The stochastic block model (SBM), first introduced in [56], is a generative model for random graphs with a community structure. It serves as a useful benchmark for clustering algorithms on graph data. When the random graph generated by an SBM is sparse with bounded expected degrees, a phase transition has been observed around the so-called Kesten-Stigum threshold: in particular, above this threshold, a wealth of algorithms are known to achieve partial reconstruction [73, 6, 30, 57, 39]. Most relevant to this line of work are spectral algorithms that use the eigenvectors of a matrix associated with the graph G to perform the reconstruction. In the sparse case, examples include the self-avoiding [69], non-backtracking [38, 62, 23], graph powering [3] or distance [78] matrices. We refer interested readers to the survey [1] for more references, including a more in-depth discussion of the Kesten-Stigum threshold. As a generalization of graphs, hypergraphs are well-studied objects in combinatorics and theoretical computer science.

Signed and directed networks are ubiquitous in real-world applications. However, there has been relatively little work proposing spectral graph neural networks (GNNs) for such networks. Here we introduce a signed directed Laplacian matrix, which we call the magnetic signed Laplacian, as a natural generalization of both the signed Laplacian on signed graphs and the magnetic Laplacian on directed graphs. We then use this matrix to construct a novel efficient spectral GNN architecture and conduct extensive experiments on both node clustering and link prediction tasks. In these experiments, we consider tasks related to signed information, tasks related to directional information, and tasks related to both signed and directional information. We demonstrate that our proposed spectral GNN is effective for incorporating both signed and directional information, and attains leading performance on a wide range of data sets. Additionally, we provide a novel synthetic network model, which we refer to as the Signed Directed Stochastic Block Model, and a number of novel real-world data sets based on lead-lag relationships in financial time series.

We consider the constrained sampling problem where the goal is to sample from a distribution $\pi(x)\propto e^{-f(x)}$ and $x$ is constrained on a convex body $\mathcal{C}\subset \mathbb{R}^d$. Motivated by penalty methods from optimization, we propose penalized Langevin Dynamics (PLD) and penalized Hamiltonian Monte Carlo (PHMC) that convert the constrained sampling problem into an unconstrained one by introducing a penalty function for constraint violations. When $f$ is smooth and the gradient is available, we show $\tilde{\mathcal{O}}(d/\varepsilon^{10})$ iteration complexity for PLD to sample the target up to an $\varepsilon$-error where the error is measured in terms of the total variation distance and $\tilde{\mathcal{O}}(\cdot)$ hides some logarithmic factors. For PHMC, we improve this result to $\tilde{\mathcal{O}}(\sqrt{d}/\varepsilon^{7})$ when the Hessian of $f$ is Lipschitz and the boundary of $\mathcal{C}$ is sufficiently smooth. To our knowledge, these are the first convergence rate results for Hamiltonian Monte Carlo methods in the constrained sampling setting that can handle non-convex $f$ and can provide guarantees with the best dimension dependency among existing methods with deterministic gradients. We then consider the setting where unbiased stochastic gradients are available. We propose PSGLD and PSGHMC that can handle stochastic gradients without Metropolis-Hasting correction steps. When $f$ is strongly convex and smooth, we obtain an iteration complexity of $\tilde{\mathcal{O}}(d/\varepsilon^{18})$ and $\tilde{\mathcal{O}}(d\sqrt{d}/\varepsilon^{39})$ respectively in the 2-Wasserstein distance. For the more general case, when $f$ is smooth and non-convex, we also provide finite-time performance bounds and iteration complexity results. Finally, we test our algorithms on Bayesian LASSO regression and Bayesian constrained deep learning problems.

Designing faster optimization algorithms is of ever-growing interest. In recent years, learning to learn methods that learn how to optimize demonstrated very encouraging results. Current approaches usually do not effectively include the dynamics of the optimization process during training. They either omit it entirely or only implicitly assume the dynamics of an isolated parameter. In this paper, we show how to utilize the dynamic mode decomposition method for extracting informative features about optimization dynamics. By employing those features, we show that our learned optimizer generalizes much better to unseen optimization problems in short. The improved generalization is illustrated on multiple tasks where training the optimizer on one neural network generalizes to different architectures and distinct datasets.

An undirected weighted graph (UWG) is frequently adopted to describe the interactions among a solo set of nodes from real applications, such as the user contact frequency from a social network services system. A graph convolutional network (GCN) is widely adopted to perform representation learning to a UWG for subsequent pattern analysis tasks such as clustering or missing data estimation. However, existing GCNs mostly neglects the latent collaborative information hidden in its connected node pairs. To address this issue, this study proposes to model the node collaborations via a symmetric latent factor analysis model, and then regards it as a node-collaboration module for supplementing the collaboration loss in a GCN. Based on this idea, a Node-collaboration-informed Graph Convolutional Network (NGCN) is proposed with three-fold ideas: a) Learning latent collaborative information from the interaction of node pairs via a node-collaboration module; b) Building the residual connection and weighted representation propagation to obtain high representation capacity; and c) Implementing the model optimization in an end-to-end fashion to achieve precise representation to the target UWG. Empirical studies on UWGs emerging from real applications demonstrate that owing to its efficient incorporation of node-collaborations, the proposed NGCN significantly outperforms state-of-the-art GCNs in addressing the task of missing weight estimation. Meanwhile, its good scalability ensures its compatibility with more advanced GCN extensions, which will be further investigated in our future studies.

