26 papers · ranked by Valyu relevance
Nikhil Goyal, Harsh Jain, Sayan Ranu
Graph generative models have been extensively studied in the data mining literature. While traditional techniques are based on generating structures that adhere to a pre-decided distribution, recent techniques have shifted towards learning this distribution directly from the data. While learning-based approaches have…
Yujia Li, Oriol Vinyals, Chris Dyer, Razvan Pascanu + 1 more
'Peter Battaglia'] Graphs are fundamental data structures which concisely capture the relational structure in many important real-world domains, such as knowledge graphs, physical and social interactions, language, and chemistry. Here we introduce a powerful new approach for learning generative models over graphs…
Jiaxuan You, Rex Ying, Xiang Ren, William L. Hamilton + 1 more
'Jure Leskovec'] Modeling and generating graphs is fundamental for studying networks in biology, engineering, and social sciences. However, modeling complex distributions over graphs and then efficiently sampling from these distributions is challenging due to the non-unique, high-dimensional nature of graphs and the…
Zhiwei Deng, Megha Nawhal, Lili Meng, Greg Mori
In this paper, we propose Continuous Graph Flow, a generative continuous flow based method that aims to model complex distributions of graph-structured data. Once learned, the model can be applied to an arbitrary graph, defining a probability density over the random variables represented by the graph. It is formulated…
Davide Bacciu, Marco Podda
—The problem of labeled graph generation is gaining attention in the Deep Learning community. The task is challenging due to the sparse and discrete nature of graph spaces. Several approaches have been proposed in the literature, most of which require to transform the graphs into sequences that encode their structure…
Dawei Zhou, Lecheng Zheng, Jiejun Xu, Jingrui He
Characterizing and modeling the distribution of a particular family of graphs are essential for the studying real-world networks in a broad spectrum of disciplines, ranging from market-basket analysis to biology, from social science to neuroscience. However, it is unclear how to model these complex graph organizations…
Faezeh Faez, Negin Hashemi Dijujin, Mahdieh Soleymani Baghshah, Hamid R. Rabiee + 1 more
'Hamid R. Rabiee' 'Sathishkumar V E'] Deep learning-based graph generation approaches have remarkable capacities for graph data modeling, allowing them to solve a wide range of real-world problems. Making these methods able to consider different conditions during the generation procedure even increases their…
Nathan Mancheun Lui, Max D Li, Matthew Ford
Deep generative models for molecular graphs offer a new avenue for property optimization in drug discovery. Optimizing differentiable models that generate molecular graphs is certainly faster, cheaper, and much more accessible than traditional methods of chemical synthesis. Recent advances in generative modeling have…
Jan H. Jensen
This paper presents a comparison of a graph-based genetic algorithm (GB-GA) and machine learning (ML) results for the optimisation of logP values with a constraint for synthetic accessibility and shows that GA is as good or better than the ML approaches for this particular property. The molecules found by GB-GA bear…
Hiroaki Iwata, Taichi Nakai, Takuto Koyama, Shigeyuki Mtsumoto + 2 more
Molecular generation is crucial for advancing drug discovery, material design, and chemical exploration. It expedites the search for new drug candidates, facilitates tailored material creation, and enhances our understanding of molecular diversity. By employing artificial intelligence techniques, such as molecular…
Wenbin Zhang, Liming Zhang, Dieter Pfoser, Liang Zhao
Deep generative models for graphs have exhibited promising performance in ever-increasing domains such as design of molecules (i.e, graph of atoms) and structure prediction of proteins (i.e., graph of amino acids). Existing work typically focuses on static rather than dynamic graphs, which are actually very important…
Malte Rørmose Damgaard, Rasmus Pedersen, Thomas Bak
Title: Summary Inspired by the “cognitive hourglass” model presented by the researchers behind the cognitive architecture called Sigma, we propose a framework for developing cognitive architectures for cognitive robotics. The main purpose of the proposed framework is to ease development of cognitive architectures by…
Yuanqi Du, Xian Liu, Shengchao Liu, Jieyu Zhang + 1 more
Discovering new structures in the chemical space is a long-standing challenge and has important applications to various fields such as chemistry, material science, and drug discovery. Deep generative models have been used in de novo molecule design to embed molecules in a meaningful latent space and then sample new…
