Histopathological analysis of Whole Slide Images (WSIs) has seen a surge in the utilization of deep learning methods, particularly Convolutional Neural Networks (CNNs). However, CNNs often fall short in capturing the intricate spatial dependencies inherent in WSIs. Graph Neural Networks (GNNs) present a promising alternative, adept at directly modeling pairwise interactions and effectively discerning the topological tissue and cellular structures within WSIs. Recognizing the pressing need for deep learning techniques that harness the topological structure of WSIs, the application of GNNs in histopathology has experienced rapid growth. In this comprehensive review, we survey GNNs in histopathology, discuss their applications, and explore emerging trends that pave the way for future advancements in the field. We begin by elucidating the fundamentals of GNNs and their potential applications in histopathology. Leveraging quantitative literature analysis, we identify four emerging trends: Hierarchical GNNs, Adaptive Graph Structure Learning, Multimodal GNNs, and Higher-order GNNs. Through an in-depth exploration of these trends, we offer insights into the evolving landscape of GNNs in histopathological analysis. Based on our findings, we propose future directions to propel the field forward. Our analysis serves to guide researchers and practitioners towards innovative approaches and methodologies, fostering advancements in histopathological analysis through the lens of graph neural networks.
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Random Projections have been widely used to generate embeddings for various graph learning tasks due to their computational efficiency. The majority of applications have been justified through the Johnson-Lindenstrauss Lemma. In this paper, we take a step further and investigate how well dot product and cosine similarity are preserved by random projections when these are applied over the rows of the graph matrix. Our analysis provides new asymptotic and finite-sample results, identifies pathological cases, and tests them with numerical experiments. We specialize our fundamental results to a ranking application by computing the probability of random projections flipping the node ordering induced by their embeddings. We find that, depending on the degree distribution, the method produces especially unreliable embeddings for the dot product, regardless of whether the adjacency or the normalized transition matrix is used. With respect to the statistical noise introduced by random projections, we show that cosine similarity produces remarkably more precise approximations.
We develop a Mean-Field (MF) view of the learning dynamics of overparametrized Artificial Neural Networks (NN) under data symmetric in law wrt the action of a general compact group $G$. We consider for this a class of generalized shallow NNs given by an ensemble of $N$ multi-layer units, jointly trained using stochastic gradient descent (SGD) and possibly symmetry-leveraging (SL) techniques, such as Data Augmentation (DA), Feature Averaging (FA) or Equivariant Architectures (EA). We introduce the notions of weakly and strongly invariant laws (WI and SI) on the parameter space of each single unit, corresponding, respectively, to $G$-invariant distributions, and to distributions supported on parameters fixed by the group action (which encode EA). This allows us to define symmetric models compatible with taking $N\to\infty$ and give an interpretation of the asymptotic dynamics of DA, FA and EA in terms of Wasserstein Gradient Flows describing their MF limits. When activations respect the group action, we show that, for symmetric data, DA, FA and freely-trained models obey the exact same MF dynamic, which stays in the space of WI laws and minimizes therein the population risk. We also give a counterexample to the general attainability of an optimum over SI laws. Despite this, quite remarkably, we show that the set of SI laws is also preserved by the MF dynamics even when freely trained. This sharply contrasts the finite-$N$ setting, in which EAs are generally not preserved by unconstrained SGD. We illustrate the validity of our findings as $N$ gets larger in a teacher-student experimental setting, training a student NN to learn from a WI, SI or arbitrary teacher model through various SL schemes. We last deduce a data-driven heuristic to discover the largest subspace of parameters supporting SI distributions for a problem, that could be used for designing EA with minimal generalization error.
