arXiv subjects

Regina Barzilay

Publications and source records attributed to Regina Barzilay.

At least 73 records · Page 4Linked to original sources

arXiv2021

Nutribullets Hybrid: Multi-document Health Summarization

We present a method for generating comparative summaries that highlights similarities and contradictions in input documents. The key challenge in creating such summaries is the lack of large parallel training data required for training typical summarization systems. To this end, we introduce a hybrid generation approach inspired by traditional concept-to-text systems. To enable accurate comparison between different sources, the model first learns to extract pertinent relations from input documents. The content planning component uses deterministic operators to aggregate these relations after identifying a subset for inclusion into a summary. The surface realization component lexicalizes this information using a text-infilling language model. By separately modeling content selection and realization, we can effectively train them with limited annotations. We implemented and tested the model in the domain of nutrition and health -- rife with inconsistencies. Compared to conventional methods, our framework leads to more faithful, relevant and aggregation-sensitive summarization -- while being equally fluent.

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arXiv2021

Nutri-bullets: Summarizing Health Studies by Composing Segments

We introduce \emph{Nutri-bullets}, a multi-document summarization task for health and nutrition. First, we present two datasets of food and health summaries from multiple scientific studies. Furthermore, we propose a novel \emph{extract-compose} model to solve the problem in the regime of limited parallel data. We explicitly select key spans from several abstracts using a policy network, followed by composing the selected spans to present a summary via a task specific language model. Compared to state-of-the-art methods, our approach leads to more faithful, relevant and diverse summarization -- properties imperative to this application. For instance, on the BreastCancer dataset our approach gets a more than 50\% improvement on relevance and faithfulness.\footnote{Our code and data is available at \url{https://github.com/darsh10/Nutribullets.}}

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arXiv2021

Get Your Vitamin C! Robust Fact Verification with Contrastive Evidence

Typical fact verification models use retrieved written evidence to verify claims. Evidence sources, however, often change over time as more information is gathered and revised. In order to adapt, models must be sensitive to subtle differences in supporting evidence. We present VitaminC, a benchmark infused with challenging cases that require fact verification models to discern and adjust to slight factual changes. We collect over 100,000 Wikipedia revisions that modify an underlying fact, and leverage these revisions, together with additional synthetically constructed ones, to create a total of over 400,000 claim-evidence pairs. Unlike previous resources, the examples in VitaminC are contrastive, i.e., they contain evidence pairs that are nearly identical in language and content, with the exception that one supports a given claim while the other does not. We show that training using this design increases robustness -- improving accuracy by 10% on adversarial fact verification and 6% on adversarial natural language inference (NLI). Moreover, the structure of VitaminC leads us to define additional tasks for fact-checking resources: tagging relevant words in the evidence for verifying the claim, identifying factual revisions, and providing automatic edits via factually consistent text generation.

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arXiv2021

Efficient Conformal Prediction via Cascaded Inference with Expanded Admission

In this paper, we present a novel approach for conformal prediction (CP), in which we aim to identify a set of promising prediction candidates -- in place of a single prediction. This set is guaranteed to contain a correct answer with high probability, and is well-suited for many open-ended classification tasks. In the standard CP paradigm, the predicted set can often be unusably large and also costly to obtain. This is particularly pervasive in settings where the correct answer is not unique, and the number of total possible answers is high. We first expand the CP correctness criterion to allow for additional, inferred "admissible" answers, which can substantially reduce the size of the predicted set while still providing valid performance guarantees. Second, we amortize costs by conformalizing prediction cascades, in which we aggressively prune implausible labels early on by using progressively stronger classifiers -- again, while still providing valid performance guarantees. We demonstrate the empirical effectiveness of our approach for multiple applications in natural language processing and computational chemistry for drug discovery.

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arXiv2020

Discovering Synergistic Drug Combinations for COVID with Biological Bottleneck Models

Drug combinations play an important role in therapeutics due to its better efficacy and reduced toxicity. Recent approaches have applied machine learning to identify synergistic combinations for cancer, but they are not applicable to new diseases with limited combination data. Given that drug synergy is closely tied to biological targets, we propose a \emph{biological bottleneck} model that jointly learns drug-target interaction and synergy. The model consists of two parts: a drug-target interaction and target-disease association module. This design enables the model to \emph{explain} how a biological target affects drug synergy. By utilizing additional biological information, our model achieves 0.78 test AUC in drug synergy prediction using only 90 COVID drug combinations for training. We experimentally tested the model predictions in the U.S. National Center for Advancing Translational Sciences (NCATS) facilities and discovered two novel drug combinations (Remdesivir + Reserpine and Remdesivir + IQ-1S) with strong synergy in vitro.

