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95 results for “Interactive Learning”
Bioactivity deep learning for structure-free compound-protein interaction
<p>CPI2M data for "<strong>Bioactivity deep learning for structure-free compound-protein interaction</strong>".</p> <p>CPI2M_main_Ki.csv: Bioactivity data with <strong>pKi </strong>activity type. Used for model training and internal validation.</p> <p>CPI2M_main_Kd.csv: Bioactivity data with <strong>pKd</strong> activity type. Used for model training and internal validation.</p> <p>CPI2M_main_EC50.csv: Bioactivity data with <strong>pEC50 </strong>activity type. Used for model training and internal validation.</p> <p>CPI2M_main_IC50.csv: Bioactivity data with <strong>pIC50 </strong>activity type. Used for model training and internal validation.</p> <p>CPI2M_few_Ki.csv: Bioactivity data with <strong>pKi </strong>activity type. Used for external validation.</p> <p>CPI2M_few_Kd.csv: Bioactivity data with <strong>pKd </strong>activity type. Used for external validation.</p> <p>CPI2M_few_EC50.csv: Bioactivity data with <strong>pEC50 </strong>activity type. Used for external validation.</p> <p>CPI2M_few_IC50.csv: Bioactivity data with <strong>pIC50 </strong>activity type. Used for external validation.</p> <p>potency.csv: BIoactivity data with <strong>pPotency </strong>activity type. Not used currently but can be potentially adopted as classification data for customized use.</p> <p>percentage.csv: BIoactivity data with <strong>Percentage Inhibition </strong>activity type. Not used currently but can be potentially adopted as classification data for customized use.</p> <p>Protein_pretrained_feat.zip: pre-calculated protein feature files with UniProt ID naming. <strong>Should be unzipped</strong> before start model training with CPI2M data.</p> <p> </p> <p>For each .csv data, columns include "<strong>smiles</strong>" (ligand SMILES), "<strong>exp_mean</strong>" (nM bioactivity), "<strong>y</strong>" (neg.log nM, final label), "<strong>cliff_mol</strong>" (whether activity cliff or not), "<strong>split</strong>" (splitting label by activity cliff), "<strong>Uniprot_id</strong>" (UniProt ID for protein), "<strong>Sequence</strong>" (wildtype sequence for protein), and "type_id" (bioactivity type token, pKi =0, pKd=1, pEC50=2, pIC50=3).</p> <p> </p> <p>Please find the project code at https://github.com/gu-yaowen/GGAP-CPI</p> <p> </p>
Using machine learning to integrate genetic and environmental data to model genotype-by-environment interactions
<p>Files generated from the study described in <a href="https://doi.org/10.1101/2024.02.08.579534">Fernandes et. al (2024)</a> .</p> <p>The file "cvs_h2s.csv" comprises the coefficient of variation and the Cullis heritability for each environment.</p> <p>The file "all_predictions.csv" contains the predictions from all the models evaluated, in different cross-validation (CV) scenarios.</p> <p>The file "coincidence_index.csv" has the Coincidence Index (CI) for each CV and models evaluated in our study.</p> <p>Our study used the multi-environment maize yield trials data from the Genomes to Fields 2022 initiative (<a href="https://doi.org/10.1186/s13104-023-06421-z">Lima et. al 2024</a>).</p>
RNA-Protein Interaction Prediction Using Network-Guided Deep Learning
<p>RNA-protein interactions are critical to various life processes, including fundamental translation and gene regulation. Identifying these interactions is vital for understanding the mechanisms underlying life processes. Then, ZHMolGraph is an advanced pipeline that integrates graph neural network sampling strategy and unsupervised large language models to enhance binding predictions for novel RNAs and proteins.</p> <div> </div>
Machine-Learning of Aerosol-Cloud-Climate Interactions Reveals an increased Cloud Fraction
<p>Data presented in the manuscript "Machine-Learning of Aerosol-Cloud-Climate Interactions Reveals an increased Cloud Fraction" by Chen et al. (2022).</p>
Learning to embed lifetime social behavior from interaction dynamics - Data
<p><strong>Interaction matrices and metadata used in "Learning to embed lifetime social behavior from interaction dynamics"</strong></p> <p>The following files are included:</p> <ul> <li>interactions_bn16_sparse.npz and interactions_bn19_sparse.npz: These are the interaction affinity matrices for the BN16 and BN19 datasets as described in the publication. The data is stored as compressed sparse tensors with time on the first, and the individuals on the second and third dimensions. The data was stored using the <a href="http://sparse.pydata.org">pydata/sparse</a> library 0.9.1</li> <li> <p>alive_bn16.csv and alive_bn19.csv: These files contain the dates of emergence (also corresponding to the dates they were introduced into the colonies) and heuristically determined number days alive for all individuals in the interaction matrices. Death dates were determined using a bayesian changepoint model and the number of