Related papers: MOSGA: Modular Open-Source Genome Annotator
1. Automated analysis of bioacoustic recordings using machine learning (ML) methods has the potential to greatly scale biodiversity monitoring efforts. The use of ML for high-stakes applications, such as conservation research, demands a…
MOOSEnger is a tool-enabled AI agent tailored to the Multiphysics Object-Oriented Simulation Environment (MOOSE). MOOSE cases are specified in HIT ".i" input files; the large object catalog and strict syntax make initial setup and debugging…
Inspired by the effectiveness of genetic algorithms and the importance of synthesizability in molecular design, we present SynGA, a simple genetic algorithm that operates directly over synthesis routes. Our method features custom crossover…
Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…
Cancer subtype classification is crucial for personalized treatment and prognostic assessment. However, effectively integrating multi-omic data remains challenging due to the heterogeneous nature of genomic, epigenomic, and transcriptomic…
The lack of annotated datasets is a major bottleneck for training new task-specific supervised machine learning models, considering that manual annotation is extremely expensive and time-consuming. To address this problem, we present MONAI…
Summary: The AptaBlocks Web Interface is focused on providing graphical, intuitive, and platform independent access to AptaBlocks, an experimentally validated algorithmic approach for the in-silico design of oligonucleotide sticky bridges.…
MRA (Multilingual Report Annotator) is a web application that translates Radiology text and annotates it with RadLex terms. Its goal is to explore the solution of translating non-English Radiology reports as a way to solve the problem of…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
Isochores are long genome segments relatively homogeneous in G+C. A heuristic algorithm based on entropic segmentation has been developed by our group, and a web server implementing all the required components is available. However, a…
Background and Objective: The lack of benchmark datasets has impeded the development of slice-to-volume registration algorithms. Such datasets are difficult to annotate, primarily due to the dimensional difference within data and the dearth…
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…
Deploying production-ready multi-agent systems (MAS) in complex industrial environments remains challenging due to limitations in scalability, observability, and autonomous evolution. We present OxyGent, an open-source framework driven by…
Multimodal learning combining pathology images and genomic sequences enhances cancer survival analysis but faces clinical implementation barriers due to limited access to genomic sequencing in under-resourced regions. To enable survival…
In the era of data-driven science, conducting computational experiments that involve analysing large datasets using heterogeneous computational clusters, is part of the everyday routine for many scientists. Moreover, to ensure the…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
We present Deep Search DocQA. This application enables information extraction from documents via a question-answering conversational assistant. The system integrates several technologies from different AI disciplines consisting of document…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
A lot of real-world phenomena are complex and cannot be captured by single task annotations. This causes a need for subsequent annotations, with interdependent questions and answers describing the nature of the subject at hand. Even in the…
In research labs, there is often a need to customise software at every step in a given bioinformatics workflow, but traditionally it has been difficult to obtain both a high degree of customisability and good performance.…