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Bio

I'm a PhD candidate in the Molecular Engineering group at the University of Cambridge. I write software and research machine learning methods to facilitate the discovery and characterisation of materials with applications to small-angle scattering. This includes:
  • developing machine learning-assisted small-angle scattering pipelines.
  • creating generative models for inorganic crystal structures, as well as structure-property models to predict their properties.
  • developing segmentation methods to detect, locate and quantify systems of particles from electron microscopy (EM) images.

Publications

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.

Posts

Spectral Graph Convolutions - Fourier Transforms (on Graphs) for the Birdwatcher

Open Source Software

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

Data

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

Fun

Numerai
I compete on Numerai, a data science tournament where I submit predictions weekly and regularly finish in the top 15% and top 5%. Links to some of my best performing models can be found below.
[numer.ai/by32]
Generative Art
I enjoy creating generative art which exploits randomness, motion and colour to produce diverse sets of examples. I have sold many of my pieces and have created a Twitter bot that randomly generates and posts every 6 hours.

Contact:

by256[at]cam.ac.uk