arXiv subjects

Octavian-Eugen Ganea

Publications and source records attributed to Octavian-Eugen Ganea.

At least 19 recordsLinked to original sources

arXiv2022

EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction

Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on heavy candidate sampling coupled with scoring, ranking, and fine-tuning steps. We challenge this paradigm with EquiBind, an SE(3)-equivariant geometric deep learning model performing direct-shot prediction of both i) the receptor binding location (blind docking) and ii) the ligand's bound pose and orientation. EquiBind achieves significant speed-ups and better quality compared to traditional and recent baselines. Further, we show extra improvements when coupling it with existing fine-tuning techniques at the cost of increased running time. Finally, we propose a novel and fast fine-tuning model that adjusts torsion angles of a ligand's rotatable bonds based on closed-form global minima of the von Mises angular distance to a given input atomic point cloud, avoiding previous expensive differential evolution strategies for energy minimization.

q-bio.BM↗

arXiv2022

Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking

Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering. We tackle rigid body protein-protein docking, i.e., computationally predicting the 3D structure of a protein-protein complex from the individual unbound structures, assuming no conformational change within the proteins happens during binding. We design a novel pairwise-independent SE(3)-equivariant graph matching network to predict the rotation and translation to place one of the proteins at the right docked position relative to the second protein. We mathematically guarantee a basic principle: the predicted complex is always identical regardless of the initial locations and orientations of the two structures. Our model, named EquiDock, approximates the binding pockets and predicts the docking poses using keypoint matching and alignment, achieved through optimal transport and a differentiable Kabsch algorithm. Empirically, we achieve significant running time improvements and often outperform existing docking software despite not relying on heavy candidate sampling, structure refinement, or templates.

cs.AI↗

arXiv2022

Crystal Diffusion Variational Autoencoder for Periodic Material Generation

Generating the periodic structure of stable materials is a long-standing challenge for the material design community. This task is difficult because stable materials only exist in a low-dimensional subspace of all possible periodic arrangements of atoms: 1) the coordinates must lie in the local energy minimum defined by quantum mechanics, and 2) global stability also requires the structure to follow the complex, yet specific bonding preferences between different atom types. Existing methods fail to incorporate these factors and often lack proper invariances. We propose a Crystal Diffusion Variational Autoencoder (CDVAE) that captures the physical inductive bias of material stability. By learning from the data distribution of stable materials, the decoder generates materials in a diffusion process that moves atomic coordinates towards a lower energy state and updates atom types to satisfy bonding preferences between neighbors. Our model also explicitly encodes interactions across periodic boundaries and respects permutation, translation, rotation, and periodic invariances. We significantly outperform past methods in three tasks: 1) reconstructing the input structure, 2) generating valid, diverse, and realistic materials, and 3) generating materials that optimize a specific property. We also provide several standard datasets and evaluation metrics for the broader machine learning community.

cs.LG↗

arXiv2021

Optimal Transport Graph Neural Networks

Current graph neural network (GNN) architectures naively average or sum node embeddings into an aggregated graph representation -- potentially losing structural or semantic information. We here introduce OT-GNN, a model that computes graph embeddings using parametric prototypes that highlight key facets of different graph aspects. Towards this goal, we successfully combine optimal transport (OT) with parametric graph models. Graph representations are obtained from Wasserstein distances between the set of GNN node embeddings and ``prototype'' point clouds as free parameters. We theoretically prove that, unlike traditional sum aggregation, our function class on point clouds satisfies a fundamental universal approximation theorem. Empirically, we address an inherent collapse optimization issue by proposing a noise contrastive regularizer to steer the model towards truly exploiting the OT geometry. Finally, we outperform popular methods on several molecular property prediction tasks, while exhibiting smoother graph representations.

