Related papers: Data navigation on the ENCODE portal
Data commons collate data with cloud computing infrastructure and commonly used software services, tools and applications to create biomedical resources for the large-scale management, analysis, harmonization, and sharing of biomedical…
Enterprise data typically involves multiple heterogeneous data sources and external data that respectively record business activities, transactions, customer demographics, status, behaviors, interactions and communications with the…
Assessing where and how information is stored in biological networks (such as neuronal and genetic networks) is a central task both in neuroscience and in molecular genetics, but most available tools focus on the network's structure as…
Encoding models that predict brain response patterns to stimuli are one way to capture this relationship between variability in bottom-up neural systems and individual's behavior or pathological state. However, they generally need a large…
NetFlow data is a popular network log format used by many network analysts and researchers. The advantages of using NetFlow over deep packet inspection are that it is easier to collect and process, and it is less privacy intrusive. Many…
Clinical coding is the task of transforming medical information in a patient's health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard…
Biological neural networks (BNNs) have been established as a powerful and adaptive substrate that offer the potential for incredibly energy and data efficient information processing with distinct learning mechanisms. Yet a core challenge to…
Objectives: The vast and complex nature of human genomic sequencing data presents challenges for effective analysis. This review aims to investigate the application of Natural Language Processing (NLP) techniques, particularly Large…
Electroencephalogram (EEG) decoding aims to identify the perceptual, semantic, and cognitive content of neural processing based on non-invasively measured brain activity. Traditional EEG decoding methods have achieved moderate success when…
Background: Everything as Code (EaC) is an emerging paradigm aiming to codify all aspects of modern software systems. Despite its growing popularity, comprehensive industry standards and peer-reviewed research clarifying its scope and…
Over the past several years, DNA sequencing has emerged as one of the driving forces in life-sciences, paving the way for affordable and accurate whole genome sequencing. As genomes represent the entirety of an organism's hereditary…
In this white paper, we present AlphaEvolve, an evolutionary coding agent that substantially enhances capabilities of state-of-the-art LLMs on highly challenging tasks such as tackling open scientific problems or optimizing critical pieces…
Identifying the complete set of functional elements within the human genome would be a windfall for multiple areas of biological research including medicine, molecular biology, and evolution. Complete knowledge of function would aid in the…
Chromosome enumeration is an essential but tedious procedure in karyotyping analysis. To automate the enumeration process, we develop a chromosome enumeration framework, DeepACEv2, based on the region based object detection scheme. The…
Medical coding translates free-text clinical documentation into standardized codes drawn from classification systems that contain tens of thousands of entries and are updated annually. It is central to billing, clinical research, and…
Visual encoding and decoding models act as gateways to understanding the neural mechanisms underlying human visual perception. Typically, visual encoding models that predict brain activity from stimuli and decoding models that reproduce…
Human genomic data carry unique information about an individual and offer unprecedented opportunities for healthcare. The clinical interpretations derived from large genomic datasets can greatly improve healthcare and pave the way for…
Our genomes influence nearly every aspect of human biology from molecular and cellular functions to phenotypes in health and disease. Human genetics studies have now associated hundreds of thousands of differences in our DNA sequence…
Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases…
Determining the types of neurons within a nervous system plays a significant role in the analysis of brain connectomics and the investigation of neurological diseases. However, the efficiency of utilizing anatomical, physiological, or…