GitHub topics: biomedical

Repositories

msamprovalaki/Exploring-Multimodal-Large-Language-Models-for-Medical-Image-Captioning

This repository includes the code for my Master Thesis, which investigates the application of Multimodal Large Language Models (MLLMs) for medical image captioning

Language: Python - Size: 5.45 MB - Last synced at: about 18 hours ago - Pushed at: about 19 hours ago - Stars: 6 - Forks: 0

khiemducdoan/MyBachelorThesis

This is my project for my Bachelor Thesis.

Language: Jupyter Notebook - Size: 24.5 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0

fedbiomed/fedbiomed

A collaborative learning framework for empowering biomedical research

Language: Python - Size: 51.9 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 51 - Forks: 9

MartinPdeS/FlowCyPy

Python package for FlowCytometry simulation and development toolbox.

Language: Jupyter Notebook - Size: 176 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 2 - Forks: 0

typedb-osi/typedb-bio

TypeDB Bio: Biomedical Knowledge Graph

Language: Python - Size: 41.1 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 86 - Forks: 33

epigen/MrBiomics

MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses

Language: R - Size: 10.2 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 50 - Forks: 1

skar-2274/Muscle-Contraction-Motion-Detection

A script to plot traces of muscle contractions from video recordings. This is part of my ongoing PhD work.

Language: Python - Size: 27.3 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

dimexideas/microinfusora

Micro Infusora de Código Abierto

Size: 1000 Bytes - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 7 - Forks: 0

zjunlp/Mol-Instructions

[ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models

Language: Python - Size: 16.5 MB - Last synced at: 4 days ago - Pushed at: 7 months ago - Stars: 275 - Forks: 15

kyegomez/Med-PaLM

Towards Generalist Biomedical AI

Language: Python - Size: 850 KB - Last synced at: 12 days ago - Pushed at: over 1 year ago - Stars: 383 - Forks: 53

hit-webinar/hit-webinar.github.io

关注医疗智能科技相关的中文网络研讨会

Language: JavaScript - Size: 135 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 3 - Forks: 1

Cardman08/Excel2eLabFTW-CSV

Convert Excel lab inventories to eLabFTW-compatible CSVs with optional structured metadata

Language: R - Size: 80.1 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

techthumb1/KGNN-Drug-Drug-Interaction-DDI-Prediction

A deep learning application for predicting drug-drug interactions using Graph Neural Networks (GraphSAGE) and BioKG, with explainable AI visualizations via D3.js.

Language: Jupyter Notebook - Size: 31.5 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 0

Abhishek-Atole/Classification-of-an-EMG-Signal-Using-CNN

Classification of EMG Signal Using Convolution Neural Network (Sliding Window Technique, Root Mean Square , Fourier Transform)

Language: Jupyter Notebook - Size: 8.73 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 1 - Forks: 0

allenai/scispacy

A full spaCy pipeline and models for scientific/biomedical documents.

Language: Python - Size: 237 MB - Last synced at: 16 days ago - Pushed at: 6 months ago - Stars: 1,814 - Forks: 234

plandes/mimicsid

MIMIC-III corpus parsing and section prediction with MedSecId (COLING paper)

Language: Python - Size: 387 KB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 4 - Forks: 0

slinusc/medical_RAG_system

Enhancing Medical Question-Answering System through Advanced Information Retrieval Strategies and Integration of GPT-3.5

Language: Jupyter Notebook - Size: 38.2 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 14 - Forks: 2

biocypher/biocypher

A unifying framework for biomedical research knowledge graphs

Language: Python - Size: 21.9 MB - Last synced at: 15 days ago - Pushed at: 17 days ago - Stars: 253 - Forks: 37

OmooLab/BioxelNodes

For scientific volumetric data visualization in Blender.

Language: Python - Size: 62 MB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 299 - Forks: 23

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.

Language: Python - Size: 32.9 MB - Last synced at: 24 days ago - Pushed at: about 1 year ago - Stars: 385 - Forks: 42

stephaniehicks/stephaniehicks.github.io

Website for Stephanie C. Hicks

Language: JavaScript - Size: 20.9 MB - Last synced at: 28 days ago - Pushed at: 29 days ago - Stars: 1 - Forks: 0

dinhngoc267/a-metric-learning-based-method-for-biomedical-entity-linking

A Metric learning-based Method for Biomedical Entity Linking

Language: Python - Size: 72.3 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

BioDataFuse/pyBiodatafuse

Python package for biodatafuse project.