stat.ML↗

arXiv2021

GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles

Prediction of a molecule's 3D conformer ensemble from the molecular graph holds a key role in areas of cheminformatics and drug discovery. Existing generative models have several drawbacks including lack of modeling important molecular geometry elements (e.g. torsion angles), separate optimization stages prone to error accumulation, and the need for structure fine-tuning based on approximate classical force-fields or computationally expensive methods such as metadynamics with approximate quantum mechanics calculations at each geometry. We propose GeoMol--an end-to-end, non-autoregressive and SE(3)-invariant machine learning approach to generate distributions of low-energy molecular 3D conformers. Leveraging the power of message passing neural networks (MPNNs) to capture local and global graph information, we predict local atomic 3D structures and torsion angles, avoiding unnecessary over-parameterization of the geometric degrees of freedom (e.g. one angle per non-terminal bond). Such local predictions suffice both for the training loss computation, as well as for the full deterministic conformer assembly (at test time). We devise a non-adversarial optimal transport based loss function to promote diverse conformer generation. GeoMol predominantly outperforms popular open-source, commercial, or state-of-the-art machine learning (ML) models, while achieving significant speed-ups. We expect such differentiable 3D structure generators to significantly impact molecular modeling and related applications.

physics.chem-ph↗

arXiv2020

Message Passing Networks for Molecules with Tetrahedral Chirality

Molecules with identical graph connectivity can exhibit different physical and biological properties if they exhibit stereochemistry-a spatial structural characteristic. However, modern neural architectures designed for learning structure-property relationships from molecular structures treat molecules as graph-structured data and therefore are invariant to stereochemistry. Here, we develop two custom aggregation functions for message passing neural networks to learn properties of molecules with tetrahedral chirality, one common form of stereochemistry. We evaluate performance on synthetic data as well as a newly-proposed protein-ligand docking dataset with relevance to drug discovery. Results show modest improvements over a baseline sum aggregator, highlighting opportunities for further architecture development.

q-bio.QM↗

arXiv2020

Computationally Tractable Riemannian Manifolds for Graph Embeddings

Representing graphs as sets of node embeddings in certain curved Riemannian manifolds has recently gained momentum in machine learning due to their desirable geometric inductive biases, e.g., hierarchical structures benefit from hyperbolic geometry. However, going beyond embedding spaces of constant sectional curvature, while potentially more representationally powerful, proves to be challenging as one can easily lose the appeal of computationally tractable tools such as geodesic distances or Riemannian gradients. Here, we explore computationally efficient matrix manifolds, showcasing how to learn and optimize graph embeddings in these Riemannian spaces. Empirically, we demonstrate consistent improvements over Euclidean geometry while often outperforming hyperbolic and elliptical embeddings based on various metrics that capture different graph properties. Our results serve as new evidence for the benefits of non-Euclidean embeddings in machine learning pipelines.

cs.LG↗

arXiv2020

Constant Curvature Graph Convolutional Networks

Interest has been rising lately towards methods representing data in non-Euclidean spaces, e.g. hyperbolic or spherical, that provide specific inductive biases useful for certain real-world data properties, e.g. scale-free, hierarchical or cyclical. However, the popular graph neural networks are currently limited in modeling data only via Euclidean geometry and associated vector space operations. Here, we bridge this gap by proposing mathematically grounded generalizations of graph convolutional networks (GCN) to (products of) constant curvature spaces. We do this by i) introducing a unified formalism that can interpolate smoothly between all geometries of constant curvature, ii) leveraging gyro-barycentric coordinates that generalize the classic Euclidean concept of the center of mass. Our class of models smoothly recover their Euclidean counterparts when the curvature goes to zero from either side. Empirically, we outperform Euclidean GCNs in the tasks of node classification and distortion minimization for symbolic data exhibiting non-Euclidean behavior, according to their discrete curvature.

cs.LG↗

arXiv2020

Mixed-curvature Variational Autoencoders

Euclidean geometry has historically been the typical "workhorse" for machine learning applications due to its power and simplicity. However, it has recently been shown that geometric spaces with constant non-zero curvature improve representations and performance on a variety of data types and downstream tasks. Consequently, generative models like Variational Autoencoders (VAEs) have been successfully generalized to elliptical and hyperbolic latent spaces. While these approaches work well on data with particular kinds of biases e.g. tree-like data for a hyperbolic VAE, there exists no generic approach unifying and leveraging all three models. We develop a Mixed-curvature Variational Autoencoder, an efficient way to train a VAE whose latent space is a product of constant curvature Riemannian manifolds, where the per-component curvature is fixed or learnable. This generalizes the Euclidean VAE to curved latent spaces and recovers it when curvatures of all latent space components go to 0.

