arXiv subjects

Regina Barzilay

Publications and source records attributed to Regina Barzilay.

At least 91 records · Page 5Linked to original sources

arXiv2019

Analyzing Learned Molecular Representations for Property Prediction

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

cs.LG↗

arXiv2019

Capturing Greater Context for Question Generation

Automatic question generation can benefit many applications ranging from dialogue systems to reading comprehension. While questions are often asked with respect to long documents, there are many challenges with modeling such long documents. Many existing techniques generate questions by effectively looking at one sentence at a time, leading to questions that are easy and not reflective of the human process of question generation. Our goal is to incorporate interactions across multiple sentences to generate realistic questions for long documents. In order to link a broad document context to the target answer, we represent the relevant context via a multi-stage attention mechanism, which forms the foundation of a sequence to sequence model. We outperform state-of-the-art methods on question generation on three question-answering datasets -- SQuAD, MS MARCO and NewsQA.

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arXiv2019

Learning to Make Generalizable and Diverse Predictions for Retrosynthesis

We propose a new model for making generalizable and diverse retrosynthetic reaction predictions. Given a target compound, the task is to predict the likely chemical reactants to produce the target. This generative task can be framed as a sequence-to-sequence problem by using the SMILES representations of the molecules. Building on top of the popular Transformer architecture, we propose two novel pre-training methods that construct relevant auxiliary tasks (plausible reactions) for our problem. Furthermore, we incorporate a discrete latent variable model into the architecture to encourage the model to produce a diverse set of alternative predictions. On the 50k subset of reaction examples from the United States patent literature (USPTO-50k) benchmark dataset, our model greatly improves performance over the baseline, while also generating predictions that are more diverse.

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arXiv2019

Hierarchical Graph-to-Graph Translation for Molecules

The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on graph-to-graph translation methods for molecular optimization. In particular, we realize coherent multi-resolution representations by interweaving the encoding of substructure components with the atom-level encoding of the original molecular graph. Moreover, our graph decoder is fully autoregressive, and interleaves each step of adding a new substructure with the process of resolving its attachment to the emerging molecule. We evaluate our model on multiple molecular optimization tasks and show that our model significantly outperforms previous state-of-the-art baselines.

physics.chem-ph↗

arXiv2019

Working Hard or Hardly Working: Challenges of Integrating Typology into Neural Dependency Parsers

This paper explores the task of leveraging typology in the context of cross-lingual dependency parsing. While this linguistic information has shown great promise in pre-neural parsing, results for neural architectures have been mixed. The aim of our investigation is to better understand this state-of-the-art. Our main findings are as follows: 1) The benefit of typological information is derived from coarsely grouping languages into syntactically-homogeneous clusters rather than from learning to leverage variations along individual typological dimensions in a compositional manner; 2) Typology consistent with the actual corpus statistics yields better transfer performance; 3) Typological similarity is only a rough proxy of cross-lingual transferability with respect to parsing.

cs.CL↗

arXiv2019

Towards Debiasing Fact Verification Models

Fact verification requires validating a claim in the context of evidence. We show, however, that in the popular FEVER dataset this might not necessarily be the case. Claim-only classifiers perform competitively with top evidence-aware models. In this paper, we investigate the cause of this phenomenon, identifying strong cues for predicting labels solely based on the claim, without considering any evidence. We create an evaluation set that avoids those idiosyncrasies. The performance of FEVER-trained models significantly drops when evaluated on this test set. Therefore, we introduce a regularization method which alleviates the effect of bias in the training data, obtaining improvements on the newly created test set. This work is a step towards a more sound evaluation of reasoning capabilities in fact verification models.

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arXiv2019

Neural Decipherment via Minimum-Cost Flow: from Ugaritic to Linear B

In this paper we propose a novel neural approach for automatic decipherment of lost languages. To compensate for the lack of strong supervision signal, our model design is informed by patterns in language change documented in historical linguistics. The model utilizes an expressive sequence-to-sequence model to capture character-level correspondences between cognates. To effectively train the model in an unsupervised manner, we innovate the training procedure by formalizing it as a minimum-cost flow problem. When applied to the decipherment of Ugaritic, we achieve a 5.5% absolute improvement over state-of-the-art results. We also report the first automatic results in deciphering Linear B, a syllabic language related to ancient Greek, where our model correctly translates 67.3% of cognates.

