Related papers: A brief overview on the BioPAX and SBML standards …
Scientific progress is driven by the deliberate articulation of what remains unknown. This study investigates the ability of large language models (LLMs) to identify research knowledge gaps in the biomedical literature. We define two…
The modeling of bio-molecular system across molecular scales remains a central challenge in scientific research. Large language models (LLMs) are increasingly applied to bio-molecular discovery, yet systematic evaluation across multi-scale…
Despite their strong linguistic capabilities, Large Language Models (LLMs) are computationally demanding and require substantial resources for fine-tuning, which is unadapted to privacy and budget constraints of many healthcare settings. To…
This article summarises a Web-book on "Complexity" that was developed to introduce undergraduate students to interesting complex systems in the biological, physical and social sciences, and the common tools, principles and concepts used for…
Verification of biomedical claims is critical for healthcare decision-making, public health policy and scientific research. We present an interactive biomedical claim verification system by integrating LLMs, transparent model explanations,…
The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted…
We introduce BiMediX2, a bilingual (Arabic-English) Bio-Medical EXpert Large Multimodal Model that supports text-based and image-based medical interactions. It enables multi-turn conversation in Arabic and English and supports diverse…
Recent advances in natural language processing (NLP) owe their success to pre-training language models on large amounts of unstructured data. Still, there is an increasing effort to combine the unstructured nature of LMs with structured…
Biomedical knowledge graphs (KGs) are widely used across research and translational settings, yet their design decisions and implementation are often opaque. Unlike ontologies that more frequently adhere to established creation principles,…
A foundation for closing the gap between biometrics in the narrower and the broader perspective is presented trough a conceptualization of biometric systems in both perspectives. A clear distinction between verification, identification and…
This paper introduces MedExQA, a novel benchmark in medical question-answering, to evaluate large language models' (LLMs) understanding of medical knowledge through explanations. By constructing datasets across five distinct medical…
Automatic Question Answering (QA) has been successfully applied in various domains such as search engines and chatbots. Biomedical QA (BQA), as an emerging QA task, enables innovative applications to effectively perceive, access and…
semanticSBML 2.0 is an online collection of services for the work with biochemical network models in SBML format.
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
Cell types are at the root of modern biology, and describing them is a core task of the Human Cell Atlas project. Surprisingly, there are no standards for reporting new cell types, leading to a gap between classes mentioned in biomedical…
Objective: Large language models (LLMs) are increasingly applied in biomedical settings, and existing benchmark datasets have played an important role in supporting model development and evaluation. However, these benchmarks often have…
Large language models (LLMs) are increasingly evident for accurate question answering across various domains. However, rigorous evaluation of their performance on complex question-answering (QA) capabilities is essential before deployment…
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…
Biosignals offer valuable insights into the physiological states of the human body. Although biosignal modalities differ in functionality, signal fidelity, sensor comfort, and cost, they are often intercorrelated, reflecting the holistic…
Despite the large-scale uptake of semantic technologies in the biomedical domain, little is known about common modelling practices in published ontologies. OWL ontologies are often published only in the crude form of sets of axioms leaving…