In the COVID-19 pandemic, a rigorous testing scheme was crucial. However, tests can be time-consuming and expensive. A machine learning-based diagnostic tool for audio recordings could enable widespread testing at low costs. In order to achieve comparability between such algorithms, the DiCOVA challenge was created. It is based on the Coswara dataset offering the recording categories cough, speech, breath and vowel phonation. Recording durations vary greatly, ranging from one second to over a minute. A base model is pre-trained on random, short time intervals. Subsequently, a Multiple Instance Learning (MIL) model based on self-attention is incorporated to make collective predictions for multiple time segments within each audio recording, taking advantage of longer durations. In order to compete in the fusion category of the DiCOVA challenge, we utilize a linear regression approach among other fusion methods to combine predictions from the most successful models associated with each sound modality. The application of the MIL approach significantly improves generalizability, leading to an AUC ROC score of 86.6% in the fusion category. By incorporating previously unused data, including the sound modality 'sustained vowel phonation' and patient metadata, we were able to significantly improve our previous results reaching a score of 92.2%.
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Data Brief
February 2025
Arabic Department, University of Sharjah, UAE.
This paper introduces the Morphologically-Analyzed and Syntactically-Annotated Quran (MASAQ) dataset, a comprehensive resource designed to address the scarcity of annotated Quranic Arabic corpora and facilitate the development of advanced Natural Language Processing (NLP) models. The Quran, being a cornerstone of classical Arabic, presents unique challenges for NLP due to its sacred nature and complex linguistic features. MASAQ provides a detailed syntactic and morphological annotation of the entire Quranic text, utilizing a rigorously verified text from Tanzil.
View Article and Find Full Text PDFFront Pharmacol
January 2025
Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, United States.
Introduction: Recent advances in 3D structure-based deep learning approaches demonstrate improved accuracy in predicting protein-ligand binding affinity in drug discovery. These methods complement physics-based computational modeling such as molecular docking for virtual high-throughput screening. Despite recent advances and improved predictive performance, most methods in this category primarily rely on utilizing co-crystal complex structures and experimentally measured binding affinities as both input and output data for model training.
View Article and Find Full Text PDFBackground: Genomic data is essential for clinical decision-making in precision oncology. Bioinformatic algorithms are widely used to analyze next-generation sequencing (NGS) data, but they face two major challenges. First, these pipelines are highly complex, involving multiple steps and the integration of various tools.
View Article and Find Full Text PDFCurr Environ Health Rep
January 2025
Institute for Society and Genetics, University of California, Boyer Hall, Room 332, 611 Charles E Young Dr E., UCLA, Los Angeles, CA, 90095, USA.
Purpose Of Review: The burgeoning field of environmental epigenetics has revealed the malleability of the epigenome and uncovered numerous instances of its sensitivity to environmental influences; however, pinpointing specific mechanisms that tie together environmental triggers, epigenetic pathways, and organismal responses has proven difficult. This article describes how Caenorhabditis elegans can fill this gap, serving as a useful model for the discovery of molecular epigenetic mechanisms that are conserved in humans.
Recent Findings: Recent results show that environmental stressors such as methylmercury, arsenite, starvation, heat, bacterial infection, and mitochondrial inhibitors can all have profound effects on the epigenome, with some insults showing epigenetic and organismal effects for multiple generations.
Commun Biol
January 2025
Computer Science Department, Technion - Israel Institute of Technology, Haifa, Israel.
The activity of miRNA varies across different cell populations and systems, as part of the mechanisms that distinguish cell types and roles in living organisms and in human health and disease. Typically, miRNA regulation drives changes in the composition and levels of protein-coding RNA and of lncRNA, with targets being down-regulated when miRNAs are active. The term "miRNA activity" is used to refer to this transcriptional effect of miRNAs.
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