cs.CL↗

arXiv2019

Path-Augmented Graph Transformer Network

Much of the recent work on learning molecular representations has been based on Graph Convolution Networks (GCN). These models rely on local aggregation operations and can therefore miss higher-order graph properties. To remedy this, we propose Path-Augmented Graph Transformer Networks (PAGTN) that are explicitly built on longer-range dependencies in graph-structured data. Specifically, we use path features in molecular graphs to create global attention layers. We compare our PAGTN model against the GCN model and show that our model consistently outperforms GCNs on molecular property prediction datasets including quantum chemistry (QM7, QM8, QM9), physical chemistry (ESOL, Lipophilictiy) and biochemistry (BACE, BBBP).

cs.LG↗

arXiv2019

Using Machine Learning and Natural Language Processing to Review and Classify the Medical Literature on Cancer Susceptibility Genes

PURPOSE: The medical literature relevant to germline genetics is growing exponentially. Clinicians need tools monitoring and prioritizing the literature to understand the clinical implications of the pathogenic genetic variants. We developed and evaluated two machine learning models to classify abstracts as relevant to the penetrance (risk of cancer for germline mutation carriers) or prevalence of germline genetic mutations. METHODS: We conducted literature searches in PubMed and retrieved paper titles and abstracts to create an annotated dataset for training and evaluating the two machine learning classification models. Our first model is a support vector machine (SVM) which learns a linear decision rule based on the bag-of-ngrams representation of each title and abstract. Our second model is a convolutional neural network (CNN) which learns a complex nonlinear decision rule based on the raw title and abstract. We evaluated the performance of the two models on the classification of papers as relevant to penetrance or prevalence. RESULTS: For penetrance classification, we annotated 3740 paper titles and abstracts and used 60% for training the model, 20% for tuning the model, and 20% for evaluating the model. The SVM model achieves 89.53% accuracy (percentage of papers that were correctly classified) while the CNN model achieves 88.95 % accuracy. For prevalence classification, we annotated 3753 paper titles and abstracts. The SVM model achieves 89.14% accuracy while the CNN model achieves 89.13 % accuracy. CONCLUSION: Our models achieve high accuracy in classifying abstracts as relevant to penetrance or prevalence. By facilitating literature review, this tool could help clinicians and researchers keep abreast of the burgeoning knowledge of gene-cancer associations and keep the knowledge bases for clinical decision support tools up to date.

cs.IR↗

arXiv2019

GraphIE: A Graph-Based Framework for Information Extraction

Most modern Information Extraction (IE) systems are implemented as sequential taggers and only model local dependencies. Non-local and non-sequential context is, however, a valuable source of information to improve predictions. In this paper, we introduce GraphIE, a framework that operates over a graph representing a broad set of dependencies between textual units (i.e. words or sentences). The algorithm propagates information between connected nodes through graph convolutions, generating a richer representation that can be exploited to improve word-level predictions. Evaluation on three different tasks --- namely textual, social media and visual information extraction --- shows that GraphIE consistently outperforms the state-of-the-art sequence tagging model by a significant margin.

cs.CL↗

arXiv2019

Cross-Lingual Alignment of Contextual Word Embeddings, with Applications to Zero-shot Dependency Parsing

We introduce a novel method for multilingual transfer that utilizes deep contextual embeddings, pretrained in an unsupervised fashion. While contextual embeddings have been shown to yield richer representations of meaning compared to their static counterparts, aligning them poses a challenge due to their dynamic nature. To this end, we construct context-independent variants of the original monolingual spaces and utilize their mapping to derive an alignment for the context-dependent spaces. This mapping readily supports processing of a target language, improving transfer by context-aware embeddings. Our experimental results demonstrate the effectiveness of this approach for zero-shot and few-shot learning of dependency parsing. Specifically, our method consistently outperforms the previous state-of-the-art on 6 tested languages, yielding an improvement of 6.8 LAS points on average.

cs.CL↗

arXiv2019

Inferring Which Medical Treatments Work from Reports of Clinical Trials

How do we know if a particular medical treatment actually works? Ideally one would consult all available evidence from relevant clinical trials. Unfortunately, such results are primarily disseminated in natural language scientific articles, imposing substantial burden on those trying to make sense of them. In this paper, we present a new task and corpus for making this unstructured evidence actionable. The task entails inferring reported findings from a full-text article describing a randomized controlled trial (RCT) with respect to a given intervention, comparator, and outcome of interest, e.g., inferring if an article provides evidence supporting the use of aspirin to reduce risk of stroke, as compared to placebo. We present a new corpus for this task comprising 10,000+ prompts coupled with full-text articles describing RCTs. Results using a suite of models --- ranging from heuristic (rule-based) approaches to attentive neural architectures --- demonstrate the difficulty of the task, which we believe largely owes to the lengthy, technical input texts. To facilitate further work on this important, challenging problem we make the corpus, documentation, a website and leaderboard, and code for baselines and evaluation available at http://evidence-inference.ebm-nlp.com/.

