Related papers: MOSGA: Modular Open-Source Genome Annotator
Data annotation is an important and necessary task for all NLP applications. Designing and implementing a web-based application that enables many annotators to annotate and enter their input into one central database is not a trivial task.…
Analysis of genomics data is central to nearly all areas of modern biology. Despite significant progress in artificial intelligence (AI) and computational methods, these technologies require significant human oversight to generate novel and…
The assessment of microbial species biodiversity is essential in ecology and evolutionary biology (Reaka-Kudla et al. 1996), but especially challenging for communities of microorganisms found in the environment (Das et al. 2006, Hillebrand…
Image based biomarker discovery typically requires an accurate segmentation of histologic structures (e.g., cell nuclei, tubules, epithelial regions) in digital pathology Whole Slide Images (WSI). Unfortunately, annotating each structure of…
Summary: TreeGrafter is a new software tool for annotating protein sequences using annotated phylogenetic trees. Cur-rently, the tool provides annotations to Gene Ontology terms, and PANTHER protein class, family and subfamily. The…
Prokaryotic organisms usually possess compact genomes, which are particularly suitable to complete sequencing with existing technologies, which led to an escalating accumulation of available genome data. In response to this ever-expanding…
Several algorithms and tools have been developed to (semi) automate the process of glycan identification by interpreting Mass Spectrometric data. However, each has limitations when annotating MSn data with thousands of MS spectra using…
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,…
Accurate identification of protein-nucleotide binding sites is fundamental to deciphering molecular mechanisms and accelerating drug discovery. However, current computational methods often struggle with suboptimal performance due to…
Collecting and annotating morphological data present significant challenges, requiring linguistic expertise, methodological rigour, and substantial resources. These barriers are particularly acute for low-resource languages and varieties.…
Annotating biomedical images for supervised learning is a complex and labor-intensive task due to data diversity and its intricate nature. In this paper, we propose an innovative method, the efficient one-pass selective annotation (EPOSA),…
The performance of current supervised AI systems is tightly connected to the availability of annotated datasets. Annotations are usually collected through annotation tools, which are often designed for specific tasks and are difficult to…
In our previous work, we demonstrated that it is feasible to perform analysis on mutation signature data without the need for downloads or installations and analyze individual patient data at scale without compromising privacy. Building on…
Manually annotated data is key to developing text-mining and information-extraction algorithms. However, human annotation requires considerable time, effort and expertise. Given the rapid growth of biomedical literature, it is paramount to…
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.…
We present POTATO, the Portable text annotation tool, a free, fully open-sourced annotation system that 1) supports labeling many types of text and multimodal data; 2) offers easy-to-configure features to maximize the productivity of both…
The code of nature, embedded in DNA and RNA genomes since the origin of life, holds immense potential to impact both humans and ecosystems through genome modeling. Genomic Foundation Models (GFMs) have emerged as a transformative approach…
In this paper, we introduce, MultiGA, an optimization framework which applies genetic algorithm principles to address complex natural language tasks and reasoning problems by sampling from a diverse population of LLMs to initialize the…
Coarse-Grained Reconfigurable Arrays (CGRAs) hold great promise as power-efficient edge accelerator, offering versatility beyond AI applications. Morpher, an open-source, architecture-adaptive CGRA design framework, is specifically designed…
Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manually refined genome annotations into account. Results: We…