AI-made Scientists (TAIS), designed to streamline the scientific discovery pipeline. TAIS comprises simulated roles, including a project manager, data engineer, and domain expert, each represented by a Large Language Model (LLM). These roles collaborate to replicate the tasks typically performed by data scientists, with a specific focus on identifying disease-predictive genes. Furthermore, we have curated a benchmark dataset to assess TAIS's effectiveness in gene identification, demonstrating our system's potential to significantly enhance the efficiency and scope of scientific exploration. Our findings represent a solid step towards automating scientific discovery through large language models.

Personalized adaptive interventions offer the opportunity to increase patient benefits, however, there are challenges in their planning and implementation. Once implemented, it is an important question whether personalized adaptive interventions are indeed clinically more effective compared to a fixed gold standard intervention. In this paper, we present an innovative N-of-1 trial study design testing whether implementing a personalized intervention by an online reinforcement learning agent is feasible and effective. Throughout, we use a new study on physical exercise recommendations to reduce pain in endometriosis for illustration. We describe the design of a contextual bandit recommendation agent and evaluate the agent in simulation studies. The results show that, first, implementing a personalized intervention by an online reinforcement learning agent is feasible. Second, such adaptive interventions have the potential to improve patients' benefits even if only few observations are available. As one challenge, they add complexity to the design and implementation process. In order to quantify the expected benefit, data from previous interventional studies is required. We expect our approach to be transferable to other interventions and clinical interventions.

In this paper, for the first time, a method is presented that can provide a fully automated surgery based on software and computer vision techniques. Then, the advantages and challenges of computerization of medical surgery are examined. Finally, the surgery related to isolated ovarian endometriosis disease has been examined, and based on the presented method, a more detailed algorithm is presented that is capable of automatically diagnosing and treating this disease during surgery as proof of our proposed method where a U-net is trained to detect the endometriosis during surgery.

Endometriosis is a common chronic gynecological disorder that has many characteristics, including the pouch of Douglas (POD) obliteration, which can be diagnosed using Transvaginal gynecological ultrasound (TVUS) scans and magnetic resonance imaging (MRI). TVUS and MRI are complementary non-invasive endometriosis diagnosis imaging techniques, but patients are usually not scanned using both modalities and, it is generally more challenging to detect POD obliteration from MRI than TVUS. To mitigate this classification imbalance, we propose in this paper a knowledge distillation training algorithm to improve the POD obliteration detection from MRI by leveraging the detection results from unpaired TVUS data. More specifically, our algorithm pre-trains a teacher model to detect POD obliteration from TVUS data, and it also pre-trains a student model with 3D masked auto-encoder using a large amount of unlabelled pelvic 3D MRI volumes. Next, we distill the knowledge from the teacher TVUS POD obliteration detector to train the student MRI model by minimizing a regression loss that approximates the output of the student to the teacher using unpaired TVUS and MRI data. Experimental results on our endometriosis dataset containing TVUS and MRI data demonstrate the effectiveness of our method to improve the POD detection accuracy from MRI.

The training set for the DotEndo machine learning algorithm was developed via DotLab's EMPOWER clinical study, a prospective, observational, multi- …

Want to seem like the smartest member of your family these holidays? Why not brag about your vast knowledge of AI? It was a big year for artificial intelligence, so here's a round-up of Cosmos' AI favourites from 2021. A team of researchers from the University of Glasgow, UK, used machine learning algorithms to find future zoonotic (originating in animals) virus threats. According to the researchers, a major stumbling block for understanding zoonotic disease has been that scientists tend to prioritise well-known zoonotic virus families based on their common features.