Specular microscopy assessment of the human corneal endothelium (CE) in Fuchs' dystrophy is challenging due to the presence of dark image regions called guttae. This paper proposes a UNet-based segmentation approach that requires minimal post-processing and achieves reliable CE morphometric assessment and guttae identification across all degrees of Fuchs' dystrophy. We cast the segmentation problem as a regression task of the cell and gutta signed distance maps instead of a pixel-level classification task as typically done with UNets. Compared to the conventional UNet classification approach, the distance-map regression approach converges faster in clinically relevant parameters. It also produces morphometric parameters that agree with the manually-segmented ground-truth data, namely the average cell density difference of -41.9 cells/mm2 (95% confidence interval (CI) [-306.2, 222.5]) and the average difference of mean cell area of 14.8 um2 (95% CI [-41.9, 71.5]). These results suggest a promising alternative for CE assessment.

The prediction of protein structures from sequences is an important task for function prediction, drug design, and related biological processes understanding. Recent advances have proved the power of language models (LMs) in processing the protein sequence databases, which inherit the advantages of attention networks and capture useful information in learning representations for proteins. The past two years have witnessed remarkable success in tertiary protein structure prediction (PSP), including evolution-based and single-sequence-based PSP. It seems that instead of using energy-based models and sampling procedures, protein language model (pLM)-based pipelines have emerged as mainstream paradigms in PSP. Despite the fruitful progress, the PSP community needs a systematic and up-to-date survey to help bridge the gap between LMs in the natural language processing (NLP) and PSP domains and introduce their methodologies, advancements and practical applications. To this end, in this paper, we first introduce the similarities between protein and human languages that allow LMs extended to pLMs, and applied to protein databases. Then, we systematically review recent advances in LMs and pLMs from the perspectives of network architectures, pre-training strategies, applications, and commonly-used protein databases. Next, different types of methods for PSP are discussed, particularly how the pLM-based architectures function in the process of protein folding. Finally, we identify challenges faced by the PSP community and foresee promising research directions along with the advances of pLMs. This survey aims to be a hands-on guide for researchers to understand PSP methods, develop pLMs and tackle challenging problems in this field for practical purposes.

This paper studies the infinite-width limit of deep linear neural networks initialized with random parameters. We obtain that, when the number of neurons diverges, the training dynamics converge (in a precise sense) to the dynamics obtained from a gradient descent on an infinitely wide deterministic linear neural network. Moreover, even if the weights remain random, we get their precise law along the training dynamics, and prove a quantitative convergence result of the linear predictor in terms of the number of neurons. We finally study the continuous-time limit obtained for infinitely wide linear neural networks and show that the linear predictors of the neural network converge at an exponential rate to the minimal $\ell_2$-norm minimizer of the risk.

This paper presents a subsampling-task paradigm for data-driven task-specific experiment design (ED) and a novel method in populationwide supervised feature selection (FS). Optimal ED, the choice of sampling points under constraints of limited acquisition-time, arises in a wide variety of scientific and engineering contexts. However the continuous optimization used in classical approaches depend on a-priori parameter choices and challenging non-convex optimization landscapes. This paper proposes to replace this strategy with a subsampling-task paradigm, analogous to populationwide supervised FS. In particular, we introduce JOFSTO, which performs JOint Feature Selection and Task Optimization. JOFSTO jointly optimizes two coupled networks: one for feature scoring, which provides the ED, the other for execution of a downstream task or process. Unlike most FS problems, e.g. selecting protein expressions for classification, ED problems typically select from highly correlated globally informative candidates rather than seeking a small number of highly informative features among many uninformative features. JOFSTO's construction efficiently identifies potentially correlated, but effective subsets and returns a trained task network. We demonstrate the approach using parameter estimation and mapping problems in clinically-relevant applications in quantitative MRI and in hyperspectral imaging. Results from simulations and empirical data show the subsampling-task paradigm strongly outperforms classical ED, and within our paradigm, JOFSTO outperforms state-of-the-art supervised FS techniques. JOFSTO extends immediately to wider image-based ED problems and other scenarios where the design must be specified globally across large numbers of acquisitions. Code will be released.

This paper introduces and studies zero-base generalized few-shot learning (zero-base GFSL), which is an extreme yet practical version of few-shot learning problem. Motivated by the cases where base data is not available due to privacy or ethical issues, the goal of zero-base GFSL is to newly incorporate the knowledge of few samples of novel classes into a pretrained model without any samples of base classes. According to our analysis, we discover the fact that both mean and variance of the weight distribution of novel classes are not properly established, compared to those of base classes. The existing GFSL methods attempt to make the weight norms balanced, which we find helps only the variance part, but discard the importance of mean of weights particularly for novel classes, leading to the limited performance in the GFSL problem even with base data. In this paper, we overcome this limitation by proposing a simple yet effective normalization method that can effectively control both mean and variance of the weight distribution of novel classes without using any base samples and thereby achieve a satisfactory performance on both novel and base classes. Our experimental results somewhat surprisingly show that the proposed zero-base GFSL method that does not utilize any base samples even outperforms the existing GFSL methods that make the best use of base data. Our implementation is available at: https://github.com/bigdata-inha/Zero-Base-GFSL.