no code implementations • 6 May 2024 • Andac Demir, Elizaveta Solovyeva, James Boylan, Mei Xiao, Fabrizio Serluca, Sebastian Hoersch, Jeremy Jenkins, Murthy Devarakonda, Bulent Kiziltan
Influenced by breakthroughs in LLMs, single-cell foundation models are emerging.
no code implementations • 12 Dec 2023 • Andac Demir, Francis Prael III, Bulent Kiziltan
We explore the underlying topologies and patterns in molecular structures by applying Vietoris-Rips persistent homology across varying scales and parameters such as atomic weight, partial charge, bond type, and chirality.
no code implementations • 17 Nov 2023 • Andac Demir, Bulent Kiziltan
In this study, we present a novel molecular fingerprint generation method based on multiparameter persistent homology.
no code implementations • 24 Apr 2023 • Andac Demir, Elie Massaad, Bulent Kiziltan
To tackle this problem, we introduce a novel loss function, namely Topology-Aware Focal Loss (TAFL), that incorporates the conventional Focal Loss with a topological constraint term based on the Wasserstein distance between the ground truth and predicted segmentation masks' persistence diagrams.
no code implementations • 8 Dec 2022 • Andac Demir, Iya Khalil, Bulent Kiziltan
One of the main challenges in electroencephalogram (EEG) based brain-computer interface (BCI) systems is learning the subject/session invariant features to classify cognitive activities within an end-to-end discriminative setting.
no code implementations • 7 Nov 2022 • Andac Demir, Baris Coskunuzer, Ignacio Segovia-Dominguez, Yuzhou Chen, Yulia Gel, Bulent Kiziltan
In computer-aided drug discovery (CADD), virtual screening (VS) is used for identifying the drug candidates that are most likely to bind to a molecular target in a large library of compounds.