daily detections of each individual</p> </li> <li> <p>rhythmicity_bn16.csv and rhythmicity_bn19.csv: These files contain the circadian rhythmicity values used in the evaluation of the method. The circadian rhythmicity is the <span class="math-tex">\(R^2\)</span> value of a sine with a 24 hour period fitted to the individuals' movement velocities over a three day window</p> </li> <li> <p>indices_bn16.csv and indices_bn19.csv: These files contain the mapping between the original marker IDs used during the recording of the data (which has gaps, because not all markers were used) and the sequential indices used in the interaction matrices. These files can therefore be used to look up the original ID of an individual based on it's index in the interaction matrix and vice versa</p> </li> <li> <p>time_spent_on_substrates.csv: This data was used for the mapping from factors to the proportion of time spent on various cell substrates (Figure 5). The positions of the individuals were accumulated by minute, and the column "location_descriptor_count" contains the total number of minutes on the respective day that the individual was detected</p> </li> </ul> <p>See <a href="https://doi.org/10.1101/2020.05.06.076943">10.1101/2020.05.06.076943</a> for more details about the bayesian changepoint model, circadian rhythmicity calculation, and location mapping.</p>
Structural Interaction Fingerprints and Machine Learning for predicting and explaining binding of small molecule ligands to RNA: a benchmark dataset
<p><b>Structural Interaction Fingerprints and Machine Learning for predicting and explaining binding of small molecule ligands to RNA: a benchmark dataset.</b></p><p>Ribonucleic acids (RNA) play crucial roles in living organisms as they are involved in key processes necessary for proper cell functioning. Some RNA molecules, such as bacterial ribosomes and precursor messenger RNA, are targets of small molecule drugs, while others, e.g., bacterial riboswitches or viral RNA motifs are considered as potential therapeutic targets. Thus, the continuous discovery of new functional RNA increases the demand for developing compounds targeting them and for methods for analyzing RNA—small molecule interactions. We recently developed fingeRNAt - a software for detecting non-covalent bonds formed within complexes of nucleic acids with different types of ligands. The program detects several non-covalent interactions, such as hydrogen and halogen bonds, ionic, Pi, inorganic ion- and water-mediated, lipophilic interactions, and encodes them as computational-friendly Structural Interaction Fingerprint (SIFt). Here we present the application of SIFts accompanied by machine learning methods for binding prediction of small molecules to RNA targets. We show that SIFt-based models outperform the classic, general-purpose scoring functions in virtual screening. We discuss the aid offered by Explainable Artificial Intelligence in the analysis of the binding prediction models, elucidating the decision-making process, and deciphering molecular recognition processes.</p>
Supporting data for "CoVEffect: Interactive System for Mining the Effects of SARS-CoV-2 Mutations and Variants Based on Deep Learning"
<p>This repository contains the datasets created and extracted for the paper:</p> <p>Giuseppe Serna García, Ruba Al Khalaf, Francesco Invernici, Stefano Ceri, and Anna Bernasconi. 2022.<br> "<strong>CoVEffect</strong>: Interactive System for Mining the <strong>Effects of SARS-CoV-2 Mutations and Variants</strong> Based on Deep Learning". (Available online at http://gmql.eu/coveffect)</p> <p>--------------------------------------------------------------------------------<br> LIST OF FILES WITH DESCRIPTION:<br> --------------------------------------------------------------------------------</p> <p>AdditionalFile1-effects-taxonomy:<br> Descriptions of legal values for the 'Effect' field, based on a categorized taxonomy.</p> <p>AdditionalFile2-levels-taxonomy:<br> Descriptions of legal values for the 'Level' field.</p> <p>AdditionalFile3-training_dataset_target:<br> List of target tuples (manually annotated) of 221 abstracts considered for training the model. For each abstract, target tuples follow the schema ID, DOI, title, entity, effect, level, type (mutation or variant), tuples_count (>1 when an effect/level is shared by multiple entities, #abstracts containing the same effect described in the tuple).</p> <p>AdditionalFile4-validation_dataset_target:<br> List of target tuples (manually annotated) of 50 abstracts considered for validating the prepared prediction model.<br> For each abstract, target tuples follow the schema defined for AdditionalFile3.</p> <p>AdditionalFile5-validation_dataset_highlighted:<br> Textual abstracts of the 50 manuscripts considered for validation; the text used to support the manual target annotations has been highlighted in yellow.