BioGeek

Staff Research engineer at @instadeepai – Machine Learning for personalized cancer vaccines, de novo peptide sequencing and signal peptides.

@instadeepaiCape Town, South Africa

Pinned Repositories

50-examples
Contains the text of a book describing interesting examples of Python programming for use in teaching. An alternate title was "The Python Teaching Cookbook".
Language:JavaScript3 1 026
adventofcode
My solutions of Advent Of Code in Python
Language:Python2 1 01
aima
Python implementation of algorithms from Russell and Norvig's Artificial Intelligence: A Modern Approach.
Language:Python8 4 04
euler
My solutions to Project Euler
Language:Python10 2 00
hackathon_indaba_senegal_2024
Language:Jupyter Notebook1 3 10
hackathon_indabaX_2024
Data and starter notebooks for the locust breeding ground prediction hackaton
Language:Jupyter Notebook3 2 04
hackathon_IndabaX_2025_mlip
Language:Jupyter Notebook54
magic
Scanner for decks of cards with bar codes printed on card edges
Language:Swift4 0 00
InstaNovo
De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments
Language:Python101 8 3224
winnow
Confidence control and FDR estimation for de novo peptide sequencing
Language:Python61

BioGeek's Repositories

BioGeek/euler
My solutions to Project Euler
Language:Python10 2 00
BioGeek/hackathon_IndabaX_2025_mlip
Language:Jupyter Notebook54
BioGeek/os-proteomics
View point in Open source in Proteomics
1 0 0
BioGeek/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell0 0
BioGeek/bpe-match
BioGeek/deep-representation-learning-book
Learning Deep Representations of Data Distributions
BioGeek/DEgym
A LLM-friendly framework for translating dynamical equations to gymnasium-compatible RL environments.
BioGeek/DeNovo_Benchmark
Benchmarking several SOTA de novo sequencing tools on the metaproteomics dataset
BioGeek/denovo_benchmarks
Language:HTML1
BioGeek/example-get-started-experiments
Get started DVC project
Language:Python
BioGeek/flash-attention
Fast and memory-efficient exact attention
Language:Python0 0
BioGeek/GlycoNovo
BioGeek/gpt-oss
gpt-oss-120b and gpt-oss-20b are two open-weight language models by OpenAI
BioGeek/InstaGeo-E2E-Geospatial-ML
A python package for end-to-end geospatial machine learning using multispectral earth observation data such as NASA HLS.
Language:Python0 0
BioGeek/InstaNovo
Language:Python0 01
BioGeek/MassNet-DDA
MassNet-DDA
BioGeek/metalic
Meta in-context learning for protein fitness prediction
BioGeek/mlip
Library for efficient training and application of Machine Learning Interatomic Potentials (MLIP)
Language:Python
BioGeek/ModernBERT
Bringing BERT into modernity via both architecture changes and scaling
Language:Python0 0
BioGeek/mojo-gpu-puzzles
Learn GPU Programming in Mojo🔥 by Solving Puzzles
BioGeek/mzpeaks
A Rust crate for mass spectral peaks
BioGeek/nanochat
The best ChatGPT that $100 can buy.
BioGeek/Ninikske
Language:CSS1
BioGeek/nucleotide-transformer
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Language:Jupyter Notebook0 0
BioGeek/PDV
PDV: an integrative proteomics data viewer
BioGeek/protein-structure-tokenizer
Official implementation of "Learning the language of protein structures"
Language:Python0 0
BioGeek/psi-ms-CV
HUPO-PSI mass spectrometry CV
BioGeek/SimMS
GPU-Accelerated Cosine Similarity for Tandem Mass Spectrometry
BioGeek/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
Language:Python0 0
BioGeek/torchtitan
A PyTorch native platform for training generative AI models