AIPatient: Simulating Patients with EHRs and LLM Powered Agentic Workflow

Simulated patient systems play a crucial role in modern medical education and research, providing safe, integrative learning environments and enabling clinical decision-making simulations. Large Language Models (LLM) could advance simulated patient systems by replicating medical conditions and patient-doctor interactions with high fidelity and low cost. However, ensuring the effectiveness and trustworthiness of these systems remains a challenge, as they require a large, diverse, and precise patient knowledgebase, along with a robust and stable knowledge diffusion to users. Here, we developed AIPatient, an advanced simulated patient system with AIPatient Knowledge Graph (AIPatient KG) as the input and the Reasoning Retrieval-Augmented Generation (Reasoning RAG) agentic workflow as the generation backbone. AIPatient KG samples data from Electronic Health Records (EHRs) in the Medical Information Mart for Intensive Care (MIMIC)-III database, producing a clinically diverse and relevant cohort of 1,495 patients with high knowledgebase validity (F1 0.89). Reasoning RAG leverages six LLM powered agents spanning tasks including retrieval, KG query generation, abstraction, checker, rewrite, and summarization. This agentic framework reaches an overall accuracy of 94.15% in EHR-based medical Question Answering (QA), outperforming benchmarks that use either no agent or only partial agent integration. Our system also presents high readability (median Flesch Reading Ease 77.23; median Flesch Kincaid Grade 5.6), robustness (ANOVA F-value 0.6126, p<0.1), and stability (ANOVA F-value 0.782, p<0.1). The promising performance of the AIPatient system highlights its potential to support a wide range of applications, including medical education, model evaluation, and system integration.

Recent advances in deep learning and language models for studying the microbiome

Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.

Characterizing Online Toxicity During the 2022 Mpox Outbreak: A Computational Analysis of Topical and Network Dynamics

Background: Online toxicity, encompassing behaviors such as harassment, bullying, hate speech, and the dissemination of misinformation, has become a pressing social concern in the digital age. The 2022 Mpox outbreak, initially termed "Monkeypox" but subsequently renamed to mitigate associated stigmas and societal concerns, serves as a poignant backdrop to this issue. Objective: In this research, we undertake a comprehensive analysis of the toxic online discourse surrounding the 2022 Mpox outbreak. Our objective is to dissect its origins, characterize its nature and content, trace its dissemination patterns, and assess its broader societal implications, with the goal of providing insights that can inform strategies to mitigate such toxicity in future crises. Methods: We collected more than 1.6 million unique tweets and analyzed them from five dimensions, including context, extent, content, speaker, and intent. Utilizing BERT-based topic modeling and social network community clustering, we delineated the toxic dynamics on Twitter. Results: We identified five high-level topic categories in the toxic online discourse on Twitter, including disease (46.6%), health policy and healthcare (19.3%), homophobia (23.9%), politics (6.0%), and racism (4.1%). Through the toxicity diffusion networks of mentions, retweets, and the top users, we found that retweets of toxic content were widespread, while influential users rarely engaged with or countered this toxicity through retweets. Conclusions: By tracking topical dynamics, we can track the changing popularity of toxic content online, providing a better understanding of societal challenges. Network dynamics spotlight key social media influencers and their intents, indicating that addressing these central figures in toxic discourse can enhance crisis communication and inform policy-making.

Prompt Design Matters for Computational Social Science Tasks but in Unpredictable Ways

Manually annotating data for computational social science tasks can be costly, time-consuming, and emotionally draining. While recent work suggests that LLMs can perform such annotation tasks in zero-shot settings, little is known about how prompt design impacts LLMs' compliance and accuracy. We conduct a large-scale multi-prompt experiment to test how model selection (ChatGPT, PaLM2, and Falcon7b) and prompt design features (definition inclusion, output type, explanation, and prompt length) impact the compliance and accuracy of LLM-generated annotations on four CSS tasks (toxicity, sentiment, rumor stance, and news frames). Our results show that LLM compliance and accuracy are highly prompt-dependent. For instance, prompting for numerical scores instead of labels reduces all LLMs' compliance and accuracy. The overall best prompting setup is task-dependent, and minor prompt changes can cause large changes in the distribution of generated labels. By showing that prompt design significantly impacts the quality and distribution of LLM-generated annotations, this work serves as both a warning and practical guide for researchers and practitioners.

