Publications (12)
Differentiable Simulation of a Liquid Argon Time Projection Chamber
Sean Gasiorowski, Yifan Chen, Youssef Nashed +5
Liquid argon time projection chambers (LArTPCs) are widely used in particle detection for their tracking and calorimetric capabilities. The particle physics community actively buil…
Heterogeneous reconstruction of deformable atomic models in Cryo-EM
Youssef Nashed, Ariana Peck, Julien Martel +6
Cryogenic electron microscopy (cryo-EM) provides a unique opportunity to study the structural heterogeneity of biomolecules. Being able to explain this heterogeneity with atomic mo…
BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery
Peter St. John, Dejun Lin, Polina Binder +89
Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increas…
Capturing dynamical correlations using implicit neural representations
Sathya Chitturi, Zhurun Ji, Alexander Petsch +16
The observation and description of collective excitations in solids is a fundamental issue when seeking to understand the physics of a many-body system. Analysis of these excitatio…
CryoAI: Amortized Inference of Poses for Ab Initio Reconstruction of 3D Molecular Volumes from Real Cryo-EM Images
Axel Levy, Frédéric Poitevin, Julien Martel +6
Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us understand the basic building blocks of life. The algorithmic chall…
Real-time sparse-sampled Ptychographic imaging through deep neural networks
Mathew J. Cherukara, Tao Zhou, Youssef Nashed +4
Ptychography has rapidly grown in the fields of X-ray and electron imaging for its unprecedented ability to achieve nano or atomic scale resolution while simultaneously retrieving…
Sparse recovery of undersampled intensity patterns for coherent diffraction imaging at high X-ray energies
Siddharth Maddali, Irene Calvo-Almazan, Jonathan Almer +5
Coherent X-ray photons with energies higher than 50 keV offer new possibilities for imaging nanoscale lattice distortions in bulk crystalline materials using Bragg peak phase retri…
A machine learning photon detection algorithm for coherent X-ray ultrafast fluctuation analysis
Sathya R. Chitturi, Nicolas G. Burdet, Youssef Nashed +8
X-ray free electron laser (XFEL) experiments have brought unique capabilities and opened new directions in research, such as creating new states of matter or directly measuring ato…
Testing the data framework for an AI algorithm in preparation for high data rate X-ray facilities
Hongwei Chen, Sathya R. Chitturi, Rajan Plumley +22
The advent of next-generation X-ray free electron lasers will be capable of delivering X-rays at a repetition rate approaching 1 MHz continuously. This will require the development…
Implicit Neural Representation as a Differentiable Surrogate for Photon Propagation in a Monolithic Neutrino Detector
Minjie Lei, Ka Vang Tsang, Sean Gasiorowski +6
Optical photons are used as signal in a wide variety of particle detectors. Modern neutrino experiments employ hundreds to tens of thousands of photon detectors to observe signal f…
Ptychopy: GPU framework for ptychographic data analysis
Ke Yue, Junjing Deng, Yi Jiang +3
X-ray ptychography imaging at synchrotron facilities like the Advanced Photon Source (APS) involves controlling instrument hardwares to collect a set of diffraction patterns from o…
Phase retrieval for Bragg coherent diffraction imaging at high X-ray energies
Siddharth Maddali, Marc Allain, Wonsuk Cha +6
Coherent X-ray beams with energies keV can potentially enable three-dimensional imaging of atomic lattice distortion fields within individual crystallites in bulk polycry…