AIMC Topic: Genomics

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The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models.

PLoS computational biology
Complex deep learning models trained on very large datasets have become key enabling tools for current research in natural language processing and computer vision. By providing pre-trained models that can be fine-tuned for specific applications, they...

Genomic language models: opportunities and challenges.

Trends in genetics : TIG
Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of natural language processing is to understand sequences of words, a major objective i...

Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets.

Cancer cell
Molecular subtypes, such as defined by The Cancer Genome Atlas (TCGA), delineate a cancer's underlying biology, bringing hope to inform a patient's prognosis and treatment plan. However, most approaches used in the discovery of subtypes are not suita...

Identification of genomic alteration and prognosis using pathomics-based artificial intelligence in oral leukoplakia and head and neck squamous cell carcinoma: a multicenter experimental study.

International journal of surgery (London, England)
BACKGROUND: Loss of chromosome 9p is an important biomarker in the malignant transformation of oral leukoplakia (OLK) to head and neck squamous cell carcinoma (HNSCC), and is associated with the prognosis of HNSCC patients. However, various challenge...

Sex identification in rainbow trout using genomic information and machine learning.

Genetics, selection, evolution : GSE
Sex identification in farmed fish is important for the management of fish stocks and breeding programs, but identification based on visual characteristics is typically difficult or impossible in juvenile or premature fish. The amount of genomic data ...

Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper.

PLoS computational biology
Antibiotic resistance is a global public health concern. Bacteria have evolved resistance to most antibiotics, which means that for any given bacterial infection, the bacteria may be resistant to one or several antibiotics. It has been suggested that...

A Systematic Approach to Prioritise Diagnostically Useful Findings for Inclusion in Electronic Health Records as Discrete Data to Improve Clinical Artificial Intelligence Tools and Genomic Research.

Clinical oncology (Royal College of Radiologists (Great Britain))
AIMS: The recent widespread use of electronic health records (EHRs) has opened the possibility for innumerable artificial intelligence (AI) tools to aid in genomics, phenomics, and other research, as well as disease prevention, diagnosis, and therapy...

Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics.

Annual review of entomology
Most insects encountered in the field are initially entomological dark matter in that they cannot be identified to species while alive. This explains the enduring quest for efficient ways to identify collected specimens. Morphological tools came firs...

Next-Gen Therapeutics: Pioneering Drug Discovery with iPSCs, Genomics, AI, and Clinical Trials in a Dish.

Annual review of pharmacology and toxicology
In the high-stakes arena of drug discovery, the journey from bench to bedside is hindered by a daunting 92% failure rate, primarily due to unpredicted toxicities and inadequate therapeutic efficacy in clinical trials. The FDA Modernization Act 2.0 he...