Popularity Prediction for Social Media over Arbitrary Time Horizons
Daniel Haimovich, Dima Karamshuk, Thomas Leeper, Evgeniy Riabenko, Milan Vojnovic
International Conference on Learning Representations (ICLR)
We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that incorporate knowledge of physical principles and features that are the complex product of several decades of research and tuning. To evaluate the model, we benchmark on the rotamer recovery task, the problem of predicting the conformation of a side chain from its context within a protein structure, which has been used to evaluate energy functions for protein design. The model achieves performance close to that of the Rosetta energy function, a state-of-the-art method widely used in protein structure prediction and design. An investigation of the model’s outputs and hidden representations finds that it captures physicochemical properties relevant to protein energy.
Daniel Haimovich, Dima Karamshuk, Thomas Leeper, Evgeniy Riabenko, Milan Vojnovic
Liqi Yan, Qifan Wang, Yiming Cu, Fuli Feng, Xiaojun Quan, Xiangyu Zhang, Dongfang Liu
Barlas Oğuz, Xilun Chen, Vladimir Karpukhin, Stan Peshterliev, Dmytro Okhonko, Michael Schlichtkrull, Sonal Gupta, Yashar Mehdad, Wen-tau Yih