Related papers: LongBEL: Long-Context and Document-Consistent Biom…

Memory embeddings are crucial for memory-augmented systems, such as OpenClaw, but their evaluation is underexplored in current text embedding benchmarks, which narrowly focus on traditional passage retrieval and fail to assess models'…

Extracting biomedical relations from large corpora of scientific documents is a challenging natural language processing task. Existing approaches usually focus on identifying a relation either in a single sentence (mention-level) or across…

Document-Level Biomedical Relation Extraction (Bio-RE) aims to identify relations between biomedical entities within extensive texts, serving as a crucial subfield of biomedical text mining. Existing Bio-RE methods struggle with…

Pre-trained language models (PLMs) have proven to be effective for document re-ranking task. However, they lack the ability to fully interpret the semantics of biomedical and health-care queries and often rely on simplistic patterns for…

Question answering is a natural language understanding task that involves reasoning over both explicit context, and unstated relevant domain knowledge. Despite the high cost of training, large language models (LLMs) -- the backbone of most…

Information extraction techniques, including named entity recognition (NER) and relation extraction (RE), are crucial in many domains to support making sense of vast amounts of unstructured text data by identifying and connecting relevant…

Large Language Models (LLMs) have been increasingly studied as neural knowledge bases for supporting knowledge-intensive applications such as question answering and fact checking. However, the structural organization of their knowledge…

The rapid increase in textual information means we need more efficient methods to sift through, organize, and understand it all. While retrieval-augmented generation (RAG) models excel in accessing information from large document…

Existing state of the art neural entity linking models employ attention-based bag-of-words context model and pre-trained entity embeddings bootstrapped from word embeddings to assess topic level context compatibility. However, the latent…

Biomedical knowledge graphs are increasingly large, dynamic, and multimodal, driven by rapid advances in biotechnology such as high-throughput sequencing. Machine learning models can infer previously unobserved biomedical relationships and…

Motivation: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network…

Background: Recent advancements in large language models (LLMs) offer potential benefits in healthcare, particularly in processing extensive patient records. However, existing benchmarks do not fully assess LLMs' capability in handling…

We introduce RelNet: a new model for relational reasoning. RelNet is a memory augmented neural network which models entities as abstract memory slots and is equipped with an additional relational memory which models relations between all…

Cross-lingual entity linking (XEL) grounds named entities in a source language to an English Knowledge Base (KB), such as Wikipedia. XEL is challenging for most languages because of limited availability of requisite resources. However, much…

Long-context modeling capabilities have garnered widespread attention, leading to the emergence of Large Language Models (LLMs) with ultra-context windows. Meanwhile, benchmarks for evaluating long-context LLMs are gradually catching up.…

Developing high-performance entity normalization algorithms that can alleviate the term variation problem is of great interest to the biomedical community. Although deep learning-based methods have been successfully applied to biomedical…

Biomedical text embeddings have primarily been developed using research literature from PubMed, yet clinical cardiology practice relies heavily on procedural knowledge and specialized terminology found in comprehensive textbooks rather than…

Training a neural network-based biomedical named entity recognition (BioNER) model usually requires extensive and costly human annotations. While several studies have employed multi-task learning with multiple BioNER datasets to reduce…

As opposed to general English, many concepts in biomedical terminology have been designed in recent history by biomedical professionals with the goal of being precise and concise. This is often achieved by concatenating meaningful…

Recent large language models (LLMs) have demonstrated exceptional performance on general-purpose text embedding tasks. While dense embeddings have dominated related research, we introduce the first lexicon-based embeddings (LENS) leveraging…