biomedical

There are 43 repositories under biomedical topic.

scispacy
allenai / scispacy
A full spaCy pipeline and models for scientific/biomedical documents.
bioinformatics biomedical custom-pipes nlp scientific-documents spacy
Language:Python 1621
alibaba-research / ChineseBLUE
Chinese Biomedical Language Understanding Evaluation benchmark (ChineseBLUE)
benchmark bert biomedical chinese medical natural-language-processing
Language:Python 516
cambridgeltl / visual-med-alpaca
Visual Med-Alpaca is an open-source, multi-modal foundation model designed specifically for the biomedical domain, built on the LLaMa-7B.
biomedical biomedical-image-processing foundation-model large-language-models multimodal
Language:Python 344
caufieldjh / awesome-bioie
🧫 A curated list of resources relevant to doing Biomedical Information Extraction (including BioNLP)
awesome awesome-list bioinformatics biomedical biomedical-data biomedical-language information-extraction medical-informatics natural-language-processing nlp text-mining
309
kyegomez / Med-PaLM
Towards Generalist Biomedical AI
biomedical deep-learning gpt4 multimodal multimodal-deep-learning multimodality opensource
Language:Python 248
zjunlp / Mol-Instructions
[ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models
ai-for-science biomedical dataset instruction-following large-language-models llama molecule natural-language-processing protein science generation mol-instruction datasets instruction instructions resource iclr2024
Language:Python 200
MousaviSajad / SleepEEGNet
SleepEEGNet: Automated Sleep Stage Scoring with Sequence to Sequence Deep Learning Approach
sleep-stage-scoring eeg deep-learning sequence-to-sequence cnn rnn tensorflow biomedical biosignals
Language:Python 192
biocypher
biocypher / biocypher
A unifying framework for biomedical research knowledge graphs
bioinformatics biomedical knowledge-graph neo4j framework ontology postgresql rdf rdfs sql ai-ready retrieval-augmented-generation biochatter
Language:Python 191
vaticle / biograkn
BioGrakn Knowledge Graph
biograkn bioinformatics biomedical knowledge-discovery knowledge-graph
180
Correr-Zhou / RepMode
[CVPR 2023 (Highlight)] Offical implementation of the paper "RepMode: Learning to Re-parameterize Diverse Experts for Subcellular Structure Prediction".
biomedical computer-vision cvpr2023 deep-learning dense-prediction machine-learning multi-task-learning
Language:Python 165
OmooLab / BioxelNodes
For scientific volumetric data visualization in Blender.
biomedical blender geometry-nodes sciart scientific-visualization visualization volume voxel
Language:Python 131
patverga / bran
Full abstract relation extraction from biological texts with bi-affine relation attention networks
biomedical relation-extraction tensorflow
Language:Python 127
Lee-Gihun / MEDIAR
(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"
biomedical cell-biology cell-segmentation instance-segmentation miscroscopy monai multi-modality multi-resolution neurips-2022 pytorch pytorch-implementation pytorch-segmentation vision-transformer
Language:Python 125
SCIRun
SCIInstitute / SCIRun
SCIRun is a Problem Solving Environment, for modeling, simulation and visualization of scientific problems. This is version 5, the upgraded version of SCIRun v4.
