Genetics

ROCAS: Root Cause Analysis of Autonomous Driving Accidents via Cyber-Physical Co-mutation

As Autonomous driving systems (ADS) have transformed our daily life, safety of ADS is of growing significance. While various testing approaches have emerged to enhance the ADS reliability, a crucial gap remains in understanding the accidents causes. Such post-accident analysis is paramount and beneficial for enhancing ADS safety and reliability. Existing cyber-physical system (CPS) root cause an...

Machine Learning Approaches for Defect Detection in a Microwell-based Medical Device

Microfluidic devices offer numerous advantages in medical applications, including the capture of single cells in microwell-based platforms for genomic analysis. As the cost of sequencing decreases, the demand for high-throughput single-cell analysis devices increases, leading to more microwells in a single device. However, their small size and large quantity increase the quality control (QC) eff...

Multi-variable control to mitigate loads in CRISPRa networks: Extended Version

The discovery of CRISPR-mediated gene activation (CRISPRa) has transformed the way in which we perform genetic screening, bioproduction and therapeu...

Optimizing Sample Size for Supervised Machine Learning with Bulk Transcriptomic Sequencing: A Learning Curve Approach

Accurate sample classification using transcriptomics data is crucial for advancing personalized medicine. Achieving this goal necessitates determini...

Understanding how chromatin folding and enzyme competition affect rugged epigenetic landscapes

Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without al...

DeepFM-Crispr: Prediction of CRISPR On-Target Effects via Deep Learning

Since the advent of CRISPR-Cas9, a groundbreaking gene-editing technology that enables precise genomic modifications via a short RNA guide sequence,...

Machine Learning-Based Prediction of Key Genes Correlated to the Subretinal Lesion Severity in a Mouse Model of Age-Related Macular Degeneration

Age-related macular degeneration (AMD) is a major cause of blindness in older adults, severely affecting vision and quality of life. Despite advance...

Unlocking Potential Binders: Multimodal Pretraining DEL-Fusion for Denoising DNA-Encoded Libraries

In the realm of drug discovery, DNA-encoded library (DEL) screening technology has emerged as an efficient method for identifying high-affinity comp...

Deep learning meets histones at the replication fork.

Epigenetic inheritance of heterochromatin requires transfer of parental H3-H4 tetramers to both daughter duplexes during replication. Three recent pap...

Explainable AI for computational pathology identifies model limitations and tissue biomarkers

Introduction: Deep learning models hold great promise for digital pathology, but their opaque decision-making processes undermine trust and hinder c...

Gene-Specific Machine Learning Models to Classify Driver Mutations in Clonal Hematopoiesis.

There is no general consensus on the set of mutations capable of driving the age-related clonal expansions in hematopoietic stem cells known as clonal...

Toward Capturing Genetic Epistasis From Multivariate Genome-Wide Association Studies Using Mixed-Precision Kernel Ridge Regression

We exploit the widening margin in tensor-core performance between [FP64/FP32/FP16/INT8,FP64/FP32/FP16/FP8/INT8] on NVIDIA [Ampere,Hopper] GPUs to bo...

Rapid GPU-Based Pangenome Graph Layout

Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pan...

FateNet: an integration of dynamical systems and deep learning for cell fate prediction.

MOTIVATION: Understanding cellular decision-making, particularly its timing and impact on the biological system such as tissue health and function, is...

Deep5hmC: predicting genome-wide 5-hydroxymethylcytosine landscape via a multimodal deep learning model.

MOTIVATION: 5-Hydroxymethylcytosine (5hmC), a crucial epigenetic mark with a significant role in regulating tissue-specific gene expression, is essent...

Gene and RNA Editing: Methods, Enabling Technologies, Applications, and Future Directions

Gene and RNA editing methods, technologies, and applications are emerging as innovative forms of therapy and medicine, offering more efficient imple...

Improving the odds: Artificial intelligence and the great plate count anomaly.

Next-generation DNA sequencing has shown that the great plate count anomaly, that is, the difference between bacteria present in the environment and t...

Scalable CNN-based classification of selective sweeps using derived allele frequencies.

MOTIVATION: Selective sweeps can successfully be distinguished from neutral genetic data using summary statistics and likelihood-based methods that an...

Progress on deep learning in genomics.

With the rapid growth of data driven by high-throughput sequencing technologies, genomics has entered an era characterized by big data, which presents...

Identification of putative coral pathogens in endangered Caribbean staghorn coral using machine learning.

Coral diseases contribute to the rapid decline in coral reefs worldwide, and yet coral bacterial pathogens have proved difficult to identify because 1...