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Ismail Alkhouri, Shijun Liang, Rongrong Wang, Qing Qu, Saiprasad Ravishankar

Deep learning (DL) methods have been extensively employed in magnetic resonance imaging (MRI) reconstruction, demonstrating remarkable performance improvements compared to traditional non-DL methods. However, recent studies have uncovered the susceptibility of these models to carefully engineered adversarial perturbations. In this paper, we tackle this issue by leveraging diffusion models. Specifically, we introduce a defense strategy that enhances the robustness of DL-based MRI reconstruction methods through the utilization of pre-trained diffusion models as adversarial purifiers. Unlike conventional state-of-the-art adversarial defense methods (e.g., adversarial training), our proposed approach eliminates the need to solve a minimax optimization problem to train the image reconstruction model from scratch, and only requires fine-tuning on purified adversarial examples. Our experimental findings underscore the effectiveness of our proposed technique when benchmarked against leading defense methodologies for MRI reconstruction such as adversarial training and randomized smoothing.

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Ismail Alkhouri, Sumit Jha, Andre Beckus, George Atia, Alvaro Velasquez, Rickard Ewetz, Arvind Ramanathan, Susmit Jha

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.

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Ismail Alkhouri, Alvaro Velasquez, George Atia

The design of additive imperceptible perturbations to the inputs of deep classifiers to maximize their misclassification rates is a central focus of adversarial machine learning. An alternative approach is to synthesize adversarial examples from scratch using GAN-like structures, albeit with the use of large amounts of training data. By contrast, this paper considers one-shot synthesis of adversarial examples; the inputs are synthesized from scratch to induce arbitrary soft predictions at the output of pre-trained models, while simultaneously maintaining high similarity to specified inputs. To this end, we present a problem that encodes objectives on the distance between the desired and output distributions of the trained model and the similarity between such inputs and the synthesized examples. We prove that the formulated problem is NP-complete. Then, we advance a generative approach to the solution in which the adversarial examples are obtained as the output of a generative network whose parameters are iteratively updated by optimizing surrogate loss functions for the dual-objective. We demonstrate the generality and versatility of the framework and approach proposed through applications to the design of targeted adversarial attacks, generation of decision boundary samples, and synthesis of low confidence classification inputs. The approach is further extended to an ensemble of models with different soft output specifications. The experimental results verify that the targeted and confidence reduction attack methods developed perform on par with state-of-the-art algorithms.

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Alvaro Velasquez, Ashutosh Trivedi, Ismail Alkhouri, Andre Beckus, George Atia

Given a Markov decision process (MDP) and a linear-time ($\omega$-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 $\omega$-regular and steady-state constraints by characterizing the solutions as an integer linear program, and experimentally evaluate our approach.

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George K. Atia, Andre Beckus, Ismail Alkhouri, Alvaro Velasquez

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, such as Linear Temporal Logic (LTL) or Computation Tree Logic (CTL), among others. While such logics are very powerful and expressive 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 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. In this paper, we explore the steady-state planning problem 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.

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Mohsen Joneidi, Ismail Alkhouri, Nazanin Rahnavard

A new paradigm for large-scale spectrum occupancy learning based on long short-term memory (LSTM) recurrent neural networks is proposed. Studies have shown that spectrum usage is a highly correlated time series. Moreover, there is a correlation for occupancy of spectrum between different frequency channels. Therefore, revealing all these correlations using learning and prediction of one-dimensional time series is not a trivial task. In this paper, we introduce a new framework for representing the spectrum measurements in a tensor format. Next, a time-series prediction method based on CANDECOMP/PARFAC (CP) tensor decomposition and LSTM recurrent neural networks is proposed. The proposed method is computationally efficient and is able to capture different types of correlation within the measured spectrum. Moreover, it is robust against noise and missing entries of sensed spectrum. The superiority of the proposed method is evaluated over a large-scale synthetic dataset in terms of prediction accuracy and computational efficiency.

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