Applying Deep Reinforcement Learning to the HP Model for Protein Structure Prediction

A central problem in computational biophysics is protein structure prediction, i.e., finding the optimal folding of a given amino acid sequence. This problem has been studied in a classical abstract model, the HP model, where the protein is modeled as a sequence of H (hydrophobic) and P (polar) amino acids on a lattice. The objective is to find conformations maximizing H-H contacts. It is known that even in this reduced setting, the problem is intractable (NP-hard). In this work, we apply deep reinforcement learning (DRL) to the two-dimensional HP model. We can obtain the conformations of best known energies for benchmark HP sequences with lengths from 20 to 50. Our DRL is based on a deep Q-network (DQN). We find that a DQN based on long short-term memory (LSTM) architecture greatly enhances the RL learning ability and significantly improves the search process. DRL can sample the state space efficiently, without the need of manual heuristics. Experimentally we show that it can find multiple distinct best-known solutions per trial. This study demonstrates the effectiveness of deep reinforcement learning in the HP model for protein folding.

Augmenting Neural Nets with Symbolic Synthesis: Applications to Few-Shot Learning

We propose symbolic learning as extensions to standard inductive learning models such as neural nets as a means to solve few shot learning problems. We device a class of visual discrimination puzzles that calls for recognizing objects and object relationships as well learning higher-level concepts from very few images. We propose a two-phase learning framework that combines models learned from large data sets using neural nets and symbolic first-order logic formulas learned from a few shot learning instance. We develop first-order logic synthesis techniques for discriminating images by using symbolic search and logic constraint solvers. By augmenting neural nets with them, we develop and evaluate a tool that can solve few shot visual discrimination puzzles with interpretable concepts.