Andre Beckus

Ismail Alkhouri, Sumit Jha, Andre Beckus et al.

Protein folding neural networks (PFNNs) such as AlphaFold predict remarkably accurate structures of proteins compared to other approaches. However, the robustness of such networks has heretofore not been explored. This is particularly relevant given the broad social implications of such technologies and the fact that biologically small perturbations in the protein sequence do not generally lead to drastic changes in the protein structure. In this paper, we demonstrate that AlphaFold does not exhibit such robustness despite its high accuracy. This raises the challenge of detecting and quantifying the extent to which these predicted protein structures can be trusted. To measure the robustness of the predicted structures, we utilize (i) the root-mean-square deviation (RMSD) and (ii) the Global Distance Test (GDT) similarity measure between the predicted structure of the original sequence and the structure of its adversarially perturbed version. We prove that the problem of minimally perturbing protein sequences to fool protein folding neural networks is NP-complete. Based on the well-established BLOSUM62 sequence alignment scoring matrix, we generate adversarial protein sequences and show that the RMSD between the predicted protein structure and the structure of the original sequence are very large when the adversarial changes are bounded by (i) 20 units in the BLOSUM62 distance, and (ii) five residues (out of hundreds or thousands of residues) in the given protein sequence. In our experimental evaluation, we consider 111 COVID-19 proteins in the Universal Protein resource (UniProt), a central resource for protein data managed by the European Bioinformatics Institute, Swiss Institute of Bioinformatics, and the US Protein Information Resource. These result in an overall GDT similarity test score average of around 34%, demonstrating a substantial drop in the performance of AlphaFold.

Suraj Singireddy, Precious Nwaorgu, Andre Beckus et al.

Reinforcement learning (RL) is a powerful tool for finding optimal policies in sequential decision processes. However, deep RL methods have two weaknesses: collecting the amount of agent experience required for practical RL problems is prohibitively expensive, and the learned policies exhibit poor generalization on tasks outside the training data distribution. To mitigate these issues, we introduce automaton distillation, a form of neuro-symbolic transfer learning in which Q-value estimates from a teacher are distilled into a low-dimensional representation in the form of an automaton. We then propose methods for generating Q-value estimates where symbolic information is extracted from a teacher's Deep Q-Network (DQN). The resulting Q-value estimates are used to bootstrap learning in the target discrete and continuous environment via a modified DQN and Twin-Delayed Deep Deterministic (TD3) loss function, respectively. We demonstrate that automaton distillation decreases the time required to find optimal policies for various decision tasks in new environments, even in a target environment different in structure from the source environment.

Adis Delanovic, Carmen Chiu, John F. Kolen et al.

Airlift operations require the timely distribution of various cargo, much of which is time sensitive and valuable. These operations, however, have to contend with sudden disruptions from weather and malfunctions, requiring immediate rescheduling. The Airlift Challenge competition seeks possible solutions via a simulator that provides a simplified abstraction of the airlift problem. The simulator uses an OpenAI gym interface that allows participants to create an algorithm for planning agent actions. The algorithm is scored using a remote evaluator against scenarios of ever-increasing difficulty. The second iteration of the competition was underway from November 2023 to April 2024. This paper describes the competition, simulation environment, and results. As a step towards applying generalized planning techniques to the problem, a temporal PDDL domain is presented for the Pickup and Delivery Problem, a model which lies at the core of the Airlift Challenge.

Taylor Dohmen, Noah Topper, George Atia et al.

The success of reinforcement learning in typical settings is predicated on Markovian assumptions on the reward signal by which an agent learns optimal policies. In recent years, the use of reward machines has relaxed this assumption by enabling a structured representation of non-Markovian rewards. In particular, such representations can be used to augment the state space of the underlying decision process, thereby facilitating non-Markovian reinforcement learning. However, these reward machines cannot capture the semantics of stochastic reward signals. In this paper, we make progress on this front by introducing probabilistic reward machines (PRMs) as a representation of non-Markovian stochastic rewards. We present an algorithm to learn PRMs from the underlying decision process and prove results around its correctness and convergence.

Alvaro Velasquez, Ismail Alkhouri, Andre Beckus et al.

Given a Markov decision process (MDP) and a linear-time ($ω$-regular or LTL) specification, the controller synthesis problem aims to compute the optimal policy that satisfies the specification. More recently, problems that reason over the asymptotic behavior of systems have been proposed through the lens of steady-state planning. This entails finding a control policy for an MDP such that the Markov chain induced by the solution policy satisfies a given set of constraints on its steady-state distribution. This paper studies a generalization of the controller synthesis problem for a linear-time specification under steady-state constraints on the asymptotic behavior. We present an algorithm to find a deterministic policy satisfying $ω$-regular and steady-state constraints by characterizing the solutions as an integer linear program, and experimentally evaluate our approach.

