Ismail Alkhouri

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.

Curie Kim, Carsten Portner, Mingju Liu et al.

Boolean satisfiability (SAT) problem, the first problem proven to be NP-complete, has become a fundamental challenge in computational complexity, with widespread applications in optimization and verification across many domains. Despite significant algorithmic advances over the past two decades, the performance of SAT solvers has improved at a limited pace. Notably, the 2025 competition winner shows only about a 2X improvement over the 2006 winner in SAT Competition performance after nearly 20 years of effort. This paper introduces GaloisSAT, a novel hybrid GPU-CPU SAT solver that integrates a differentiable SAT solving engine powered by modern machine learning infrastructure on GPUs, followed by a traditional CDCL-based SAT solving stage on CPUs. GaloisSAT is benchmarked against the latest versions of state-of-the-art solvers, Kissat and CaDiCaL, using the SAT Competition 2024 benchmark suite. Results demonstrate substantial improvements in the official SAT Competition metric PAR-2 (penalized average runtime with a timeout of 5,000 seconds and a penalty factor of 2). Specifically, GaloisSAT achieves an 8.41X speedup in the satisfiable category and a 1.29X speedup in the unsatisfiable category compared to the strongest baselines.

Evan Bell, Shijun Liang, Ismail Alkhouri et al.

Deep Image Prior (DIP) has recently emerged as a promising one-shot neural-network based image reconstruction method. However, DIP has seen limited application to 3D image reconstruction problems. In this work, we introduce Tada-DIP, a highly effective and fully 3D DIP method for solving 3D inverse problems. By combining input-adaptation and denoising regularization, Tada-DIP produces high-quality 3D reconstructions while avoiding the overfitting phenomenon that is common in DIP. Experiments on sparse-view X-ray computed tomography reconstruction validate the effectiveness of the proposed method, demonstrating that Tada-DIP produces much better reconstructions than training-data-free baselines and achieves reconstruction performance on par with a supervised network trained using a large dataset with fully-sampled volumes.

Ismail R. Alkhouri, George K. Atia, Alvaro Velasquez

The success of machine learning solutions for reasoning about discrete structures has brought attention to its adoption within combinatorial optimization algorithms. Such approaches generally rely on supervised learning by leveraging datasets of the combinatorial structures of interest drawn from some distribution of problem instances. Reinforcement learning has also been employed to find such structures. In this paper, we propose a radically different approach in that no data is required for training the neural networks that produce the solution. In particular, we reduce the combinatorial optimization problem to a neural network and employ a dataless training scheme to refine the parameters of the network such that those parameters yield the structure of interest. We consider the combinatorial optimization problems of finding maximum independent sets and maximum cliques in a graph. In principle, since these problems belong to the NP-hard complexity class, our proposed approach can be used to solve any other NP-hard problem. Additionally, we propose a universal graph reduction procedure to handle large scale graphs. The reduction exploits community detection for graph partitioning and is applicable to any graph type and/or density. Experimental evaluation on both synthetic graphs and real-world benchmarks demonstrates that our method performs on par with or outperforms state-of-the-art heuristic, reinforcement learning, and machine learning based methods without requiring any data.

Chaoyan Huang, Cheng-Han Huang, Ismail R. Alkhouri et al.

Recently, Deep Image Prior (DIP) has demonstrated strong capabilities for solving inverse imaging problems (IIPs) by optimizing a randomly initialized convolutional neural network in a training-data-free regime. However, DIP suffers from overfitting to noisy measurements due to network over-parameterization, making early stopping (ES) essential. The most successful ES method tracks fluctuations in the running variance of the network output to detect overfitting. However, in many applications, these fluctuations may appear prematurely, leading to unstable reconstructions. In this paper, we first show that nearly optimal DIP early stopping can be achieved when two independent noisy copies of the degraded image are available. Motivated by this observation, and since obtaining two fully independent copies is infeasible, we propose an overfitting detection framework based on constructing pseudo self-referenced images, resulting in three IIP-specific algorithms. Our approach is further supported by theoretical results on single-reference validation, pseudo-validation estimation, and the impact of shared noise. Across different IIPs, ranging from natural image restoration to medical image reconstruction, and under varying noise levels and noise types, our methods consistently outperform existing DIP early stopping approaches, all without requiring an accurate estimate of the noise level.

