Related papers: BIOMERO: BioImage analysis in OMERO
We introduce SoftTiger, a clinical large language model (CLaM) designed as a foundation model for healthcare workflows. The narrative and unstructured nature of clinical notes is a major obstacle for healthcare intelligentization. We…
The rapid growth of data in the recent years has led to the development of complex learning algorithms that are often used to make decisions in real world. While the positive impact of the algorithms has been tremendous, there is a need to…
We present FairHealth, an open-source Python library that provides a unified, modular framework for trustworthy machine learning in healthcare applications, with particular focus on low-resource and low-income country (LMIC) settings such…
Open science represents a transformative research approach essential for enhancing sustainability and impact. Data generation encompasses various methods, from automated processes to human-driven inputs, creating a rich and diverse…
The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration…
A large number of services for research data management strive to adhere to the FAIR guiding principles for scientific data management and stewardship. To evaluate these services and to indicate possible improvements, use-case-centric…
Three key properties that are desired of trustworthy machine learning models deployed in high-stakes environments are fairness, explainability, and an ability to account for various kinds of "drift". While drifts in model accuracy, for…
This chapter addresses the forth paradigm of materials research -- big-data driven materials science. Its concepts and state-of-the-art are described, and its challenges and chances are discussed. For furthering the field, Open Data and an…
Open science movement has established reproducibility, transparency, and validation of research outputs as essential norms for conducting scientific research. It advocates for open access to research outputs, especially research data, to…
The Fast Healthcare Interoperability Resources (FHIR) standard has emerged as a widely adopted specification for exchanging structured clinical data across healthcare systems. However, raw FHIR resources are often complex, verbose, and…
The explosive growth of data fuels data-driven research, facilitating progress across diverse domains. The FAIR principles emerge as a guiding standard, aiming to enhance the findability, accessibility, interoperability, and reusability of…
Inference on time series data is a common requirement in many scientific disciplines and internet of things (IoT) applications, yet there are few resources available to domain scientists to easily, robustly, and repeatably build such…
Large language models (LLMs) and large multimodal models (LMMs) promise to accelerate biomedical discovery, yet their reliability remains unclear. We introduce ARIEL (AI Research Assistant for Expert-in-the-Loop Learning), an open-source…
Over the past decade, deep learning (DL) research in computer vision has been growing rapidly, with many advances in DL-based image analysis methods for biomedical problems. In this work, we introduce MMV_Im2Im, a new open-source python…
Biomedical challenges have become the de facto standard for benchmarking biomedical image analysis algorithms. While the number of challenges is steadily increasing, surprisingly little effort has been invested in ensuring high quality…
Modern biomedical applications often involve time-series data, from high-throughput phenotyping of model organisms, through to individual disease diagnosis and treatment using biomedical data streams. Data and tools for time-series analysis…
The advent of foundation models (FMs) in healthcare offers unprecedented opportunities to enhance medical diagnostics through automated classification and segmentation tasks. However, these models also raise significant concerns about their…
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…
Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…
Traditional neuroimage analysis pipelines involve computationally intensive, time-consuming optimization steps, and thus, do not scale well to large cohort studies with thousands or tens of thousands of individuals. In this work we propose…