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5 results for “DNA language models”
Transfer learning and DNA language models enhance transcription factor binding predictions
<p>This is the dataset for replicating the results of the paper called "Transfer learning and DNA language models enhance transcription factor binding predictions" by Ekin Deniz Aksu and Martin Vingron.</p> <p>See https://github.com/ekinda/tfbs_prediction_paper</p>
Species-aware DNA language modeling - data
<p>Data accompanying the publication Species-aware DNA language modeling.</p> <p>For code, see: https://github.com/DennisGankin/species-aware-DNA-LM (for the latest version) or the code.zip file.</p> <p>The data directory contains model checkpoints, baselines models, evaluation results and datasets used for training, testing and downstream tasks. It has the following structure:</p> <p>data/ Datasets and subdirectories</p> <p> - data/results/ Results from different test runs</p> <p> - data/models/ Model checkpoints</p> <p> - data/baselines/ Baseline models</p>
Data from: Markovian language model of the DNA and its information content
This work proposes a Markovian memoryless model for the DNA that simplifies enormously the complexity of it. We encode nucleotide sequences into symbolic sequences, called words, from which we establish meaningful length of words and groups of words that share symbolic similarities. Interpreting a node to represent a group of similar words and edges to represent their functional connectivity allows us to construct a network of the grammatical rules governing the appearance of groups of words in the DNA. Our model allows us to predict the transition between groups of words in the DNA with unprecedented accuracy, and to easily calculate many informational quantities to better characterize the DNA. In addition, we reduce the DNA of known bacteria to a network of only tens of nodes, show how our model can be used to detect similar (or dissimilar) genes in different organisms, and which sequences of symbols are responsible for most of the information content of the DNA. Therefore, the DNA can indeed be treated as a language, a Markovian language, where a 'word' is an element of a group, and its grammar represents the rules behind the probability of transitions between any two groups.
Data from: Markovian language model of the DNA and its information content
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DNA language models reveal the architecture of nucleotide dependencies in genomes
GEO Series GSE271937. Escherichia coli. 1 samples. Type: Other.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.