Related papers: GRAPHENE: A Precise Biomedical Literature Retrieva…

Deep neural networks (DNNs) are known for extracting useful information from large amounts of data. However, the representations learned in DNNs are typically hard to interpret, especially in dense layers. One crucial issue of the classical…

Recent advancements in Large Language Models (LLMs) have significantly improved their performance across various Natural Language Processing (NLP) tasks. However, LLMs still struggle with generating non-factual responses due to limitations…

Currently, there is a rapidly increasing need for high-quality biomedical knowledge graphs (BioKG) that provide direct and precise biomedical knowledge. In the context of COVID-19, this issue is even more necessary to be highlighted.…

We present a novel graph neural network (GNN) architecture for retrieval-augmented generation (RAG) that leverages query-aware attention mechanisms and learned scoring heads to improve retrieval accuracy on complex, multi-hop questions.…

Safe and trustworthy use of Large Language Models (LLM) in the processing of healthcare documents and scientific papers could substantially help clinicians, scientists and policymakers in overcoming information overload and focusing on the…

Graph Neural Networks (GNNs) perform effectively when training and testing graphs are drawn from the same distribution, but struggle to generalize well in the face of distribution shifts. To address this issue, existing mainstreaming graph…

This paper presents the first deep reinforcement learning (DRL) framework to estimate the optimal Dynamic Treatment Regimes from observational medical data. This framework is more flexible and adaptive for high dimensional action and state…

While large language models (LLMs) demonstrate impressive capabilities, their reliance on parametric knowledge often leads to factual inaccuracies. Retrieval-Augmented Generation (RAG) mitigates this by leveraging external documents, yet…

Graph generation is a fundamental task with broad applications, such as drug discovery. Recently, discrete flow matching-based graph generation, \aka, graph flow model (GFM), has emerged due to its superior performance and flexible…

In the brain, the structure of a network of neurons defines how these neurons implement the computations that underlie the mind and the behavior of animals and humans. Provided that we can describe the network of neurons as a graph, we can…

Biomedical Knowledge Graphs (BKGs) integrate diverse datasets to elucidate complex relationships within the biomedical field. Effective link prediction on these graphs can uncover valuable connections, such as potential novel drug-disease…

Large Language Models (LLMs) integrated with Retrieval-Augmented Generation (RAG) techniques have exhibited remarkable performance across a wide range of domains. However, existing RAG approaches primarily operate on unstructured data and…

Graph Neural Networks (GNNs) are effective tools for graph representation learning. Most GNNs rely on a recursive neighborhood aggregation scheme, named message passing, thereby their theoretical expressive power is limited to the…

Self-supervised learning provides a promising path towards eliminating the need for costly label information in representation learning on graphs. However, to achieve state-of-the-art performance, methods often need large numbers of…

Recently, graph neural networks (GNNs) have been widely used for document classification. However, most existing methods are based on static word co-occurrence graphs without sentence-level information, which poses three challenges:(1) word…

Recent advances in machine learning, particularly Large Language Models (LLMs) such as BERT and GPT, provide rich contextual embeddings that improve text representation. However, current document clustering approaches often ignore the…

The Precision Medicine Initiative states that treatments for a patient should take into account not only the patient's disease, but his/her specific genetic variation as well. The vast biomedical literature holds the potential for…

Background : Knowledge is evolving over time, often as a result of new discoveries or changes in the adopted methods of reasoning. Also, new facts or evidence may become available, leading to new understandings of complex phenomena. This is…

Drug repurposing plays a critical role in accelerating treatment discovery, especially for complex and rare diseases. Biomedical knowledge graphs (KGs), which encode rich clinical associations, have been widely adopted to support this task.…

We present the DEREK (Deep Extraction & Reasoning Engine for Knowledge) Module, a secure and scalable Retrieval-Augmented Generation pipeline designed specifically for enterprise document question answering. Designed and implemented by…