Ran He, Jie Cao, Tieniu Tan
Generative artificial intelligence (GAI) has recently achieved significant success, enabling anyone to create texts, images, videos and even computer codes while providing insights that might not be possible with traditional tools. To stimulate future research, this work provides a brief summary of the ongoing and…
Stefan Lenz, Moritz Hess, Harald Binder
Background The best way to calculate statistics from medical data is to use the data of individual patients. In some settings, this data is difficult to obtain due to privacy restrictions. In Germany, for example, it is not possible to pool routine data from different hospitals for research purposes without the consent…
Manfred Jaeger
Reasoning about graphs, and learning from graph data is a field of artificial intelligence that has recently received much attention in the machine learning areas of graph representation learning and graph neural networks. Graphs are also the underlying structures of interest in a wide range of more traditional fields…
Francesca Pia Panaccione, Sofia Mongardi, Marco Masseroli, Pietro Pinoli + 2 more
'Pietro Pinoli' 'Chandan K. Sen' 'George Truskey'] The advancement of computational genomics has significantly enhanced the use of data-driven solutions in disease prediction and precision medicine. Yet, challenges such as data scarcity, privacy constraints, and biases persist. Synthetic data generation offers a…
Joshua Levy, Carly Bobak, Brock Christensen, Louis Vaickus + 1 more
Network analysis methods are useful to better understand and contextualize relationships between entities. While statistical and machine learning prediction models generally assume independence between actors, network-based statistical methods for social network data allow for dyadic dependence between actors. While…
Daniel M. Gonçalves, André Patrício, Rafael S. Costa, Rui Henriques
The growing availability and complexity of omics data have driven the development of specialized algorithms for modeling molecular systems. Although graph-based learning methods effectively represent biological interactions, they often neglect the statistical information embedded in node and edge annotations. To…
David Buterez, Jon Paul Janet, Steven Kiddle, Pietro Liò
We investigate the potential of graph neural networks for transfer learning and improving molecular property prediction on sparse and expensive to acquire high-fidelity data by leveraging low-fidelity measurements as an inexpensive proxy for a targeted property ofinterest. This problem arises in discovery processes…
Riccardo Smeriglio, Joana Rosell-Mirmi, Petia Radeva, Jordi Abante
Current genotype-to-phenotype models, such as poly-genic risk scores, only account for linear relationships between genotype and phenotype and ignore epistatic interactions, limiting the complexity of the diseases that can be properly characterized. Protein-protein interaction networks have the potential to improve the…
Liying Chen, Satwik Acharyya, Chunyu Luo, Yang Ni + 1 more
Probabilistic graphical models are powerful and widely used tools to quantify, visualize and interpret dependencies in complex biological systems such as highthroughput genomics and proteomics. However, most existing graphical modeling methods assume homogeneity within and across samples which restricts their broad…
Philipp Renz, Dries Van Rompaey, Jörg Kurt Wegner, Sepp Hochreiter + 1 more
There has been a wave of generative models for molecules triggered by advances in the field of Deep Learning. These generative models are often used to optimize chemical compounds towards particular properties or a desired biological activity. The evaluation of generative models remains challenging and suggested…
Jens Nußberger, Frederic Boesel, Stefan Lenz, Harald Binder + 1 more
Deep generative models can be trained to represent the joint distribution of data, such as measurements of single nucleotide polymorphisms (SNPs) from several individuals. Subsequently, synthetic observations are obtained by drawing from this distribution. This has been shown to be useful for several tasks, such as…
Alejandro A. Edera, Georgina Stegmayer, Diego H. Milone
Unsupervised learning of node representations from knowledge graphs is critical for numerous downstream tasks, ranging from large-scale graph analysis to measuring semantic similarity between nodes. This study presents gGN as a novel representation that defines graph nodes as Gaussian distributions. Unlike existing…
Jie Lin, Mingyuan Xu, Hongming Chen
Shape-based virtual screening is a widely utilized method in ligand-based de novo drug design, aiming to identify molecules in chemical libraries that share similar 3D shapes but simultaneously possess novel 2D chemical structures compared to the reference compound. As an emerging technology, generative model is an…