Ismail Alkhouri, Cedric Le Denmat, Yingjie Li et al.

Combinatorial Optimization (CO) addresses many important problems, including the challenging Maximum Independent Set (MIS) problem. Alongside exact and heuristic solvers, differentiable approaches have emerged, often using continuous relaxations of ReLU-based or quadratic objectives. Noting that an MIS in a graph is a Maximum Clique (MC) in its complement, we propose a new quadratic formulation for MIS by incorporating an MC term, improving convergence and exploration. We show that every maximal independent set corresponds to a local minimizer, derive conditions with respect to the MIS size, and characterize stationary points. To tackle the non-convexity of the objective, we propose optimizing several initializations in parallel using momentum-based gradient descent, complemented by an efficient MIS checking criterion derived from our theory. We dub our method as parallelized Clique-Informed Quadratic Optimization for MIS (pCQO-MIS). Our experimental results demonstrate the effectiveness of the proposed method compared to exact, heuristic, sampling, and data-centric approaches. Notably, our method avoids the out-of-distribution tuning and reliance on (un)labeled data required by data-centric methods, while achieving superior MIS sizes and competitive runtime relative to their inference time. Additionally, a key advantage of pCQO-MIS is that, unlike exact and heuristic solvers, the runtime scales only with the number of nodes in the graph, not the number of edges. Our code is available at the GitHub repository: https://github.com/ledenmat/pCQO-mis-benchmark/tree/refactor.

Xitong Zhang, Ismail R. Alkhouri, Rongrong Wang

Deep Neural Networks (DNNs) have achieved remarkable success in addressing many previously unsolvable tasks. However, the storage and computational requirements associated with DNNs pose a challenge for deploying these trained models on resource-limited devices. Therefore, a plethora of compression and pruning techniques have been proposed in recent years. Low-rank decomposition techniques are among the approaches most utilized to address this problem. Compared to post-training compression, compression-promoted training is still under-explored. In this paper, we present a theoretically-justified technique termed Low-Rank Induced Training (LoRITa), that promotes low-rankness through the composition of linear layers and compresses by using singular value truncation. This is achieved without the need to change the structure at inference time or require constrained and/or additional optimization, other than the standard weight decay regularization. Moreover, LoRITa eliminates the need to (i) initialize with pre-trained models, (ii) specify rank selection prior to training, and (iii) compute SVD in each iteration. Our experimental results (i) demonstrate the effectiveness of our approach using MNIST on Fully Connected Networks, CIFAR10 on Vision Transformers, and CIFAR10/100 and ImageNet on Convolutional Neural Networks, and (ii) illustrate that we achieve either competitive or state-of-the-art results when compared to leading structured pruning and low-rank training methods in terms of FLOPs and parameters drop. Our code is available at \url{https://github.com/XitongSystem/LoRITa/tree/main}.

Huijie Zhang, Yifu Lu, Ismail Alkhouri et al.

Diffusion models, emerging as powerful deep generative tools, excel in various applications. They operate through a two-steps process: introducing noise into training samples and then employing a model to convert random noise into new samples (e.g., images). However, their remarkable generative performance is hindered by slow training and sampling. This is due to the necessity of tracking extensive forward and reverse diffusion trajectories, and employing a large model with numerous parameters across multiple timesteps (i.e., noise levels). To tackle these challenges, we present a multi-stage framework inspired by our empirical findings. These observations indicate the advantages of employing distinct parameters tailored to each timestep while retaining universal parameters shared across all time steps. Our approach involves segmenting the time interval into multiple stages where we employ custom multi-decoder U-net architecture that blends time-dependent models with a universally shared encoder. Our framework enables the efficient distribution of computational resources and mitigates inter-stage interference, which substantially improves training efficiency. Extensive numerical experiments affirm the effectiveness of our framework, showcasing significant training and sampling efficiency enhancements on three state-of-the-art diffusion models, including large-scale latent diffusion models. Furthermore, our ablation studies illustrate the impact of two important components in our framework: (i) a novel timestep clustering algorithm for stage division, and (ii) an innovative multi-decoder U-net architecture, seamlessly integrating universal and customized hyperparameters.