c-plus-plus visualization mesh-generation scientific-computing scientific-visualization scientific-computations dataflow-programming python linear-systems forward-problem inverse-problems biomedical open-source boost-libraries cmake qt5 qt6
Language:C++ 125
dlab-berkeley / R-Deep-Learning
Workshop (6 hours): Deep learning in R using Keras. Building & training deep nets, image classification, transfer learning, text analysis, visualization
deep-learning keras tensorflow cloudml biomedical nlp
Language:R 118
medtype
svjan5 / medtype
MedType: Improving Medical Entity Linking with Semantic Type Prediction
bert-as-service biomedical deep-learning entity-linking medical pytorch state-of-the-art
Language:Python 115
grimmlab / MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
microbiome microbiome-analysis microbiome-workflow biomedical best-practices pipeline bioinformatics amplicon-sequencing assembly 16s-rrna metagenomics
Language:Shell 101
dreji18 / Bio-Epidemiology-NER
Recognize bio-medical entities from a text corpus
biomedical epidemiology ner nlp transformers
Language:Python 100
amzn / amazon-weak-ner-needle
Named Entity Recognition with Small Strongly Labeled and Large Weakly Labeled Data
bert ner biomedical biomedical-named-entity-recognition weakly-supervised-learning weak-supervision distant-supervision
Language:Python 99
typedb-osi / typedb-bio
TypeDB Bio: Biomedical Knowledge Graph
bioinformatics biomedical drug-discovery knowledge-base knowledge-discovery knowledge-graph
Language:Python 73
som-shahlab / trove
Weakly supervised medical named entity classification
bert biomedical learning-with-noisy-labels ner ontology pseudo-labeling text-classification umls umls-metathesaurus weak-supervision weakly-supervised-learning
Language:Python 68
GanjinZero / KeBioLM
Improving Biomedical Pretrained Language Models with Knowledge [BioNLP 2021]
language-model pre-training nlp biomedical
Language:Python 63
PlusLabNLP / GEANet-BioMed-Event-Extraction
Code for the paper Biomedical Event Extraction with Hierarchical Knowledge Graphs
event-extraction biomedical covid-19 cord-19 natural-language-processing bert multitask-learning deep-learning
Language:Python 60
BorgwardtLab / S3M
A software package for statistically significant shapelet mining
biomedical biomedical-data-science shapelets significant-pattern-mining time-series time-series-analysis time-series-analysis-tool
Language:C++ 52
farabio
tuttelikz / farabio
:robot: PyTorch toolkit for biomedical imaging :heart:
deep-learning pytorch python biomedical-imaging biomedical models datasets
Language:Python 51
GanjinZero / BioBART
BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model [ACL-BioNLP 2022]
biomedical generative pretrained-language-model
Language:Python 50
GCY / wxECGAnalyzer
This project is for Electrocardiogram(ECG) signal algorithms design and validation, include preprocessing, QRS-Complex detection, embedded system validation, ECG segmentation, label your machine learning dataset, and clinical trial...etc.
qrs-detection heart-rate-variability ecg tompkins labeling pan-tompkins electrocardiogram signal chen-algorithm stm32f4 adaptive-thresholding qrs-complex biomedical ecg-signal ecg-segmentation adaptive-threshold-algorithm biomedical-signal-processing biomedical-engineering
Language:C 45
GCY / Atrial-Fibrillation-Detection-Blood-Pressure-Monitor-Oscillometric-Method-
Atrial Fibrillation Detection Blood Pressure Monitor (Oscillometric Method)
blood-pressure-monitor blood-pressure atrial-fibrillation pid-control pid-codes stm32f4 stm32 biomedical blood-pressure-measurment atrial-fibrillation-detection mercury-manometer motor-drive bpm biomedical-engineering biomedical-signal-processing
Language:C 42
IBT-FMI / SAMRI
Small Animal Magnetic Resonance Imaging via Python.
biomedical fmri functional-connectivity dwi bids fsl neuroimaging small-animals rodent registration
Language:Python 42
HemoCell
UvaCsl / HemoCell
HemoCell is a high-performance suspension code for simulating blood flows developed by the Computational Science Lab at the University of Amsterdam.
biomedical blood-flow hemodynamics hpc lattice-boltzmann
Language:C++ 42
BMDSoftware / neji
Flexible and powerful platform for biomedical information extraction from text
text-mining named-entity-recognition biomedical information-extraction concept-extraction java
Language:JavaScript 39
ericspod / Eidolon
Biomedical Visualization and Analysis Framework
python biomedical rendering data-analysis data-visualization king-college-london medical-imaging medical-image-computing image-registration irtk mirtk pyqt4 ogre3d dicom nifti brc 3d-graphics visualization
Language:Python 38
wangmengsd / pdd-graph
PDD Graph : Bridging MIMIC-III and Linked Data Cloud
linked-open-data rdf-store biomedical emr ehr icu patient drugs diseases
Language:CSS 36
kbogas / medknow
Medical Relations and Entities Extraction
nlp biomedical neo4j semrep metamap relation-extraction umls
Language:Python 35
hemelb-codes / hemelb
A high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries
lattice-boltzmann hemodynamics blood-vessels hpc biomedical
Language:C++ 33
fedbiomed
fedbiomed / fedbiomed
A collaborative learning framework for empowering biomedical research
ai biomedical clinical federated learning analytics collaborative
Language:Python 32