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We introduce PathBench-MIL, an open-source AutoML and benchmarking framework for multiple instance learning (MIL) in histopathology. The system automates end-to-end MIL pipeline construction, including preprocessing, feature extraction, and…

Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale…

Biomedical knowledge graphs (KGs) hold rich information on entities such as diseases, drugs, and genes. Predicting missing links in these graphs can boost many important applications, such as drug design and repurposing. Recent work has…

Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…

Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…

In systems biology modeling, important steps include model parameterization, uncertainty quantification, and evaluation of agreement with experimental observations. To help modelers perform these steps, we developed the software…

This paper proposes LayoutLLM, a more flexible document analysis method for understanding imaged documents. Visually Rich Document Understanding tasks, such as document image classification and information extraction, have gained…

In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…

Modeling biological sequences such as DNA, RNA, and proteins is crucial for understanding complex processes like gene regulation and protein synthesis. However, most current models either focus on a single type or treat multiple types of…

The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…

This paper introduces a novel method for translating Business Process Model and Notation (BPMN) diagrams into executable X-Klaim code for Multi-Robot Systems (MRSs). Merging the clarity of BPMN with the operational strength of X-Klaim, we…

Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis…

Existing biomedical benchmarks do not provide end-to-end infrastructure for training, evaluation, and inference of models that integrate multimodal biological data and a broad range of machine learning tasks in therapeutics. We present…

Summary Brain Predictability toolbox (BPt) represents a unified framework of machine learning (ML) tools designed to work with both tabulated data (in particular brain, psychiatric, behavioral, and physiological variables) and neuroimaging…

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…

Recently, there has been a significant upsurge of interest in leveraging large language models (LLMs) to assist scientific discovery. However, most LLMs only focus on general science, while they lack domain-specific knowledge, such as…

We present Cephalo, a series of multimodal vision large language models (V-LLMs) designed for materials science applications, integrating visual and linguistic data for enhanced understanding. A key innovation of Cephalo is its advanced…

Summary: Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks.…

Business Process Model and Notation (BPMN) is a widely used standard for modelling business processes. While automated planning has been proposed as a method for simulating and reasoning about BPMN workflows, most implementations remain…

Machine learning (ML) offers powerful methods for detecting and modeling associations often in data with large feature spaces and complex associations. Many useful tools/packages (e.g. scikit-learn) have been developed to make the various…