Disentangling Logic: The Role of Context in Large Language Model Reasoning Capabilities

This study intends to systematically disentangle pure logic reasoning and text understanding by investigating the contrast across abstract and contextualized logical problems from a comprehensive set of domains. We explore whether LLMs demonstrate genuine reasoning capabilities across various domains when the underlying logical structure remains constant. We focus on two main questions (1) Can abstract logical problems alone accurately benchmark an LLM's reasoning ability in real-world scenarios, disentangled from contextual support in practical settings? (2) Does fine-tuning LLMs on abstract logic problem generalize to contextualized logic problems and vice versa? To investigate these questions, we focus on standard propositional logic, specifically propositional deductive and abductive logic reasoning. In particular, we construct instantiated datasets for deductive and abductive reasoning with 4 levels of difficulty, encompassing 12 distinct categories or domains based on the categorization of Wikipedia. Our experiments aim to provide insights into disentangling context in logical reasoning and the true reasoning capabilities of LLMs and their generalization potential. The code and dataset are available at: https://github.com/agiresearch/ContextHub.

BattleAgent: Multi-modal Dynamic Emulation on Historical Battles to Complement Historical Analysis

This paper presents BattleAgent, an emulation system that combines the Large Vision-Language Model and Multi-agent System. This novel system aims to simulate complex dynamic interactions among multiple agents, as well as between agents and their environments, over a period of time. It emulates both the decision-making processes of leaders and the viewpoints of ordinary participants, such as soldiers. The emulation showcases the current capabilities of agents, featuring fine-grained multi-modal interactions between agents and landscapes. It develops customizable agent structures to meet specific situational requirements, for example, a variety of battle-related activities like scouting and trench digging. These components collaborate to recreate historical events in a lively and comprehensive manner while offering insights into the thoughts and feelings of individuals from diverse viewpoints. The technological foundations of BattleAgent establish detailed and immersive settings for historical battles, enabling individual agents to partake in, observe, and dynamically respond to evolving battle scenarios. This methodology holds the potential to substantially deepen our understanding of historical events, particularly through individual accounts. Such initiatives can also aid historical research, as conventional historical narratives often lack documentation and prioritize the perspectives of decision-makers, thereby overlooking the experiences of ordinary individuals. BattelAgent illustrates AI's potential to revitalize the human aspect in crucial social events, thereby fostering a more nuanced collective understanding and driving the progressive development of human society.

Large Language Models in Biomedical and Health Informatics: A Bibliometric Review

Large Language Models (LLMs) have rapidly become important tools in Biomedical and Health Informatics (BHI), enabling new ways to analyze data, treat patients, and conduct research. This bibliometric review aims to provide a panoramic view of how LLMs have been used in BHI by examining research articles and collaboration networks from 2022 to 2023. It further explores how LLMs can improve Natural Language Processing (NLP) applications in various BHI areas like medical diagnosis, patient engagement, electronic health record management, and personalized medicine. To do this, our bibliometric review identifies key trends, maps out research networks, and highlights major developments in this fast-moving field. Lastly, it discusses the ethical concerns and practical challenges of using LLMs in BHI, such as data privacy and reliable medical recommendations. Looking ahead, we consider how LLMs could further transform biomedical research as well as healthcare delivery and patient outcomes. This bibliometric review serves as a resource for stakeholders in healthcare, including researchers, clinicians, and policymakers, to understand the current state and future potential of LLMs in BHI.