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arXiv2019

Junction Tree Variational Autoencoder for Molecular Graph Generation

We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings instead of graphs. Our junction tree variational autoencoder generates molecular graphs in two phases, by first generating a tree-structured scaffold over chemical substructures, and then combining them into a molecule with a graph message passing network. This approach allows us to incrementally expand molecules while maintaining chemical validity at every step. We evaluate our model on multiple tasks ranging from molecular generation to optimization. Across these tasks, our model outperforms previous state-of-the-art baselines by a significant margin.

cs.LG↗

arXiv2019

Learning Multimodal Graph-to-Graph Translation for Molecular Optimization

We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be optimized in different ways, there are multiple viable translations for each input graph. A key challenge is therefore to model diverse translation outputs. Our primary contributions include a junction tree encoder-decoder for learning diverse graph translations along with a novel adversarial training method for aligning distributions of molecules. Diverse output distributions in our model are explicitly realized by low-dimensional latent vectors that modulate the translation process. We evaluate our model on multiple molecular optimization tasks and show that our model outperforms previous state-of-the-art baselines.

cs.LG↗

arXiv2018

Grounding Language for Transfer in Deep Reinforcement Learning

In this paper, we explore the utilization of natural language to drive transfer for reinforcement learning (RL). Despite the wide-spread application of deep RL techniques, learning generalized policy representations that work across domains remains a challenging problem. We demonstrate that textual descriptions of environments provide a compact intermediate channel to facilitate effective policy transfer. Specifically, by learning to ground the meaning of text to the dynamics of the environment such as transitions and rewards, an autonomous agent can effectively bootstrap policy learning on a new domain given its description. We employ a model-based RL approach consisting of a differentiable planning module, a model-free component and a factorized state representation to effectively use entity descriptions. Our model outperforms prior work on both transfer and multi-task scenarios in a variety of different environments. For instance, we achieve up to 14% and 11.5% absolute improvement over previously existing models in terms of average and initial rewards, respectively.

cs.CL↗

arXiv2018

Multi-Source Domain Adaptation with Mixture of Experts

We propose a mixture-of-experts approach for unsupervised domain adaptation from multiple sources. The key idea is to explicitly capture the relationship between a target example and different source domains. This relationship, expressed by a point-to-set metric, determines how to combine predictors trained on various domains. The metric is learned in an unsupervised fashion using meta-training. Experimental results on sentiment analysis and part-of-speech tagging demonstrate that our approach consistently outperforms multiple baselines and can robustly handle negative transfer.

cs.CL↗

arXiv2018

Deriving Machine Attention from Human Rationales

Attention-based models are successful when trained on large amounts of data. In this paper, we demonstrate that even in the low-resource scenario, attention can be learned effectively. To this end, we start with discrete human-annotated rationales and map them into continuous attention. Our central hypothesis is that this mapping is general across domains, and thus can be transferred from resource-rich domains to low-resource ones. Our model jointly learns a domain-invariant representation and induces the desired mapping between rationales and attention. Our empirical results validate this hypothesis and show that our approach delivers significant gains over state-of-the-art baselines, yielding over 15% average error reduction on benchmark datasets.

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arXiv2017

Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network

The prediction of organic reaction outcomes is a fundamental problem in computational chemistry. Since a reaction may involve hundreds of atoms, fully exploring the space of possible transformations is intractable. The current solution utilizes reaction templates to limit the space, but it suffers from coverage and efficiency issues. In this paper, we propose a template-free approach to efficiently explore the space of product molecules by first pinpointing the reaction center -- the set of nodes and edges where graph edits occur. Since only a small number of atoms contribute to reaction center, we can directly enumerate candidate products. The generated candidates are scored by a Weisfeiler-Lehman Difference Network that models high-order interactions between changes occurring at nodes across the molecule. Our framework outperforms the top-performing template-based approach with a 10\% margin, while running orders of magnitude faster. Finally, we demonstrate that the model accuracy rivals the performance of domain experts.

cs.LG↗