Jorge Aguilera-Iparraguirre

Bio: Jorge Aguilera-Iparraguirre is an academic researcher from Harvard University. The author has contributed to research in topics: OLED & Encoder. The author has an hindex of 16, co-authored 22 publications receiving 5041 citations. Previous affiliations of Jorge Aguilera-Iparraguirre include Ruhr University Bochum & Karlsruhe Institute of Technology.

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

Abstract: We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended spaces of chemical compounds. A deep neural network was trained on hundreds of thousands of existing chemical structures to construct three coupled functions: an encoder, a decoder, and a predictor. The encoder converts the discrete representation of a molecule into a real-valued continuous vector, and the decoder converts these continuous vectors back to discrete molecular representations. The predictor estimates chemical properties from the latent continuous vector representation of the molecule. Continuous representations of molecules allow us to automatically generate novel chemical structures by performing simple operations in the latent space, such as decoding random vectors, perturbing known chemical structures, or interpolating between molecules. Continuous represent...

Convolutional networks on graphs for learning molecular fingerprints

Abstract: We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.

Automatic chemical design using a data-driven continuous representation of molecules

Abstract: We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended spaces of chemical compounds. A deep neural network was trained on hundreds of thousands of existing chemical structures to construct three coupled functions: an encoder, a decoder and a predictor. The encoder converts the discrete representation of a molecule into a real-valued continuous vector, and the decoder converts these continuous vectors back to discrete molecular representations. The predictor estimates chemical properties from the latent continuous vector representation of the molecule. Continuous representations allow us to automatically generate novel chemical structures by performing simple operations in the latent space, such as decoding random vectors, perturbing known chemical structures, or interpolating between molecules. Continuous representations also allow the use of powerful gradient-based optimization to efficiently guide the search for optimized functional compounds. We demonstrate our method in the domain of drug-like molecules and also in the set of molecules with fewer that nine heavy atoms.

Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approach

Abstract: A high-throughput virtual screening approach is used to select molecules with efficient, thermally activated delayed fluorescence. The good performance of several selected emitters in organic LED applications has also been confirmed experimentally.

Convolutional Networks on Graphs for Learning Molecular Fingerprints

Abstract: We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.

A Comprehensive Survey on Graph Neural Networks

Abstract: Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications, where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on the existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this article, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art GNNs into four categories, namely, recurrent GNNs, convolutional GNNs, graph autoencoders, and spatial–temporal GNNs. We further discuss the applications of GNNs across various domains and summarize the open-source codes, benchmark data sets, and model evaluation of GNNs. Finally, we propose potential research directions in this rapidly growing field.

Modeling Relational Data with Graph Convolutional Networks

Abstract: Knowledge graphs enable a wide variety of applications, including question answering and information retrieval. Despite the great effort invested in their creation and maintenance, even the largest (e.g., Yago, DBPedia or Wikidata) remain incomplete. We introduce Relational Graph Convolutional Networks (R-GCNs) and apply them to two standard knowledge base completion tasks: Link prediction (recovery of missing facts, i.e. subject-predicate-object triples) and entity classification (recovery of missing entity attributes). R-GCNs are related to a recent class of neural networks operating on graphs, and are developed specifically to handle the highly multi-relational data characteristic of realistic knowledge bases. We demonstrate the effectiveness of R-GCNs as a stand-alone model for entity classification. We further show that factorization models for link prediction such as DistMult can be significantly improved through the use of an R-GCN encoder model to accumulate evidence over multiple inference steps in the graph, demonstrating a large improvement of 29.8% on FB15k-237 over a decoder-only baseline.

Graph Convolutional Neural Networks for Web-Scale Recommender Systems

Abstract: Recent advancements in deep neural networks for graph-structured data have led to state-of-the-art performance on recommender system benchmarks. However, making these methods practical and scalable to web-scale recommendation tasks with billions of items and hundreds of millions of users remains an unsolved challenge. Here we describe a large-scale deep recommendation engine that we developed and deployed at Pinterest. We develop a data-efficient Graph Convolutional Network (GCN) algorithm, which combines efficient random walks and graph convolutions to generate embeddings of nodes (i.e., items) that incorporate both graph structure as well as node feature information. Compared to prior GCN approaches, we develop a novel method based on highly efficient random walks to structure the convolutions and design a novel training strategy that relies on harder-and-harder training examples to improve robustness and convergence of the model. We also develop an efficient MapReduce model inference algorithm to generate embeddings using a trained model. Overall, we can train on and embed graphs that are four orders of magnitude larger than typical GCN implementations. We show how GCN embeddings can be used to make high-quality recommendations in various settings at Pinterest, which has a massive underlying graph with 3 billion nodes representing pins and boards, and 17 billion edges. According to offline metrics, user studies, as well as A/B tests, our approach generates higher-quality recommendations than comparable deep learning based systems. To our knowledge, this is by far the largest application of deep graph embeddings to date and paves the way for a new generation of web-scale recommender systems based on graph convolutional architectures.

Geometric Deep Learning: Going beyond Euclidean data

Abstract: Many scientific fields study data with an underlying structure that is non-Euclidean. Some examples include social networks in computational social sciences, sensor networks in communications, functional networks in brain imaging, regulatory networks in genetics, and meshed surfaces in computer graphics. In many applications, such geometric data are large and complex (in the case of social networks, on the scale of billions) and are natural targets for machine-learning techniques. In particular, we would like to use deep neural networks, which have recently proven to be powerful tools for a broad range of problems from computer vision, natural-language processing, and audio analysis. However, these tools have been most successful on data with an underlying Euclidean or grid-like structure and in cases where the invariances of these structures are built into networks used to model them.

Graph Neural Networks: A Review of Methods and Applications

Abstract: Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures (like the dependency trees of sentences and the scene graphs of images) is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are neural models that capture the dependence of graphs via message passing between the nodes of graphs. In recent years, variants of GNNs such as graph convolutional network (GCN), graph attention network (GAT), graph recurrent network (GRN) have demonstrated ground-breaking performances on many deep learning tasks. In this survey, we propose a general design pipeline for GNN models and discuss the variants of each component, systematically categorize the applications, and propose four open problems for future research.