NPHardEval4V: A Dynamic Reasoning Benchmark of Multimodal Large Language Models

Understanding the reasoning capabilities of Multimodal Large Language Models (MLLMs) is an important area of research. In this study, we introduce a dynamic benchmark, NPHardEval4V, aimed at addressing the existing gaps in evaluating the pure reasoning abilities of MLLMs. Our benchmark aims to provide a venue to disentangle the effect of various factors such as image recognition and instruction following, from the overall performance of the models, allowing us to focus solely on evaluating their reasoning abilities. It is built by converting textual description of questions from NPHardEval to image representations. Our findings reveal significant discrepancies in reasoning abilities across different models and highlight the relatively weak performance of MLLMs compared to LLMs in terms of reasoning. We also investigate the impact of different prompting styles, including visual, text, and combined visual and text prompts, on the reasoning abilities of MLLMs, demonstrating the different impacts of multimodal inputs in model performance. Unlike traditional benchmarks, which focus primarily on static evaluations, our benchmark will be updated monthly to prevent overfitting and ensure a more authentic and fine-grained evaluation of the models. We believe that this benchmark can aid in understanding and guide the further development of reasoning abilities in MLLMs. The benchmark dataset and code are available at https://github.com/lizhouf/NPHardEval4V

NPHardEval: Dynamic Benchmark on Reasoning Ability of Large Language Models via Complexity Classes

Complex reasoning ability is one of the most important features of current LLMs, which has also been leveraged to play an integral role in complex decision-making tasks. Therefore, the investigation into the reasoning capabilities of Large Language Models (LLMs) is critical: numerous benchmarks have been established to assess the reasoning abilities of LLMs. However, current benchmarks are inadequate in offering a rigorous evaluation of the full extent of reasoning abilities that LLMs are capable of achieving. They are also prone to the risk of overfitting, as these benchmarks, being publicly accessible and static, allow models to potentially tailor their responses to specific benchmark metrics, thereby inflating their performance. Addressing these limitations, our research introduces a new benchmark, named NPHardEval. This benchmark is designed to evaluate the reasoning abilities of LLMs across a broad spectrum of 900 algorithmic questions, extending up to the NP-Hard complexity class. These questions are meticulously chosen to represent a wide range of complexity class below the NP-hard complexity class, offering a rigorous measure of the reasoning ability of LLMs. Through this study, we shed light on the current state of reasoning in LLMs, providing an objective and rigorous perspective through the comparison of LLMs' performance across complex classes. Moreover, this benchmark is designed with a dynamic update mechanism, where the datapoints are refreshed on a monthly basis. Such regular updates play a crucial role in mitigating the risk of LLMs overfitting to the benchmark, promoting a more accurate and reliable assessment of their reasoning capabilities. The benchmark dataset and code of NPHardEval are available at https://github.com/casmlab/NPHardEval.

War and Peace : Large Language Model-based Multi-Agent Simulation of World Wars

Can we avoid wars at the crossroads of history? This question has been pursued by individuals, scholars, policymakers, and organizations throughout human history. In this research, we attempt to answer the question based on the recent advances of Artificial Intelligence (AI) and Large Language Models (LLMs). We propose \textbf{WarAgent}, an LLM-powered multi-agent AI system, to simulate the participating countries, their decisions, and the consequences, in historical international conflicts, including the World War I (WWI), the World War II (WWII), and the Warring States Period (WSP) in Ancient China. By evaluating the simulation effectiveness, we examine the advancements and limitations of cutting-edge AI systems' abilities in studying complex collective human behaviors such as international conflicts under diverse settings. In these simulations, the emergent interactions among agents also offer a novel perspective for examining the triggers and conditions that lead to war. Our findings offer data-driven and AI-augmented insights that can redefine how we approach conflict resolution and peacekeeping strategies. The implications stretch beyond historical analysis, offering a blueprint for using AI to understand human history and possibly prevent future international conflicts. Code and data are available at \url{https://github.com/agiresearch/WarAgent}.