Federated Learning (FL) in the Internet of Things (IoT) environments can enhance machine learning by utilising decentralised data, but at the same time, it might introduce significant privacy and security concerns due to the constrained nature of IoT devices. This represents a research challenge that we aim to address in this paper. We systematically analysed recent literature to identify privacy threats in FL within IoT environments, and evaluate the defensive measures that can be employed to mitigate these threats. Using a Systematic Literature Review (SLR) approach, we searched five publication databases (Scopus, IEEE Xplore, Wiley, ACM, and Science Direct), collating relevant papers published between 2017 and April 2024, a period which spans from the introduction of FL until now. Guided by the PRISMA protocol, we selected 49 papers to focus our systematic review on. We analysed these papers, paying special attention to the privacy threats and defensive measures -- specifically within the context of IoT -- using inclusion and exclusion criteria tailored to highlight recent advances and critical insights. We identified various privacy threats, including inference attacks, poisoning attacks, and eavesdropping, along with defensive measures such as Differential Privacy and Secure Multi-Party Computation. These defences were evaluated for their effectiveness in protecting privacy without compromising the functional integrity of FL in IoT settings. Our review underscores the necessity for robust and efficient privacy-preserving strategies tailored for IoT environments. Notably, there is a need for strategies against replay, evasion, and model stealing attacks. Exploring lightweight defensive measures and emerging technologies such as blockchain may help improve the privacy of FL in IoT, leading to the creation of FL models that can operate under variable network conditions.
Deep Gaussian processes (DGPs) provide a robust paradigm for Bayesian deep learning. In DGPs, a set of sparse integration locations called inducing points are selected to approximate the posterior distribution of the model. This is done to reduce computational complexity and improve model efficiency. However, inferring the posterior distribution of inducing points is not straightforward. Traditional variational inference approaches to posterior approximation often lead to significant bias. To address this issue, we propose an alternative method called Denoising Diffusion Variational Inference (DDVI) that uses a denoising diffusion stochastic differential equation (SDE) to generate posterior samples of inducing variables. We rely on score matching methods for denoising diffusion model to approximate score functions with a neural network. Furthermore, by combining classical mathematical theory of SDEs with the minimization of KL divergence between the approximate and true processes, we propose a novel explicit variational lower bound for the marginal likelihood function of DGP. Through experiments on various datasets and comparisons with baseline methods, we empirically demonstrate the effectiveness of DDVI for posterior inference of inducing points for DGP models.
We introduce FedDM, a novel training framework designed for the federated training of diffusion models. Our theoretical analysis establishes the convergence of diffusion models when trained in a federated setting, presenting the specific conditions under which this convergence is guaranteed. We propose a suite of training algorithms that leverage the U-Net architecture as the backbone for our diffusion models. These include a basic Federated Averaging variant, FedDM-vanilla, FedDM-prox to handle data heterogeneity among clients, and FedDM-quant, which incorporates a quantization module to reduce the model update size, thereby enhancing communication efficiency across the federated network. We evaluate our algorithms on FashionMNIST (28x28 resolution), CIFAR-10 (32x32 resolution), and CelebA (64x64 resolution) for DDPMs, as well as LSUN Church Outdoors (256x256 resolution) for LDMs, focusing exclusively on the imaging modality. Our evaluation results demonstrate that FedDM algorithms maintain high generation quality across image resolutions. At the same time, the use of quantized updates and proximal terms in the local training objective significantly enhances communication efficiency (up to 4x) and model convergence, particularly in non-IID data settings, at the cost of increased FID scores (up to 1.75x).
We introduce LLM-ARC, a neuro-symbolic framework designed to enhance the logical reasoning capabilities of Large Language Models (LLMs), by combining them with an Automated Reasoning Critic (ARC). LLM-ARC employs an Actor-Critic method where the LLM Actor generates declarative logic programs along with tests for semantic correctness, while the Automated Reasoning Critic evaluates the code, runs the tests and provides feedback on test failures for iterative refinement. Implemented using Answer Set Programming (ASP), LLM-ARC achieves a new state-of-the-art accuracy of 88.32% on the FOLIO benchmark which tests complex logical reasoning capabilities. Our experiments demonstrate significant improvements over LLM-only baselines, highlighting the importance of logic test generation and iterative self-refinement. We achieve our best result using a fully automated self-supervised training loop where the Actor is trained on end-to-end dialog traces with Critic feedback. We discuss potential enhancements and provide a detailed error analysis, showcasing the robustness and efficacy of LLM-ARC for complex natural language reasoning tasks.