</p> <p>AdditionalFile6-validation_dataset_prediction:<br> List of predicted annotations of 50 abstracts considered for validating the prepared prediction model. The file is split in 4 TSV, respectively for entity (a), effect (b), level (c), and whole tuple predictions (d).</p> <p>AdditionalFile7-keywords_query_list:<br> Keyword-based search run on the CORD-19 dataset to extract a relevant subset of abstracts regarding the scope of interest of CoVEffect. The Boolean logic used to combine keywords is explained in the section 'Annotations of the biology-related CORD-19 cluster'.</p> <p>AdditionalFile8-CORD-19_batch_dataset_metadata:<br> Metadata of the 7,230 papers extracted by the keyword-based query in AdditionalFile7.<br> These abstracts have been annotated by the prediction framework.</p> <p>AdditionalFile9-CORD-19_batch_dataset_prediction:<br> List of predicted annotations of 7,230 abstracts extracted from the biology-related cluster of CORD-19.</p> <p>AdditionalFile10-test_dataset_target:<br> List of target tuples (manually annotated) of 100 abstracts randomly selected from the 7,230 extracted as in AdditionalFile8.<br> For each abstract, target tuples follow the schema defined for AdditionalFile3.</p> <p>AdditionalFile11-test_dataset_prediction:<br> List of predicted annotations of 100 abstracts considered for testing the prediction model on a subset of the CORD-19 biology-related cluster. As AdditionalFile6, it is split in 4 TSV, respectively for entity (a), effect (b), level (c), and whole tuple predictions (d).</p>
Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations
<p>MD simulations used in the studies of the publication "<strong>Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations</strong>"</p>
Capturing functional relations in fluid-structure interaction via machine learning
<p>While fluid-structure interaction (FSI) problems are ubiquitous in various applications from cell-biology to aerodynamics, they involve huge computational overhead. In this paper, we adopt a machine learning (ML)-based strategy to bypass the detailed FSI analysis that requires cumbersome simulations in solving the Navier-Stokes (N-S) equations. To mimic the effect of fluid on an immersed beam, we have introduced dissipation into the beam model with time-varying forces acting on it. The forces in a discretized setup have been decoupled via an appropriate linear algebraic operation, which generates the ground truth force/moment data for the ML analysis. The adopted ML technique, symbolic regression, generates computationally tractable functional forms to represent the force/moment with respect to space and time. These estimates are fed into the dissipative beam model to generate the immersed beam's deflections over time, which are in conformity with the detailed FSI solutions. Numerical results demonstrate that the ML-estimated continuous force and moment functions are able to accurately predict the beam deflections under different discretizations.</p>
Data from: Neural interactions in the human frontal cortex dissociate reward and punishment learning
<p>How human prefrontal and insular regions interact while maximizing rewards and minimizing punishments is unknown. Capitalizing on human intracranial recordings, we demonstrate that the functional specificity toward reward or punishment learning is better disentangled by interactions compared to local representations. Prefrontal and insular cortices display non-selective neural populations to reward and punishment. The non-selective responses, however, give rise to context-specific interareal interactions. We identify a reward subsystem with redundant interactions between the orbitofrontal and ventromedial prefrontal cortices, with a driving role of the latter. In addition, we find a punishment subsystem with redundant interactions between the insular and dorsolateral cortices, with a driving role of the insula. Finally, switching between reward and punishment learning is mediated by synergistic interactions between the two subsystems. These results provide a unifying explanation of distributed cortical representations and interactions supporting reward and punishment learning.</p>
Success in Mobile and Ubiquitous Learning: Indicators of Effectiveness-Figure 7. Level of interactivity of the studies
<p>Figure 7 presents the level of interactivity in using mobile devices. Sixty percent of the cases involved only one-way access for information either online or offline, while 8% involved social interaction with information exchange among learners. Also 32% of the cases included both levels of interactivity in learning.</p>
Deep learning model for characterizing protein-RNA interactions from sequence at single-base resolution
