Related papers: MOSGA: Modular Open-Source Genome Annotator
The Gene Ontology (GO) project is the largest resource for cataloguing gene function. The combination of solid conceptual underpinnings and a practical set of features have made the GO a widely adopted resource in the research community and…
Missense variant interpretation remains challenging because pathogenicity depends on heterogeneous evidence from population frequency, evolutionary conservation, transcript context, amino acid substitution severity, prior pathogenicity…
Cancer prognosis is a critical task that involves predicting patient outcomes and survival rates. To enhance prediction accuracy, previous studies have integrated diverse data modalities, such as clinical notes, medical images, and genomic…
Background. Biological networks have growing importance for the interpretation of high-throughput "omics" data. Statistical and combinatorial methods allow to obtain mechanistic insights through the extraction of smaller subnetwork modules.…
Motivation: Ontologies are widely used in biology for data annotation, integration, and analysis. In addition to formally structured axioms, ontologies contain meta-data in the form of annotation axioms which provide valuable pieces of…
This paper presents an ensemble part-of-speech tagging approach for source code identifiers. Ensemble tagging is a technique that uses machine-learning and the output from multiple part-of-speech taggers to annotate natural language text at…
The evolution of User Interface design has emphasized the need for efficient, reusable, and editable components to ensure an efficient design process. This research introduces CoGen, a system that uses machine learning techniques to…
Testing is widely recognized as an important stage of the software development lifecycle. Effective software testing can provide benefits such as bug finding, preventing regressions, and documentation. In terms of documentation, unit tests…
Tag-Pag is an application designed to simplify the categorization of web pages, a task increasingly common for researchers who scrape web pages to analyze individuals' browsing patterns or train machine learning classifiers. Unlike existing…
This chapter presents SMuGA, an integration of symbiogenesis with the Multiset Genetic Algorithm (MuGA). The symbiogenetic approach used here is based on the host-parasite model with the novelty of varying the length of parasites along the…
A novel reconfigurable intelligent surface (RIS) aided non-orthogonal multiple access (NOMA) downlink transmission framework is proposed. We formulate a long-term stochastic optimization problem that involves a joint optimization of NOMA…
Miniature DNA sequencing hardware has begun to succeed in mobile contexts, driving demand for efficient machine learning at the edge. This domain leverages deep learning techniques familiar from speech and time-series analysis for both…
Reusing and making sense of other scientists' computational notebooks. However, making sense of existing notebooks is a struggle, as these reference notebooks are often exploratory, have messy structures, include multiple alternatives, and…
The surge in demand for cost-effective, durable long-term archival media, coupled with density limitations of contemporary magnetic media, has resulted in synthetic DNA emerging as a promising new alternative. Despite its benefits, storing…
The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). However, with increasing…
Deep learning algorithms, often critiqued for their 'black box' nature, traditionally fall short in providing the necessary transparency for trusted clinical use. This challenge is particularly evident when such models are deployed in local…
User interface design is a complex task that involves designers examining a wide range of options. We present Spacewalker, a tool that allows designers to rapidly search a large design space for an optimal web UI with integrated support.…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
Digital pathology has become a standard in the pathology workflow due to its many benefits. These include the level of detail of the whole slide images generated and the potential immediate sharing of cases between hospitals. Recent…
Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is…