Multimodality Representation Learning, as a technique of learning to embed information from different modalities and their correlations, has achieved remarkable success on a variety of applications, such as Visual Question Answering (VQA), Natural Language for Visual Reasoning (NLVR), and Vision Language Retrieval (VLR). Among these applications, cross-modal interaction and complementary information from different modalities are crucial for advanced models to perform any multimodal task, e.g., understand, recognize, retrieve, or generate optimally. Researchers have proposed diverse methods to address these tasks. The different variants of transformer-based architectures performed extraordinarily on multiple modalities. This survey presents the comprehensive literature on the evolution and enhancement of deep learning multimodal architectures to deal with textual, visual and audio features for diverse cross-modal and modern multimodal tasks. This study summarizes the (i) recent task-specific deep learning methodologies, (ii) the pretraining types and multimodal pretraining objectives, (iii) from state-of-the-art pretrained multimodal approaches to unifying architectures, and (iv) multimodal task categories and possible future improvements that can be devised for better multimodal learning. Moreover, we prepare a dataset section for new researchers that covers most of the benchmarks for pretraining and finetuning. Finally, major challenges, gaps, and potential research topics are explored. A constantly-updated paperlist related to our survey is maintained at //github.com/marslanm/multimodality-representation-learning.
The rapid development of deep learning has made a great progress in segmentation, one of the fundamental tasks of computer vision. However, the current segmentation algorithms mostly rely on the availability of pixel-level annotations, which are often expensive, tedious, and laborious. To alleviate this burden, the past years have witnessed an increasing attention in building label-efficient, deep-learning-based segmentation algorithms. This paper offers a comprehensive review on label-efficient segmentation methods. To this end, we first develop a taxonomy to organize these methods according to the supervision provided by different types of weak labels (including no supervision, coarse supervision, incomplete supervision and noisy supervision) and supplemented by the types of segmentation problems (including semantic segmentation, instance segmentation and panoptic segmentation). Next, we summarize the existing label-efficient segmentation methods from a unified perspective that discusses an important question: how to bridge the gap between weak supervision and dense prediction -- the current methods are mostly based on heuristic priors, such as cross-pixel similarity, cross-label constraint, cross-view consistency, cross-image relation, etc. Finally, we share our opinions about the future research directions for label-efficient deep segmentation.
Causal Machine Learning (CausalML) is an umbrella term for machine learning methods that formalize the data-generation process as a structural causal model (SCM). This allows one to reason about the effects of changes to this process (i.e., interventions) and what would have happened in hindsight (i.e., counterfactuals). We categorize work in \causalml into five groups according to the problems they tackle: (1) causal supervised learning, (2) causal generative modeling, (3) causal explanations, (4) causal fairness, (5) causal reinforcement learning. For each category, we systematically compare its methods and point out open problems. Further, we review modality-specific applications in computer vision, natural language processing, and graph representation learning. Finally, we provide an overview of causal benchmarks and a critical discussion of the state of this nascent field, including recommendations for future work.
State-of-the-art Convolutional Neural Network (CNN) benefits a lot from multi-task learning (MTL), which learns multiple related tasks simultaneously to obtain shared or mutually related representations for different tasks. The most widely-used MTL CNN structure is based on an empirical or heuristic split on a specific layer (e.g., the last convolutional layer) to minimize different task-specific losses. However, this heuristic sharing/splitting strategy may be harmful to the final performance of one or multiple tasks. In this paper, we propose a novel CNN structure for MTL, which enables automatic feature fusing at every layer. Specifically, we first concatenate features from different tasks according to their channel dimension, and then formulate the feature fusing problem as discriminative dimensionality reduction. We show that this discriminative dimensionality reduction can be done by 1x1 Convolution, Batch Normalization, and Weight Decay in one CNN, which we refer to as Neural Discriminative Dimensionality Reduction (NDDR). We perform ablation analysis in details for different configurations in training the network. The experiments carried out on different network structures and different task sets demonstrate the promising performance and desirable generalizability of our proposed method.
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