<p> </p> <p><a href="https://zenodo.org/api/records/14021440/draft/files/encode_eclip.h5/content" target="_blank" rel="noopener noreferrer">encode_eclip.h5</a> - This file contains the training, validation, and test data for the Reformer model.</p> <p><a href="https://zenodo.org/api/records/14021440/draft/files/encode_eclip_bc.h5/content" target="_blank" rel="noopener noreferrer">encode_eclip_bc.h5</a> - This file contains the training, validation, and test data for the Reformer-BC model.</p> <p><a href="https://zenodo.org/api/records/14027315/draft/files/Reformer-code.zip/content" target="_blank" rel="noopener">Reformer-code.zip</a> - This file contains the training code of Reformer.</p>
CNN models and training, validation and test datasets for "PlotMI: interpretation of pairwise interactions and positional preferences learned by a deep learning model from sequence data"
<p>Convolutional neural network (CNN) models and their respective training, validation and test datasets used in manuscript:</p> <p>Tuomo Hartonen, Teemu Kivioja and Jussi Taipale, "PlotMI: interpretation of pairwise interactions and positional preferences learned by a deep learning model from sequence data"</p>
BISCUIT: Causal Representation Learning from Binary Interactions
<p>This repository contains the datasets from the paper "BISCUIT: Causal Representation Learning from Binary Interactions" (<a href="https://phlippe.github.io/BISCUIT/">link</a>) by Phillip Lippe, Sara Magliacane, Sindy Löwe, Yuki M. Asano, Taco Cohen, Efstratios Gavves. </p> <p><strong>iTHOR Embodied AI </strong>- The Embodied AI dataset is generated with the iTHOR simulator. We use the default kitchen environment, FloorPlan10, and position the robot in front of the kitchen counter. The robot interacts with different objects in the environment, including a Microwave, cabinet, stove, and an egg. For more details on the dataset, see <a href="https://github.com/phlippe/BISCUIT">our GitHub repository</a> and the appendix of our paper.</p> <p><strong>CausalWorld </strong>- The CausalWorld environment implements a tri-finger robot which can interact with a cube in the center of a stage. We additionally introduce causal variables for the friction parameters of the stage, floor and cube, as well as color changes. For more details on the dataset as well as the code to generate this dataset, see <a href="https://github.com/phlippe/BISCUIT">our GitHub repository</a> and the appendix of our paper.</p> <p><strong>Voronoi</strong> - The Voronoi benchmark allows for creating causal systems with arbitrary number of causal variables and causal graphs. We provide datasets with 6 and 9 variables, as well as systems with minimal number of interactions. For details, see <a href="https://github.com/phlippe/BISCUIT">our GitHub repository</a> and our paper.</p>
Data and analytical codes for: Learning beyond-pairwise interactions enables the bottom-up prediction of microbial community structure
<p>Data and analytical codes for: Ishizawa et al. (2023) Learning beyond-pairwise interactions enables the bottom-up prediction of microbial community structure, bioRxiv, 2023.07.04.546222</p> <p> https://www.biorxiv.org/content/10.1101/2023.07.04.546222v1</p> <p> </p>
Capturing functional relations in fluid-structure interaction via machine learning
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Data from: Neural interactions in the human frontal cortex dissociate reward and punishment learning
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The dataset used in the article "Evidential Deep Learning for Guided Drug-Target Interaction Prediction"
<p>The file consists of two parts, the first part is the feature file used for model training and the second part is the saved model.</p> <p>bond_angle file is the feature file for the drugbank dataset, KIBA file is the feature file for the kiba dataset, davis is the feature file for the davis dataset. case_drugbank is the dungbank feature file for the independent test set and case_len_drug is the feature file for the patent validation dataset in the TKIs feature file.len_vs is the feature file for TKIs virtual screening dataset.</p> <p>In the runs folder, the models saved by random division on the Drugbank, KIBA, and Davis datasets are stored.</p> <p>The <a href="https://zenodo.org/api/records/14056305/draft/files/bert_weights_encoderMedium_10.h5/content" target="_blank" rel="noopener noreferrer">bert_weights_encoderMedium_10.h5</a> is the parameter for the small molecule pre-training model, MG-BERT.</p>
LABind: Identifying Protein Binding Ligand-Aware Sites via Learning Interactions Between Ligand and Protein
<p>This dataset contains the three datasets used in LABind. For each dataset, we have saved the corresponding FASTA sequence files, the associated labels (0 for non-binding and 1 for binding), and the corresponding PDB files.</p>
PIGNet: A physics-informed deep learning model toward generalized drug-target interaction predictions
<p>Training, test datasets of the paper "PIGNet: A physics-informed deep learning model toward generalized drug-target interaction predictions".</p>
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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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.