cs.LG↗

arXiv2019

Noise Contrastive Variational Autoencoders

We take steps towards understanding the "posterior collapse (PC)" difficulty in variational autoencoders (VAEs),~i.e. a degenerate optimum in which the latent codes become independent of their corresponding inputs. We rely on calculus of variations and theoretically explore a few popular VAE models, showing that PC always occurs for non-parametric encoders and decoders. Inspired by the popular noise contrastive estimation algorithm, we propose NC-VAE where the encoder discriminates between the latent codes of real data and of some artificially generated noise, in addition to encouraging good data reconstruction abilities. Theoretically, we prove that our model cannot reach PC and provide novel lower bounds. Our method is straightforward to implement and has the same run-time as vanilla VAE. Empirically, we showcase its benefits on popular image and text datasets.

cs.LG↗

arXiv2019

Breaking the Softmax Bottleneck via Learnable Monotonic Pointwise Non-linearities

The Softmax function on top of a final linear layer is the de facto method to output probability distributions in neural networks. In many applications such as language models or text generation, this model has to produce distributions over large output vocabularies. Recently, this has been shown to have limited representational capacity due to its connection with the rank bottleneck in matrix factorization. However, little is known about the limitations of Linear-Softmax for quantities of practical interest such as cross entropy or mode estimation, a direction that we explore here. As an efficient and effective solution to alleviate this issue, we propose to learn parametric monotonic functions on top of the logits. We theoretically investigate the rank increasing capabilities of such monotonic functions. Empirically, our method improves in two different quality metrics over the traditional Linear-Softmax layer in synthetic and real language model experiments, adding little time or memory overhead, while being comparable to the more computationally expensive mixture of Softmaxes.

cs.LG↗

arXiv2019

Riemannian Adaptive Optimization Methods

Several first order stochastic optimization methods commonly used in the Euclidean domain such as stochastic gradient descent (SGD), accelerated gradient descent or variance reduced methods have already been adapted to certain Riemannian settings. However, some of the most popular of these optimization tools - namely Adam , Adagrad and the more recent Amsgrad - remain to be generalized to Riemannian manifolds. We discuss the difficulty of generalizing such adaptive schemes to the most agnostic Riemannian setting, and then provide algorithms and convergence proofs for geodesically convex objectives in the particular case of a product of Riemannian manifolds, in which adaptivity is implemented across manifolds in the cartesian product. Our generalization is tight in the sense that choosing the Euclidean space as Riemannian manifold yields the same algorithms and regret bounds as those that were already known for the standard algorithms. Experimentally, we show faster convergence and to a lower train loss value for Riemannian adaptive methods over their corresponding baselines on the realistic task of embedding the WordNet taxonomy in the Poincare ball.

cs.LG↗

arXiv2018

Poincaré GloVe: Hyperbolic Word Embeddings

Words are not created equal. In fact, they form an aristocratic graph with a latent hierarchical structure that the next generation of unsupervised learned word embeddings should reveal. In this paper, justified by the notion of delta-hyperbolicity or tree-likeliness of a space, we propose to embed words in a Cartesian product of hyperbolic spaces which we theoretically connect to the Gaussian word embeddings and their Fisher geometry. This connection allows us to introduce a novel principled hypernymy score for word embeddings. Moreover, we adapt the well-known Glove algorithm to learn unsupervised word embeddings in this type of Riemannian manifolds. We further explain how to solve the analogy task using the Riemannian parallel transport that generalizes vector arithmetics to this new type of geometry. Empirically, based on extensive experiments, we prove that our embeddings, trained unsupervised, are the first to simultaneously outperform strong and popular baselines on the tasks of similarity, analogy and hypernymy detection. In particular, for word hypernymy, we obtain new state-of-the-art on fully unsupervised WBLESS classification accuracy.

