uDiG-DIP: Unrolled Diffusion-Guided Deep Image Prior For Medical Image Reconstruction

Deep learning (DL) methods have been extensively applied to various image recovery problems, including magnetic resonance imaging (MRI) and computed tomography (CT) reconstruction. Beyond supervised models, other approaches have been recently explored including two key recent schemes: Deep Image Prior (DIP) that is an unsupervised scan-adaptive method that leverages the network architecture as implicit regularization but can suffer from noise overfitting, and diffusion models (DMs), where the sampling procedure of a pre-trained generative model is modified to allow sampling from the measurement-conditioned distribution through approximations. In this paper, we propose combining DIP and DMs for MRI and CT reconstruction, motivated by (i) the impact of the DIP network input and (ii) the use of DMs as diffusion purifiers (DPs). Specifically, we propose an unrolled procedure that iteratively optimizes the DIP network with a DM-refined adaptive input using a loss with data consistency and autoencoding terms. We term the approach unrolled Diffusion-Guided DIP (uDiG-DIP). Our experimental results demonstrate that uDiG-DIP achieves superior reconstruction results compared to leading DM-based baselines and the original DIP for MRI and CT tasks.

SITCOM: Step-wise Triple-Consistent Diffusion Sampling for Inverse Problems

Diffusion models (DMs) are a class of generative models that allow sampling from a distribution learned over a training set. When applied to solving inverse imaging problems (IPs), the reverse sampling steps of DMs are typically modified to approximately sample from a measurement-conditioned distribution in the image space. However, these modifications may be unsuitable for certain settings (such as in the presence of measurement noise) and non-linear tasks, as they often struggle to correct errors from earlier sampling steps and generally require a large number of optimization and/or sampling steps. To address these challenges, we state three conditions for achieving measurement-consistent diffusion trajectories. Building on these conditions, we propose a new optimization-based sampling method that not only enforces the standard data manifold measurement consistency and forward diffusion consistency, as seen in previous studies, but also incorporates backward diffusion consistency that maintains a diffusion trajectory by optimizing over the input of the pre-trained model at every sampling step. By enforcing these conditions, either implicitly or explicitly, our sampler requires significantly fewer reverse steps. Therefore, we refer to our accelerated method as Step-wise Triple-Consistent Sampling (SITCOM). Compared to existing state-of-the-art baseline methods, under different levels of measurement noise, our extensive experiments across five linear and three non-linear image restoration tasks demonstrate that SITCOM achieves competitive or superior results in terms of standard image similarity metrics while requiring a significantly reduced run-time across all considered tasks.

Dataless Quadratic Neural Networks for the Maximum Independent Set Problem

Combinatorial Optimization (CO) plays a crucial role in addressing various significant problems, among them the challenging Maximum Independent Set (MIS) problem. In light of recent advancements in deep learning methods, efforts have been directed towards leveraging data-driven learning approaches, typically rooted in supervised learning and reinforcement learning, to tackle the NP-hard MIS problem. However, these approaches rely on labeled datasets, exhibit weak generalization, and often depend on problem-specific heuristics. Recently, ReLU-based dataless neural networks were introduced to address combinatorial optimization problems. This paper introduces a novel dataless quadratic neural network formulation, featuring a continuous quadratic relaxation for the MIS problem. Notably, our method eliminates the need for training data by treating the given MIS instance as a trainable entity. More specifically, the graph structure and constraints of the MIS instance are used to define the structure and parameters of the neural network such that training it on a fixed input provides a solution to the problem, thereby setting it apart from traditional supervised or reinforcement learning approaches. By employing a gradient-based optimization algorithm like ADAM and leveraging an efficient off-the-shelf GPU parallel implementation, our straightforward yet effective approach demonstrates competitive or superior performance compared to state-of-the-art learning-based methods. Another significant advantage of our approach is that, unlike exact and heuristic solvers, the running time of our method scales only with the number of nodes in the graph, not the number of edges.

Improving Efficiency of Diffusion Models via Multi-Stage Framework and Tailored Multi-Decoder Architectures

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.

Robust MRI Reconstruction by Smoothed Unrolling (SMUG)

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.

Diffusion-based Adversarial Purification for Robust Deep MRI Reconstruction

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.

On the Robustness of AlphaFold: A COVID-19 Case Study

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.

BOSS: Bidirectional One-Shot Synthesis of Adversarial Examples

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.

Controller Synthesis for Omega-Regular and Steady-State Specifications

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.

Verifiable Planning in Expected Reward Multichain MDPs

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.