Language: Python - Size: 39.4 MB - Last synced at: 18 days ago - Pushed at: 19 days ago - Stars: 6 - Forks: 10

chop-dbhi/data-models

Collection of various biomedical data models in parseable formats.

Size: 9.3 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 28 - Forks: 8

hemelb-codes/hemelb

A high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries

Language: C++ - Size: 46.6 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 38 - Forks: 14

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.

Language: C++ - Size: 172 MB - Last synced at: 17 days ago - Pushed at: 28 days ago - Stars: 131 - Forks: 73

malbiruk/PubMedSummarizer

LLM-assistant that searches PubMed, retrieves abstracts or full-texts, and generates answers using OpenAI ChatGPT. Features a custom RAG pipeline, semantic search, and knowledge graph generation.

Language: Python - Size: 474 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 1

LIRuixuan0407/Biomedical-OOP-in-CPP

Language: Jupyter Notebook - Size: 1.67 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

typedb/biograkn 📦

BioGrakn Knowledge Graph

Size: 89.3 MB - Last synced at: 24 days ago - Pushed at: over 4 years ago - Stars: 183 - Forks: 52

ChiShengChen/pytorch_deep_learning_medimg_tutorial

This project simply implements three common deep learning models (VGG16, ResNet18, ViT) for medical image classification tasks using the PathMNIST dataset.

Language: Python - Size: 60.5 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 16 - Forks: 0

Alex-J-Conroy/sleep-stage-prediction

Predicts sleep vs awake states using wearable ENMO data and ML models.

Language: Jupyter Notebook - Size: 1.95 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

KVSlab/morphMan

A collection of tools for manipulation of morphological features in patient-specific geometries

Language: Python - Size: 59.5 MB - Last synced at: about 24 hours ago - Pushed at: 8 months ago - Stars: 32 - Forks: 13

caufieldjh/awesome-bioie

🧫 A curated list of resources relevant to doing Biomedical Information Extraction (including BioNLP)

Size: 588 KB - Last synced at: 25 days ago - Pushed at: about 1 year ago - Stars: 371 - Forks: 33

kyegomez/SimpleUnet

An simple implementation of Unet because all the implementations i've seen are wayy tooo complicated.

Language: Python - Size: 205 KB - Last synced at: 30 days ago - Pushed at: 7 months ago - Stars: 9 - Forks: 1

dreji18/Bio-Epidemiology-NER

Recognize bio-medical entities from a text corpus

Language: Python - Size: 16.3 MB - Last synced at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 120 - Forks: 9

alisonmitchell/Biomedical-Knowledge-Graph

Information extraction from unstructured text to build a knowledge graph using techniques from traditional NLP to pre-trained transformers and LLMs for NER and Linking, and Relation Extraction.

Language: Jupyter Notebook - Size: 26.3 MB - Last synced at: 2 months ago - Pushed at: 6 months ago - Stars: 8 - Forks: 0

mikeroyal/CNT-Guide

Carbon Nanotubes (CNTs) Guide

Language: MATLAB - Size: 47.9 KB - Last synced at: 29 days ago - Pushed at: over 3 years ago - Stars: 8 - Forks: 1

CHAVI-India/draw

Multi-Site DICOM AutoSegmentation with Parallel NNUNet models

Language: Python - Size: 6.58 MB - Last synced at: 29 days ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0

LUKE-ZZ/thuthesis-biomedical

清华大学生物，医学，药学等相关专业的毕业论文latex模板。也适用于其他专业。适合本硕博毕业论文和博后报告。本模板在tuna协会的thuthesis项目基础上，增补了和生医药相关同学的内容，也增添了对latex新手更加友好的注释。

Size: 3.4 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 18 - Forks: 3

A specialized image analysis tool for automated detection and analysis of dendritic spines in neuronal images. 2D Span Auto streamlines workflow for neuroscience researchers with intuitive modules for image processing, dendrite extraction, and morphological analysis. The software features multiple denoising and binarization methods, accurate spine

