Batu Yildirim | CV Google Scholar Github Twitter LinkedIn


I'm a Research Engineer at InstaDeep in the BioAI team. Previously, I did a PhD in the Molecular Engineering group at the University of Cambridge, where I researched machine learning methods and wrote software for characterization and generation of atomic and nano structures.


Multi-task Scattering-Model Classification and Parameter Regression of Nanostructures from Small-Angle Scattering Data
Batuhan Yildirim, James Doutch and Jacqueline M. Cole
Under review (2023)
Calculating Small-Angle Scattering Intensity Functions from Electron Micrsocopy Images
Batuhan Yildirim, Adam Washington, James Doutch and Jacqueline M. Cole
RSC Adv. (2022)
[paper] [code]
Bayesian Particle Instance Segmentation for Electron Microscopy Image Quantification
Batuhan Yildirim and Jacqueline M. Cole
J. Chem. Inf. Model. (2021)
[paper] [code] [demo]
3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning
Callum J. Court*, Batuhan Yildirim*, Apoorv Jain and Jacqueline M. Cole
J. Chem. Inf. Model. (2020)
*Equal Contribution
[paper] [code]
ImageDataExtractor: A Tool To Extract and Quantify Data from Microscopy Images
Karim T. Mukaddem, Edward J. Beard, Batuhan Yildirim, and Jacqueline M. Cole
J. Chem. Inf. Model. (2019)
[paper] [code] [site]

If you'd like to read any of my publications but can't get past the paywalls, feel free to email me and I'll send you a copy.


Exploring Standard Errors and Their Assumptions: Implications to Ensembles and Randomized Controlled Trials
Spectral Graph Convolutions - Fourier Transforms (on Graphs) for the Birdwatcher

Open Source Software

A Python library for fast computation of 2D and 3D radial distribution functions.
imagedataextractor 2.0
A Python library for nanoparticle electron microscopy image quantification.
[site] [Github]
Open source projects that I have contributed to include TorchEnsemble and ChemDataExtractor.


Electron Microscopy Particle Segmentation (EMPS) Dataset
A diverse collection of 465 electron micrographs and their corresponding particle instance segmentation maps.
[download] [Github]


I compete on Numerai, a quant machine learning tournament where I submit predictions weekly. I achieved the ranks of master (2nd) in 2022 and expert (26th) in 2023. Profile: by256

Contact: by256[at]