Batu Yildirim

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.

Publications

• Multi-task Scattering-Model Classification and Parameter Regression of Nanostructures from Small-Angle Scattering Data
  Batuhan Yildirim, James Doutch and Jacqueline M. Cole
  RSC Digit. Discov. (2024)
  [paper] [code]
• 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]

Posts

• Mutliple Regression: Maximum Likelihood Estimation, Ordinary Least Squares and Ridge Regression
• Standard Errors and Their Assumptions: Implications to Ensembles and Randomized Controlled Trials
• Spectral Graph Convolutions - Fourier Transforms (on Graphs)

Software

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

Datasets

• SAS-55M-20k
  A dataset of 1.1 million theoretical 1-D SAS intensities with scattering-model class labels and their continuous parameters.
  [download] [GitHub]
• Electron Microscopy Particle Segmentation (EMPS) Dataset
  A diverse collection of 465 electron micrographs and their corresponding particle instance segmentation maps.
  [download] [GitHub]

Fun

• Numer.ai
  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]