New method infers co-expression networks robustly from multiple studies.
problem Challenges in inferring co-expression networks from transcriptome data.
method Robust method based on multivariate t-distribution with shared precision matrix.
result Identifies co-expression matrix up to scaling factor.
Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are locally co-regulated by shared biological mechanisms. To do this, we de…
We present a technique to characterize differentially expressed genes in terms of their position in a high-dimensional co-expression network. The set-up of Gaussian graphical models is used to construct representations of the co-expression network in such a way that redundancy and the propagation of spurious informatio…
The paper develops a test for independence of selected Gaussian variables after thresholding correlations.
problem Testing independence of selected Gaussian variables after thresholding correlations.
method The approach involves conditioning on the selection event and using a new characterization of the conditioning event in terms of canonical correlation.
result The proposed test has higher power than a naive approach that ignores selection effects.
Convolutional Neural Networks (CNNs) are a popular deep learning architecture widely applied in different domains, in particular in classifying over images, for which the concept of convolution with a filter comes naturally. Unfortunately, the requirement of a distance (or, at least, of a neighbourhood function) in the…
Bayesian methods detect clusters in noisy data more reliably.
problem Noisy data distorts traditional clustering methods, leading to unreliable results.
method Bayesian community detection using Minimum Description Length principle.
result Bayesian methods identify more robust clusters in noisy data.
Estimates complex dependency structures in multi-omics data.
problem Graphical model estimation from multi-omics data with scalability and consistency.
method Pseudolikelihood-based graphical model framework with ℓ1-penalized empirical risk. result Estimates partial correlation network from dual-omic liver cancer data.
Most network-based protein (or gene) function prediction methods are based on the assumption that the labels of two adjacent proteins in the network are likely to be the same. However, assuming the pairwise relationship between proteins or genes is not complete, the information a group of genes that show very similar p…
We study the challenges of applying deep learning to gene expression data. We find experimentally that there exists non-linear signal in the data, however is it not discovered automatically given the noise and low numbers of samples used in most research. We discuss how gene interaction graphs (same pathway, protein-pr…
A new multi-task learning estimator improves Gaussian graphical regression model fitting.
problem High error rate in fitting Gaussian graphical regression models due to separate node-wise lasso regressions.
method Proposes a multi-task learning estimator with cross-task group sparsity and within-task element-wise sparsity penalties, solved via an efficient augmented Lagrangian algorithm.
result Error rate improvement over separate node-wise lasso estimates, demonstrated through simulations and application to gene co-expression network study.
In the biclustering problem, we seek to simultaneously group observations and features. While biclustering has applications in a wide array of domains, ranging from text mining to collaborative filtering, the problem of identifying structure in high dimensional genomic data motivates this work. In this context, biclust…
Paper develops statistical tests for covariance matrix regression on manifold.
problem Regression with random covariance matrices in Fréchet space.
method Develops Wasserstein F-tests for Bures-Wasserstein manifold.
result Asymptotic null distribution and power of the test.
Proposes a convex method to estimate GGMs with covariates.
problem Improving conditional independence structure estimation with covariates.
method Convex optimization framework for joint estimation of mean and precision matrix.
result Improved theoretical guarantees and practical utility demonstrated.
Spectral sparsification improves Gaussian graphical models under MTP2 constraints.
problem Learning accurate, sparse graphs from data under MTP2 constraints.
method Spectral graph sparsification applied to Gaussian graphical models.
result Spectral-MTP2 preserves MTP2 and approximates the original model well.
We consider the problem of learning a high-dimensional multi-task regression model, under sparsity constraints induced by presence of grouping structures on the input covariates and on the output predictors. This problem is primarily motivated by expression quantitative trait locus (eQTL) mapping, of which the goal is …
While linear mixed model (LMM) has shown a competitive performance in correcting spurious associations raised by population stratification, family structures, and cryptic relatedness, more challenges are still to be addressed regarding the complex structure of genotypic and phenotypic data. For example, geneticists hav…
Method learns shared and specific factors in multi-study gene expression data.
problem Understanding shared and specific factors in high-dimensional multi-study data.
method Nonlinear multi-study factor model with sparse variational autoencoder.
result Method recovers meaningful shared and specific factors in platelet gene expression data.