George K. Atia, Andre Beckus, Ismail Alkhouri et al.

The planning domain has experienced increased interest in the formal synthesis of decision-making policies. This formal synthesis typically entails finding a policy which satisfies formal specifications in the form of some well-defined logic. While many such logics have been proposed with varying degrees of expressiveness and complexity in their capacity to capture desirable agent behavior, their value is limited when deriving decision-making policies which satisfy certain types of asymptotic behavior in general system models. In particular, we are interested in specifying constraints on the steady-state behavior of an agent, which captures the proportion of time an agent spends in each state as it interacts for an indefinite period of time with its environment. This is sometimes called the average or expected behavior of the agent and the associated planning problem is faced with significant challenges unless strong restrictions are imposed on the underlying model in terms of the connectivity of its graph structure. In this paper, we explore this steady-state planning problem that consists of deriving a decision-making policy for an agent such that constraints on its steady-state behavior are satisfied. A linear programming solution for the general case of multichain Markov Decision Processes (MDPs) is proposed and we prove that optimal solutions to the proposed programs yield stationary policies with rigorous guarantees of behavior.

Andre Beckus, George K. Atia

We consider an approach for community detection in time-varying networks. At its core, this approach maintains a small sketch graph to capture the essential community structure found in each snapshot of the full network. We demonstrate how the sketch can be used to explicitly identify six key community events which typically occur during network evolution: growth, shrinkage, merging, splitting, birth and death. Based on these detection techniques, we formulate a community detection algorithm which can process a network concurrently exhibiting all processes. One advantage afforded by the sketch-based algorithm is the efficient handling of large networks. Whereas detecting events in the full graph may be computationally expensive, the small size of the sketch allows changes to be quickly assessed. A second advantage occurs in networks containing clusters of disproportionate size. The sketch is constructed such that there is equal representation of each cluster, thus reducing the possibility that the small clusters are lost in the estimate. We present a new standardized benchmark based on the stochastic block model which models the addition and deletion of nodes, as well as the birth and death of communities. When coupled with existing benchmarks, this new benchmark provides a comprehensive suite of tests encompassing all six community events. We provide analysis and a set of numerical results demonstrating the advantages of our approach both in run time and in the handling of small clusters.

Andre Beckus, Alexandru Tamasan, George K. Atia

We consider the non-line-of-sight (NLOS) imaging of an object using the light reflected off a diffusive wall. The wall scatters incident light such that a lens is no longer useful to form an image. Instead, we exploit the 4D spatial coherence function to reconstruct a 2D projection of the obscured object. The approach is completely passive in the sense that no control over the light illuminating the object is assumed and is compatible with the partially coherent fields ubiquitous in both the indoor and outdoor environments. We formulate a multi-criteria convex optimization problem for reconstruction, which fuses the reflected field's intensity and spatial coherence information at different scales. Our formulation leverages established optics models of light propagation and scattering and exploits the sparsity common to many images in different bases. We also develop an algorithm based on the alternating direction method of multipliers to efficiently solve the convex program proposed. A means for analyzing the null space of the measurement matrices is provided as well as a means for weighting the contribution of individual measurements to the reconstruction. This paper holds promise to advance passive imaging in the challenging NLOS regimes in which the intensity does not necessarily retain distinguishable features and provides a framework for multi-modal information fusion for efficient scene reconstruction.

Mostafa Rahmani, Andre Beckus, Adel Karimian et al.

This article explores and analyzes the unsupervised clustering of large partially observed graphs. We propose a scalable and provable randomized framework for clustering graphs generated from the stochastic block model. The clustering is first applied to a sub-matrix of the graph's adjacency matrix associated with a reduced graph sketch constructed using random sampling. Then, the clusters of the full graph are inferred based on the clusters extracted from the sketch using a correlation-based retrieval step. Uniform random node sampling is shown to improve the computational complexity over clustering of the full graph when the cluster sizes are balanced. A new random degree-based node sampling algorithm is presented which significantly improves upon the performance of the clustering algorithm even when clusters are unbalanced. This framework improves the phase transitions for matrix-decomposition-based clustering with regard to computational complexity and minimum cluster size, which are shown to be nearly dimension-free in the low inter-cluster connectivity regime. A third sampling technique is shown to improve balance by randomly sampling nodes based on spatial distribution. We provide analysis and numerical results using a convex clustering algorithm based on matrix completion.