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With the recent advances in machine learning for quantum chemistry, it is now possible to predict the chemical properties of compounds and to generate novel molecules. Existing generative models mostly use a string- or graph-based…

Biomolecules · Quantitative Biology 2020-10-14 Vitali Nesterov , Mario Wieser , Volker Roth

We consider the problem of graph generation guided by network statistics, i.e., the generation of graphs which have given values of various numerical measures that characterize networks, such as the clustering coefficient and the number of…

Social and Information Networks · Computer Science 2023-03-02 Jérôme Kunegis , Jun Sun , Eiko Yoneki

The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…

Machine Learning · Computer Science 2025-04-25 Binon Teji , Swarup Roy

Regularization has become a primary tool for developing reliable estimators of the covariance matrix in high-dimensional settings. To curb the curse of dimensionality, numerous methods assume that the population covariance (or inverse…

Methodology · Statistics 2018-02-19 Jacob Bien

Deep generative models have been used in recent years to learn coherent latent representations in order to synthesize high-quality images. In this work, we propose a neural network to learn a generative model for sampling consistent indoor…

Computer Vision and Pattern Recognition · Computer Science 2020-08-24 Pulak Purkait , Christopher Zach , Ian Reid

Deep learning methods are achieving ever-increasing performance on many artificial intelligence tasks. A major limitation of deep models is that they are not amenable to interpretability. This limitation can be circumvented by developing…

Machine Learning · Computer Science 2022-07-05 Hao Yuan , Haiyang Yu , Shurui Gui , Shuiwang Ji

Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…

Discrete Mathematics · Computer Science 2022-08-29 Jakob L. Andersen , Rolf Fagerberg , Juri Kolčák , Christophe V. F. P. Laurent , Daniel Merkle , Nikolai Nøjgaard

Proposing an effective and flexible matrix to represent a graph is a fundamental challenge that has been explored from multiple perspectives, e.g., filtering in Graph Fourier Transforms. In this work, we develop a novel and general…

Machine Learning · Computer Science 2023-05-11 Mingqi Yang , Wenjie Feng , Yanming Shen , Bryan Hooi

When adopting a model-based formulation, solving inverse problems encountered in multiband imaging requires to define spatial and spectral regularizations. In most of the works of the literature, spectral information is extracted from the…

Image and Video Processing · Electrical Eng. & Systems 2023-07-03 Min Zhao , Nicolas Dobigeon , Jie Chen

Despite the remarkable generative capabilities of language models in producing naturalistic language, their effectiveness on explicit manipulation and generation of linguistic structures remain understudied. In this paper, we investigate…

Computation and Language · Computer Science 2024-06-26 Xinyue Cui , Swabha Swayamdipta

Invertible flow-based generative models are an effective method for learning to generate samples, while allowing for tractable likelihood computation and inference. However, the invertibility requirement restricts models to have the same…

Machine Learning · Computer Science 2020-02-21 Abhishek Kumar , Ben Poole , Kevin Murphy

Providing a human-understandable explanation of classifiers' decisions has become imperative to generate trust in their use for day-to-day tasks. Although many works have addressed this problem by generating visual explanation maps, they…

Machine Learning · Computer Science 2021-06-22 Martin Charachon , Paul-Henry Cournède , Céline Hudelot , Roberto Ardon

Electronic Health Records (EHR) are high-dimensional data with implicit connections among thousands of medical concepts. These connections, for instance, the co-occurrence of diseases and lab-disease correlations can be informative when…

Machine Learning · Computer Science 2021-03-29 Weicheng Zhu , Narges Razavian

Graph-matching metrics such as Smatch are the de facto standard for evaluating neural semantic parsers, yet they capture surface overlap rather than logical equivalence. We reassess evaluation by pairing graph-matching with automated…

Computation and Language · Computer Science 2025-10-14 Hayate Funakura , Hyunsoo Kim , Koji Mineshima

This paper develops an innovative method that enables neural networks to generate and utilize knowledge graphs, which describe their concept-level knowledge and optimize network parameters through alignment with human-provided knowledge.…

Machine Learning · Computer Science 2024-04-29 Tangrui Li , Jun Zhou

Graph autoencoders (GAE) and variational graph autoencoders (VGAE) emerged as two powerful groups of unsupervised node embedding methods, with various applications to graph-based machine learning problems such as link prediction and…

Machine Learning · Computer Science 2025-06-19 Guillaume Salha-Galvan

Objective: This paper investigates how generative models, trained on ground-truth images, can be used \changes{as} priors for inverse problems, penalizing reconstructions far from images the generator can produce. The aim is that learned…

Image and Video Processing · Electrical Eng. & Systems 2023-08-07 Margaret Duff , Ivor J. A. Simpson , Matthias J. Ehrhardt , Neill D. F. Campbell

In real world domains, most graphs naturally exhibit a hierarchical structure. However, data-driven graph generation is yet to effectively capture such structures. To address this, we propose a novel approach that recursively generates…

Machine Learning · Computer Science 2023-06-01 Mahdi Karami , Jun Luo

As the amount of textual data has been rapidly increasing over the past decade, efficient similarity search methods have become a crucial component of large-scale information retrieval systems. A popular strategy is to represent original…

Information Retrieval · Computer Science 2017-08-14 Suthee Chaidaroon , Yi Fang

Graph convolutional neural networks (GCNs) generalize tradition convolutional neural networks (CNNs) from low-dimensional regular graphs (e.g., image) to high dimensional irregular graphs (e.g., text documents on word embeddings). Due to…

Machine Learning · Computer Science 2021-03-30 Mehrnaz Najafi , Philip S. Yu