Language: C++ - Size: 13.7 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

zekaouinoureddine/BioMed-LLaMa-3

BioMed-LLaMa-3: Instruction-Efficient Fine-Tuning of Large Language Models for Improved Biomedical Language Understanding

Size: 182 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Yijia-Xiao/Know2BIO

Know2BIO: A Comprehensive Dual-View Benchmark for Evolving Biomedical Knowledge Graphs

Language: Python - Size: 74.1 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 4

sauravmishra1710/UNet-Plus-Plus---Brain-Tumor-Segmentation

Brain tumor segmentation using UNet++ Architecture . Implementation of the paper titled - UNet++: A Nested U-Net Architecture for Medical Image Segmentation @ https://arxiv.org/abs/1807.10165

Language: Jupyter Notebook - Size: 36.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 15 - Forks: 1

fairdataihub/FAIR-AMD-OCT-paper-code

Code associated with the paper on FAIR assessment of AMD-related datasets containing OCT data

Language: Jupyter Notebook - Size: 1.27 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

AstraBert/BioMedicalPapersBot

A Gradio bot to retrieve PubMed papers' title, doi, authors and publication date based on general search terms or on specific publication names

Language: Python - Size: 321 KB - Last synced at: 4 days ago - Pushed at: 7 months ago - Stars: 3 - Forks: 1

biodatlab/biodatlab.github.io

Website for Biomedical and Data (Bio-Dat) lab at Mahidol University, Thailand

Language: JavaScript - Size: 69.8 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 18 - Forks: 16

lasigeBioTM/BENT

Biomedical Term Annotator

Language: Python - Size: 6.48 MB - Last synced at: 19 days ago - Pushed at: 3 months ago - Stars: 9 - Forks: 1

qanastek/DrBERT

DrBERT: A Robust Pre-trained Model in French for Biomedical and Clinical domains

Language: Python - Size: 87.9 KB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 19 - Forks: 1

geniusrise/awesome-healthcare-datasets

Healthcare and biomedical datasets, for AI/ML

Size: 42 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 26 - Forks: 7

sclayton33/awesome-biomedical-stuff

Collection of resources to help make biomedical research easier and more efficient.

Size: 1.39 MB - Last synced at: 30 days ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

AxelFougues/Lodestone-biomagnet-tools

Practical biomagnet stimulators for science, development and entertainment! Open source!

Size: 98.5 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 9 - Forks: 0

kimiarezaei/Heart-Rate-features

Language: Jupyter Notebook - Size: 1.89 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

SPerekrestova/BiomedNER 📦

MaaS for MedsRecognition Project. Uses a pre-trained SciSpacy biomedical NER model and RxNorm mapping for pipeline

Language: Python - Size: 39.1 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

kbogas/medknow

Medical Relations and Entities Extraction

Language: Python - Size: 118 KB - Last synced at: 8 days ago - Pushed at: almost 3 years ago - Stars: 36 - Forks: 13

kaledhoshme123/kaledhoshme123

Size: 46.9 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

marcelomaurin/doctor

Sistema de Analise Biomédica.

Language: C - Size: 542 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

BorgwardtLab/S3M

A software package for statistically significant shapelet mining

Language: C++ - Size: 2.88 MB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 53 - Forks: 8

wangmengsd/pdd-graph

PDD Graph : Bridging MIMIC-III and Linked Data Cloud

Language: CSS - Size: 1.15 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 37 - Forks: 5

NathanLeroux-git/OnlineTransformerWithSpikingNeurons

This code is the implementation of the Spiking Online Transformer of the paper "Online Transformers with Spiking Neurons for Fast Prosthetic Hand Control". It predicts finger position using a surface Elecromyography regression.

Language: Python - Size: 91.8 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 6 - Forks: 0

engnadeau/cv

My personal CV that's automatically generated using the following tech stack: LaTeX, XeTeX, GitHub Actions, Docker, GitHub Pages, Jamstack

Language: TeX - Size: 2.19 MB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 2

fasombi/RhysCornelious.github.io-BuddyEnhancedv1 Fork of RhysCornelious/RhysCornelious.github.io

I forked my friend Rhys Cornelious's portfolio to boost its visibility through optimized SEO practices and make his innovative projects more accessible. This also leverages GitHub's domain authority, aiming to rank his work higher in search queries, showcasing his passion and skills to a wider audience.