Shijun Liang, Van Hoang Minh Nguyen, Jinghan Jia et al.

As the popularity of deep learning (DL) in the field of magnetic resonance imaging (MRI) continues to rise, recent research has indicated that DL-based MRI reconstruction models might be excessively sensitive to minor input disturbances, including worst-case additive perturbations. This sensitivity often leads to unstable, aliased images. This raises the question of how to devise DL techniques for MRI reconstruction that can be robust to train-test variations. To address this problem, we propose a novel image reconstruction framework, termed Smoothed Unrolling (SMUG), which advances a deep unrolling-based MRI reconstruction model using a randomized smoothing (RS)-based robust learning approach. RS, which improves the tolerance of a model against input noises, has been widely used in the design of adversarial defense approaches for image classification tasks. Yet, we find that the conventional design that applies RS to the entire DL-based MRI model is ineffective. In this paper, we show that SMUG and its variants address the above issue by customizing the RS process based on the unrolling architecture of a DL-based MRI reconstruction model. Compared to the vanilla RS approach, we show that SMUG improves the robustness of MRI reconstruction with respect to a diverse set of instability sources, including worst-case and random noise perturbations to input measurements, varying measurement sampling rates, and different numbers of unrolling steps. Furthermore, we theoretically analyze the robustness of our method in the presence of perturbations.

Gabriel Maliakal, Ismail Alkhouri, Alvaro Velasquez et al.

The Maximum Cut (MaxCut) problem is NP-Complete, and obtaining its optimal solution is NP-hard in the worst case. As a result, heuristic-based algorithms are commonly used, though their design often requires significant domain expertise. More recently, learning-based methods trained on large (un)labeled datasets have been proposed; however, these approaches often struggle with generalizability and scalability. A well-known approximation algorithm for MaxCut is the Goemans-Williamson (GW) algorithm, which relaxes the Quadratic Unconstrained Binary Optimization (QUBO) formulation into a semidefinite program (SDP). The GW algorithm then applies hyperplane rounding by uniformly sampling a random hyperplane to convert the SDP solution into binary node assignments. In this paper, we propose a training-data-free approach based on a non-episodic reinforcement learning formulation, in which an agent learns to select improved rounding hyperplanes that yield better cuts than those produced by the GW algorithm. By optimizing over a Markov Decision Process (MDP), our method consistently achieves better cuts across large-scale graphs with varying densities and degree distributions.

Xiang Li, Soo Min Kwon, Shijun Liang et al.

Diffusion models have recently gained traction as a powerful class of deep generative priors, excelling in a wide range of image restoration tasks due to their exceptional ability to model data distributions. To solve image restoration problems, many existing techniques achieve data consistency by incorporating additional likelihood gradient steps into the reverse sampling process of diffusion models. However, the additional gradient steps pose a challenge for real-world practical applications as they incur a large computational overhead, thereby increasing inference time. They also present additional difficulties when using accelerated diffusion model samplers, as the number of data consistency steps is limited by the number of reverse sampling steps. In this work, we propose a novel diffusion-based image restoration solver that addresses these issues by decoupling the reverse process from the data consistency steps. Our method involves alternating between a reconstruction phase to maintain data consistency and a refinement phase that enforces the prior via diffusion purification. Our approach demonstrates versatility, making it highly adaptable for efficient problem-solving in latent space. Additionally, it reduces the necessity for numerous sampling steps through the integration of consistency models. The efficacy of our approach is validated through comprehensive experiments across various image restoration tasks, including image denoising, deblurring, inpainting, and super-resolution.

Ismail R. Alkhouri, Alvaro Velasquez, George K. 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.

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.

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.