CLSB models system dynamics from cross-sectional data with population-level regularization.
problem Challenges in modeling system dynamics from limited cross-sectional samples and heterogeneous individual behaviors.
method Introduces CLSB framework for learning dynamics, regularized for population-level temporal variations.
result Empirically superior in single-cell sequencing data analyses, e.g., simulating cell development and drug response.
RFN improves GCNs for road networks, outperforming state-of-the-art by 21%-40%.
problem Leveraging the structure of road networks effectively in machine learning tasks.
method Introducing RFN, a novel GCN specifically designed for road networks.
result RFN outperforms state-of-the-art GCNs by 21%-40% on road network tasks.
This survey clarifies dynamic network terminology and reviews GNN models for dynamic networks.
problem Ambiguity in dynamic network terminology and lack of GNN models for dynamic networks.
method Established consistent terminology and notation for dynamic networks, reviewed GNN models.
result Comprehensive survey of dynamic graph neural network models.
From the perspective of network analysis, the ubiquitous networks are comprised of regular and irregular components, which makes uncovering the complexity of network structures to be a fundamental challenge. Exploring the regular information and identifying the roles of microscopic elements in network data can help us …
DCNs mimic neuronal networks for improved neural classification.
problem Lack of topological similarity between DNNs and biological neural networks.
method Developed DCNs with topologies inspired by real-world neuronal networks.
result High classification accuracy achieved by DCNs.
Chemical networks outperform spiking neural networks in classification tasks.
problem Learning tasks with spiking neural networks require hidden layers, which are computationally expensive.
method Used deterministic mass-action kinetics to prove chemical reaction networks without hidden layers can solve tasks previously solved by spiking neural networks.
result A chemical reaction network without hidden layers outperforms a spiking neural network with hidden layers in a handwritten digit classification task.
Deep ReLU networks can be simplified to a three-layer model.
problem Understanding the behavior of deep neural networks.
method Constructive proof and algorithm to transform deep networks into shallow ones.
result Deep ReLU networks can be represented by a simpler three-layer structure.
Tackles network structure inference from time series data using GNN.
problem Inferring network structure from incomplete or no information.
method Gumbel Graph Network (GGN) model for network reconstruction and completion.
result GGN can reconstruct up to 100% network structure and infer missing parts with up to 90% accuracy.
This paper explores loss landscapes of sparse neural networks, finding unique characteristics compared to dense networks.
problem Understanding the loss landscape of sparse neural networks, especially one-hidden-layer networks.
method Analyzes sparse networks with dense and sparse final layers, focusing on linear and non-linear models.
result Sparse networks can have no spurious valleys under certain conditions, but spurious valleys and minima can exist for wide sparse networks.
New approach learns latent motifs in networks for mesoscale structure analysis.
problem Understanding large-scale behavior in complex systems through mesoscale structures.
method Network dictionary learning (NDL) combining network sampling and nonnegative matrix factorization.
result Networks can be approximated using a small set of latent motifs.
A challenging problem in complex networks is the network reconstruction problem from data. This work deals with a class of networks denoted as conserved networks, in which a flow associated with every edge and the flows are conserved at all non-source and non-sink nodes. We propose a novel polynomial time algorithm to …
Social network analysis is an important problem in data mining. A fundamental step for analyzing social networks is to encode network data into low-dimensional representations, i.e., network embeddings, so that the network topology structure and other attribute information can be effectively preserved. Network represen…
Taking inspiration from biological evolution, we explore the idea of "Can deep neural networks evolve naturally over successive generations into highly efficient deep neural networks?" by introducing the notion of synthesizing new highly efficient, yet powerful deep neural networks over successive generations via an ev…
SyNGLER generates synthetic networks efficiently while preserving key structural properties.
problem Efficiently generating realistic synthetic networks with preserved structural properties.
method SyNGLER uses latent space network models to learn and reconstruct node embeddings, then generates synthetic networks.
result SyNGLER produces synthetic networks that better preserve key network characteristics than existing approaches.
Secret neural networks hidden within trained models.
problem Excess capacity in neural networks allows embedding secret models.
method Novel framework for hiding secret neural networks within carrier networks.
result Detection of hidden networks is computationally infeasible.