Language: HTML - Size: 18.2 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

ddsssoftware/ddss

Differential Diagnosis Support System

Language: CSS - Size: 24.4 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

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.

Language: C - Size: 12.3 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 53 - Forks: 22

amzn/amazon-weak-ner-needle 📦

Named Entity Recognition with Small Strongly Labeled and Large Weakly Labeled Data

Language: Python - Size: 104 KB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 100 - Forks: 27

TheChymera/behaviopy

Behavioral data analysis and plotting in Python.

Language: Python - Size: 144 KB - Last synced at: about 2 months ago - Pushed at: almost 5 years ago - Stars: 26 - Forks: 14

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

Language: R - Size: 64.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 124 - Forks: 37

carpentries-incubator/fair-for-busy-biologists

A short course on FAIR and data managment for biomedical research

Size: 50.8 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 1 - Forks: 0

sdsc-ordes/demo-biomedit-workflow

Proof of concept workflow for running tasks in a restricted hospital environment.

Language: Nextflow - Size: 601 KB - Last synced at: 21 days ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0

GCY/Atrial-Fibrillation-Detection-Blood-Pressure-Monitor-Oscillometric-Method-

Atrial Fibrillation Detection Blood Pressure Monitor (Oscillometric Method)

Language: C - Size: 37 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 48 - Forks: 18

GCY/Pulse-Oximeter-with-MAX3010X

This project is MAX3010x library for STM32F4

Language: C - Size: 19.1 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 28 - Forks: 11

sirisacademic/AIObioEnts

AIObioEnts, and all-in-one biomedical named-entity recognition following the all-in-one NER scheme

Language: Python - Size: 42.7 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

sourceduty/Medical_Equipment

♿ Research and development of medical equipment.

Size: 28.2 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0

SyedAshhadIbrar/ECG-Signal-Processing-Artifact-and-Noise-Removal

This repository contains a method on enhancing ECG (Electrocardiography) signal quality by removing common artifacts and noise using wavelet-based processing. The project processes 30-minute ECG recordings, targeting issues like powerline interference, baseline drift, EMG noise, and motion artifacts.

Language: Python - Size: 2.12 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

khaihernlow/Shen-Biomedical-Website

Language: JavaScript - Size: 1.81 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

GanjinZero/BioBART

BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model [ACL-BioNLP 2022]

Language: Python - Size: 117 KB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 52 - Forks: 4

plandes/dsprov

Provenience of discharge summaries Pythonic access (BioNLP paper)

Language: Python - Size: 170 KB - Last synced at: 9 days ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

hpi-dhc/ggponc

GGPONC - The German Clinical Guideline Corpus for Oncology

Language: Jupyter Notebook - Size: 860 KB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 2 - Forks: 2

raamana/pyradigm

Research data management in biomedical and machine learning applications

Language: Python - Size: 7.25 MB - Last synced at: about 24 hours ago - Pushed at: about 2 years ago - Stars: 29 - Forks: 12

kbogas/DDI_BLKG

Drug-Drug Interaction Prediction on a Biomedical Literature Knowledge Graph

Language: Python - Size: 362 KB - Last synced at: 8 days ago - Pushed at: 12 months ago - Stars: 8 - Forks: 4

RJi86/PankVision-3D

Fully Automatic Pancreas Segmentation using 3D Computer Vision Neural Networks

Language: Jupyter Notebook - Size: 13.6 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 0

fairdataihub/codefair-BOSC-2024

Material for the codefair presentations at BOSC 2024

Size: 1.74 MB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

WheelsAndScripts/gene-expression-analysis

A biomedical data mining project. The goal is to identify groups of genes that exhibit similar expression patterns within an RNA sequence of Saccharomyces cerevisiae (a species of yeast). These groups often indicate that the genes may share similar biological functions.

Language: Python - Size: 280 KB - Last synced at: 7 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0