cs.CL↗

arXiv2018

Learning and Evaluating Sparse Interpretable Sentence Embeddings

Previous research on word embeddings has shown that sparse representations, which can be either learned on top of existing dense embeddings or obtained through model constraints during training time, have the benefit of increased interpretability properties: to some degree, each dimension can be understood by a human and associated with a recognizable feature in the data. In this paper, we transfer this idea to sentence embeddings and explore several approaches to obtain a sparse representation. We further introduce a novel, quantitative and automated evaluation metric for sentence embedding interpretability, based on topic coherence methods. We observe an increase in interpretability compared to dense models, on a dataset of movie dialogs and on the scene descriptions from the MS COCO dataset.

cs.CL↗

arXiv2018

End-to-End Neural Entity Linking

Entity Linking (EL) is an essential task for semantic text understanding and information extraction. Popular methods separately address the Mention Detection (MD) and Entity Disambiguation (ED) stages of EL, without leveraging their mutual dependency. We here propose the first neural end-to-end EL system that jointly discovers and links entities in a text document. The main idea is to consider all possible spans as potential mentions and learn contextual similarity scores over their entity candidates that are useful for both MD and ED decisions. Key components are context-aware mention embeddings, entity embeddings and a probabilistic mention - entity map, without demanding other engineered features. Empirically, we show that our end-to-end method significantly outperforms popular systems on the Gerbil platform when enough training data is available. Conversely, if testing datasets follow different annotation conventions compared to the training set (e.g. queries/ tweets vs news documents), our ED model coupled with a traditional NER system offers the best or second best EL accuracy.

cs.CL↗

arXiv2018

Hyperbolic Neural Networks

Hyperbolic spaces have recently gained momentum in the context of machine learning due to their high capacity and tree-likeliness properties. However, the representational power of hyperbolic geometry is not yet on par with Euclidean geometry, mostly because of the absence of corresponding hyperbolic neural network layers. This makes it hard to use hyperbolic embeddings in downstream tasks. Here, we bridge this gap in a principled manner by combining the formalism of Möbius gyrovector spaces with the Riemannian geometry of the Poincaré model of hyperbolic spaces. As a result, we derive hyperbolic versions of important deep learning tools: multinomial logistic regression, feed-forward and recurrent neural networks such as gated recurrent units. This allows to embed sequential data and perform classification in the hyperbolic space. Empirically, we show that, even if hyperbolic optimization tools are limited, hyperbolic sentence embeddings either outperform or are on par with their Euclidean variants on textual entailment and noisy-prefix recognition tasks.

cs.LG↗

arXiv2018

Hyperbolic Entailment Cones for Learning Hierarchical Embeddings

Learning graph representations via low-dimensional embeddings that preserve relevant network properties is an important class of problems in machine learning. We here present a novel method to embed directed acyclic graphs. Following prior work, we first advocate for using hyperbolic spaces which provably model tree-like structures better than Euclidean geometry. Second, we view hierarchical relations as partial orders defined using a family of nested geodesically convex cones. We prove that these entailment cones admit an optimal shape with a closed form expression both in the Euclidean and hyperbolic spaces, and they canonically define the embedding learning process. Experiments show significant improvements of our method over strong recent baselines both in terms of representational capacity and generalization.

cs.LG↗

arXiv2018

Web2Text: Deep Structured Boilerplate Removal

Web pages are a valuable source of information for many natural language processing and information retrieval tasks. Extracting the main content from those documents is essential for the performance of derived applications. To address this issue, we introduce a novel model that performs sequence labeling to collectively classify all text blocks in an HTML page as either boilerplate or main content. Our method uses a hidden Markov model on top of potentials derived from DOM tree features using convolutional neural networks. The proposed method sets a new state-of-the-art performance for boilerplate removal on the CleanEval benchmark. As a component of information retrieval pipelines, it improves retrieval performance on the ClueWeb12 collection.

cs.IR↗