Adithya Murali

Kaiyuan Yang, Houjing Huang, Olafs Vandans et al.

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.

Adithya Murali, Lucas Peña, Ranjit Jhala et al.

Several practical tools for automatically verifying functional programs (e.g., Liquid Haskell and Leon for Scala programs) rely on a heuristic based on unrolling recursive function definitions followed by quantifier-free reasoning using SMT solvers. We uncover foundational theoretical properties of this heuristic, revealing that it can be generalized and formalized as a technique that is in fact complete for reasoning with combined First-Order theories of algebraic datatypes and background theories, where background theories support decidable quantifier-free reasoning. The theory developed in this paper explains the efficacy of these heuristics when they succeed, explains why they fail when they fail, and the precise role that user help plays in making proofs succeed.

Abhishek Uppar, Omar Muhammad, Sumanth Prabhu et al.

We consider the problem of \emph{verification modulo tested library contracts} as a step towards automating the verification of client programs that use complex libraries. We formulate this problem as the synthesis of modular contracts for the library methods used by the client that are adequate to prove the client correct, and that also pass the scrutiny of a testing engine that tests the library against these contracts. We also consider a new form of method contracts called \emph{contextual contracts} that arise in this setting that hold in the context of the client program, and can often be simpler and easier to infer than classical modular contracts. We provide a counterexample-guided learning framework to solve this problem, in which the synthesizer interacts with a constraint solver as well as the testing engine in order to infer adequate modular/contextual method contracts and inductive invariants for the client. The main synthesis engines we use are generalizing CHC solvers that are realized using ICE learning algorithms. We realize this framework in a tool called \vmtlc and show its efficacy on benchmarks where clients call large libraries.

Adithya Murali, Atharva Sehgal, Paul Krogmeier et al.

We consider the problem of combining machine learning models to perform higher-level cognitive tasks with clear specifications. We propose the novel problem of Visual Discrimination Puzzles (VDP) that requires finding interpretable discriminators that classify images according to a logical specification. Humans can solve these puzzles with ease and they give robust, verifiable, and interpretable discriminators as answers. We propose a compositional neurosymbolic framework that combines a neural network to detect objects and relationships with a symbolic learner that finds interpretable discriminators. We create large classes of VDP datasets involving natural and artificial images and show that our neurosymbolic framework performs favorably compared to several purely neural approaches.

Umang Mathur, Adithya Murali, Paul Krogmeier et al.

We investigate the decidability of automatic program verification for programs that manipulate heaps, and in particular, decision procedures for proving memory safety for them. We extend recent work that identified a decidable subclass of uninterpreted programs to a class of alias-aware programs that can update maps. We apply this theory to develop verification algorithms for memory safety--- determining if a heap-manipulating program that allocates and frees memory locations and manipulates heap pointers does not dereference an unallocated memory location. We show that this problem is decidable when the initial allocated heap forms a forest data-structure and when programs are streaming-coherent, which intuitively restricts programs to make a single pass over a data-structure. Our experimental evaluation on a set of library routines that manipulate forest data-structures shows that common single-pass algorithms on data-structures often fall in the decidable class, and that our decision procedure is efficient in verifying them.