AIMC Topic: Software

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Leveraging fundus images for on device eye disease diagnosis with AI powered lightweight software hardware framework.

Scientific reports
Vision loss due to illness can result from various medical conditions that affect the eyes. Advanced devices like OCT and ultra-widefield retinal cameras are expensive, making them less accessible in resource-limited settings. While eye image capture...

DPDispatcher: Scalable HPC Task Scheduling for AI-Driven Science.

Journal of chemical information and modeling
Artificial intelligence (AI) is reshaping computational science, but AI-driven workflows routinely span heterogeneous tasks executed across diverse high-performance computing (HPC) systems. We introduce DPDispatcher, an open-source Python framework f...

ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling.

Nature communications
Accurate detection of somatic variants in tumors is of critical importance and remains challenging. Current methods typically require matched normal samples for reliable detection, which are often unavailable in real-world research and clinical scena...

Natural language processing of gene descriptions for overrepresentation analysis with GeneTEA.

Genome biology
Overrepresentation analysis is used to identify biological enrichment in a list of genes. Here, we introduce GeneTEA, a model that ingests free-text gene descriptions and incorporates natural language processing methods to learn a sparse gene-by-term...

OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman species.

eLife
The SpliceAI deep learning system is currently one of the most accurate methods for identifying splicing signals directly from DNA sequences. However, its utility is limited by its reliance on older software frameworks and human-centric training data...

GlyTrait: A Versatile Bioinformatics Tool for Glycomics Analysis.

Journal of proteome research
We developed GlyTrait, a Python-based framework designed to enhance Glycomics analysis through the innovative calculation and interpretation of derived traits from -glycome data. Glycomics research often grapples with the interpretability and biologi...

EasyGeSe - a resource for benchmarking genomic prediction methods.

BMC genomics
BACKGROUND: Genomic prediction is a widely used method to predict phenotypes from genotypic data. Advances in both biological and computer science have enabled the generation of vast amounts of data and the development of new algorithms, specifically...

Optimizing network bandwidth slicing identification: NADAM-enhanced CNN and VAE data preprocessing for enhanced interpretability.

PloS one
Communication networks of the future will rely heavily on network slicing (NS), a technology that enables the creation of distinct virtual networks within a shared physical infrastructure. This capability is critical for meeting the diverse quality o...

AIPred: comprehensive prediction and analysis of non-histone acetylation via protein language model and interpretable machine learning.

BMC biology
BACKGROUND: Non-histone lysine acetylation is a widespread protein post-translational modification that regulates almost all key cellular processes, and its dysregulation is closely associated with various human diseases. Precise identification of no...

TEMC-Cas: Accurate Cas Protein Classification via Combined Contrastive Learning and Protein Language Models.

ACS synthetic biology
The accurate classification of Cas proteins is crucial for understanding CRISPR-Cas systems and developing genome-editing tools. Here, we present TEMC-Cas, a deep learning framework for accurate classification of Cas proteins that combines a finely t...