We propose a novel deep learning model for joint document-level entity disambiguation, which leverages learned neural representations. Key components are entity embeddings, a neural attention mechanism over local context windows, and a differentiable joint inference stage for disambiguation. Our approach thereby combines benefits of deep learning with more traditional approaches such as graphical models and probabilistic mention-entity maps. Extensive experiments show that we are able to obtain competitive or stateof-the-art accuracy at moderate computational costs.

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.

Many fundamental problems in natural language processing rely on determining what entities appear in a given text. Commonly referenced as entity linking, this step is a fundamental component of many NLP tasks such as text understanding, automatic summarization, semantic search or machine translation. Name ambiguity, word polysemy, context dependencies and a heavy-tailed distribution of entities contribute to the complexity of this problem.We here propose a probabilistic approach that makes use of an effective graphical model to perform collective entity disambiguation. Input mentions (i.e., linkable token spans) are disambiguated jointly across an entire document by combining a document-level prior of entity co-occurrences with local information captured from mentions and their surrounding context. The model is based on simple sufficient statistics extracted from data, thus relying on few parameters to be learned.Our method does not require extensive feature engineering, nor an expensive training procedure. We use loopy belief propagation to perform approximate inference. The low complexity of our model makes this step sufficiently fast for real-time usage. We demonstrate the accuracy of our approach on a wide range of benchmark datasets, showing that it matches, and in many cases outperforms, existing stateof-the-art methods.

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.

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.