Natural graph networks are a new class of graph neural networks that are more flexible and scalable.
problem Traditional graph neural networks are limited by equivariance to node permutations.
method Introduced natural graph networks, which are more flexible and scalable than conventional graph neural networks.
result Natural graph networks are as scalable as conventional message passing graph neural networks but more flexible.
The structure of complex networks has been of interest in many scientific and engineering disciplines over the decades. A number of studies in the field have been focused on finding the common properties among different kinds of networks such as heavy-tail degree distribution, small-worldness and modular structure and …
Convolutional networks outperform fully-connected ones in certain tasks.
problem Understanding the computational advantage of convolutional networks over fully-connected networks.
method Demonstrated a computational advantage through a specific problem class.
result Convolutional networks can solve certain problems that fully-connected networks cannot, even with gradient descent.
Proposes a graph neural network for traffic forecasting in WANs.
problem Traffic forecasting challenges in WANs due to dynamic and large data volumes.
method Dynamic diffusion convolutional recurrent neural networks for multistep traffic forecasting.
result Significant improvements in forecasting accuracy compared to classical methods.
Researchers derive exact priors for finite Bayesian neural networks.
problem Understanding non-Gaussian priors in finite Bayesian neural networks.
method Analytical derivation of function space priors for finite fully-connected feedforward networks.
result Exact solutions for priors of finite networks, including Meijer G-function for linear networks and mixtures for ReLU networks.
i-cNRL learns network differences with interpretability.
problem Comparing unique network characteristics.
method Contrastive network representation learning (cNRL) integrating machine learning schemes.
result i-cNRL reveals unique network patterns with interpretability.
Deep and wide networks are shown to be equivalent in terms of their capability.
problem The relationship between the width and depth of neural networks.
method Formulated transforms to map networks, used polynomial representations.
result Deep and wide networks are quasi-equivalent with an arbitrarily small error.
We show that deep networks are better than shallow networks at approximating functions that can be expressed as a composition of functions described by a directed acyclic graph, because the deep networks can be designed to have the same compositional structure, while a shallow network cannot exploit this knowledge. Thu…
DCGANs generate drainage networks quickly from samples.
problem High computational costs in generating large numbers of drainage networks.
method DCGANs trained with connectivity-informed directional information.
result Connectivity-informed DCGANs outperform other methods in reproducing accurate drainage networks.
A network embedding consists of a vector representation for each node in the network. Its usefulness has been shown in many real-world application domains, such as social networks and web networks. Directed networks with text associated with each node, such as software package dependency networks, are commonplace. Howe…
Quantum neural network and tensor network models outperform classical models in Japanese stock market predictions.
problem Improving stock return predictions using quantum and quantum-inspired machine learning.
method Evaluation of quantum neural network and tensor network models against classical models like linear and neural networks.
result Tensor network model outperforms classical models in Japanese stock market, including linear and neural network models.
Study deep maxout networks and their equivalence to Gaussian processes.
problem Understanding neural networks with infinite width.
method Derive equivalence between deep maxout networks and Gaussian processes, characterize maxout kernel, and provide efficient numerical implementation.
result Bayesian inference based on deep maxout network kernel leads to competitive results compared to finite-width counterparts and deep neural network kernels.
Machine learning improves network classification and model selection.
problem Quantifying suitability of generative models for network structures.
method Interpretable machine learning to classify simulated networks based on features and interactions.
result Specific network features and their interactions are crucial for distinguishing generative models.
Study shows effective resistance distance yields more accurate network barycenter than Hamming distance.
problem Identifying the best metric for computing the Fréchet mean network.
method Compared the effectiveness of Hamming distance and effective resistance distance in capturing network topology.
result Effective resistance distance produces a more accurate Fréchet mean network.
Model-based neural networks generalize better than ReLU networks for sparse recovery.
problem Understanding and quantifying the superior generalization of model-based neural networks.
method Using complexity measures like global and local Rademacher complexities, the paper provides theoretical bounds on generalization and estimation errors.
result Model-based neural networks exhibit higher generalization capabilities for sparse recovery problems compared to ReLU networks.
A new method predicts links better across various networks.
problem Adaptive link prediction for diverse network types.
method MOLI method using local information from neighbors of different distances.
result MOLI outperforms other link prediction algorithms.