Related papers: DEMETER: Efficient simultaneous curation of genome…
The cost and accuracy of simulating complex physical systems using the Finite Element Method (FEM) scales with the resolution of the underlying mesh. Adaptive meshes improve computational efficiency by refining resolution in critical…
Identifying biomarkers in medical images is vital for a wide range of biotech applications. However, recent Transformer and CNN based methods often struggle with variations in morphology and staining, which limits their feature extraction…
The growing volume of omics and clinical data generated for neurodegenerative diseases (NDs) requires new approaches for their curation so they can be ready-to-use in bioinformatics. NeuroEmbed is an approach for the engineering of…
Motivation: Illumina Sequencing data can provide high coverage of a genome by relatively short (100 bp150 bp) reads at a low cost. Our goal is to produce trimmed and error-corrected reads to improve genome assemblies. Our error correction…
Real-time object detection is crucial for real-world applications as it requires high accuracy with low latency. While Detection Transformers (DETR) have demonstrated significant performance improvements, current real-time DETR models are…
Many neuroscientific applications require robust and accurate localization of neurons. It is still an unsolved problem because of the enormous variation in intensity, texture, spatial overlap, morphology and background artifacts. In…
Deploying dense retrieval models efficiently is becoming increasingly important across various industries. This is especially true for enterprise search services, where customizing search engines to meet the time demands of different…
Nowadays, due to the increasing amount of experimental data obtained by sequencing, the most interest is focused on determining the functions and characteristics of its individual parts of the genome instead of determining the nucleotide…
In this contribution, a semi-automatic segmentation algorithm for (medical) image analysis is presented. More precise, the approach belongs to the category of interactive contouring algorithms, which provide real-time feedback of the…
Specialised transformers-based models (such as BioBERT and BioMegatron) are adapted for the biomedical domain based on publicly available biomedical corpora. As such, they have the potential to encode large-scale biological knowledge. We…
Partition refinement is a method for minimizing automata and transition systems of various types. Recently, a new partition refinement algorithm and associated tool CoPaR were developed that are generic in the transition type of the input…
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
Swift and accurate blood smear analysis is an effective diagnostic method for leukemia and other hematological malignancies. However, manual leukocyte count and morphological evaluation using a microscope is time-consuming and prone to…
Identifying immune checkpoint inhibitor (ICI) studies in genomic repositories like Gene Expression Omnibus (GEO) is vital for cancer research yet remains challenging due to semantic ambiguity, extreme class imbalance, and limited labeled…
Tracking statements in the commit history of a project is in many cases useful for supporting various software maintenance, comprehension, and evolution tasks. A high level of accuracy can facilitate the adoption of code tracking tools by…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
While computer vision has proven valuable for medical image segmentation, its application faces challenges such as limited dataset sizes and the complexity of effectively leveraging unlabeled images. To address these challenges, we present…
Purpose: Bone metastasis have a major impact on the quality of life of patients and they are diverse in terms of size and location, making their segmentation complex. Manual segmentation is time-consuming, and expert segmentations are…
Monitoring biodiversity is paramount to manage and protect natural resources. Collecting images of organisms over large temporal or spatial scales is a promising practice to monitor the biodiversity of natural ecosystems, providing large…
Next generation sequencing technology rapidly produces massive volume of data and quality control of this sequencing data is essential to any genomic analysis. Here we present MEEPTOOLS, which is a collection of open-source tools based on…