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arXiv2020

Blank Language Models

We propose Blank Language Model (BLM), a model that generates sequences by dynamically creating and filling in blanks. The blanks control which part of the sequence to expand, making BLM ideal for a variety of text editing and rewriting tasks. The model can start from a single blank or partially completed text with blanks at specified locations. It iteratively determines which word to place in a blank and whether to insert new blanks, and stops generating when no blanks are left to fill. BLM can be efficiently trained using a lower bound of the marginal data likelihood. On the task of filling missing text snippets, BLM significantly outperforms all other baselines in terms of both accuracy and fluency. Experiments on style transfer and damaged ancient text restoration demonstrate the potential of this framework for a wide range of applications.

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arXiv2020

CapWAP: Captioning with a Purpose

The traditional image captioning task uses generic reference captions to provide textual information about images. Different user populations, however, will care about different visual aspects of images. In this paper, we propose a new task, Captioning with a Purpose (CapWAP). Our goal is to develop systems that can be tailored to be useful for the information needs of an intended population, rather than merely provide generic information about an image. In this task, we use question-answer (QA) pairs---a natural expression of information need---from users, instead of reference captions, for both training and post-inference evaluation. We show that it is possible to use reinforcement learning to directly optimize for the intended information need, by rewarding outputs that allow a question answering model to provide correct answers to sampled user questions. We convert several visual question answering datasets into CapWAP datasets, and demonstrate that under a variety of scenarios our purposeful captioning system learns to anticipate and fulfill specific information needs better than its generic counterparts, as measured by QA performance on user questions from unseen images, when using the caption alone as context.

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arXiv2020

Deciphering Undersegmented Ancient Scripts Using Phonetic Prior

Most undeciphered lost languages exhibit two characteristics that pose significant decipherment challenges: (1) the scripts are not fully segmented into words; (2) the closest known language is not determined. We propose a decipherment model that handles both of these challenges by building on rich linguistic constraints reflecting consistent patterns in historical sound change. We capture the natural phonological geometry by learning character embeddings based on the International Phonetic Alphabet (IPA). The resulting generative framework jointly models word segmentation and cognate alignment, informed by phonological constraints. We evaluate the model on both deciphered languages (Gothic, Ugaritic) and an undeciphered one (Iberian). The experiments show that incorporating phonetic geometry leads to clear and consistent gains. Additionally, we propose a measure for language closeness which correctly identifies related languages for Gothic and Ugaritic. For Iberian, the method does not show strong evidence supporting Basque as a related language, concurring with the favored position by the current scholarship.

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arXiv2020

Enforcing Predictive Invariance across Structured Biomedical Domains

Many biochemical applications such as molecular property prediction require models to generalize beyond their training domains (environments). Moreover, natural environments in these tasks are structured, defined by complex descriptors such as molecular scaffolds or protein families. Therefore, most environments are either never seen during training, or contain only a single training example. To address these challenges, we propose a new regret minimization (RGM) algorithm and its extension for structured environments. RGM builds from invariant risk minimization (IRM) by recasting simultaneous optimality condition in terms of predictive regret, finding a representation that enables the predictor to compete against an oracle with hindsight access to held-out environments. The structured extension adaptively highlights variation due to complex environments via specialized domain perturbations. We evaluate our method on multiple applications: molecular property prediction, protein homology and stability prediction and show that RGM significantly outperforms previous state-of-the-art baselines.

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arXiv2020

Educating Text Autoencoders: Latent Representation Guidance via Denoising

Generative autoencoders offer a promising approach for controllable text generation by leveraging their latent sentence representations. However, current models struggle to maintain coherent latent spaces required to perform meaningful text manipulations via latent vector operations. Specifically, we demonstrate by example that neural encoders do not necessarily map similar sentences to nearby latent vectors. A theoretical explanation for this phenomenon establishes that high capacity autoencoders can learn an arbitrary mapping between sequences and associated latent representations. To remedy this issue, we augment adversarial autoencoders with a denoising objective where original sentences are reconstructed from perturbed versions (referred to as DAAE). We prove that this simple modification guides the latent space geometry of the resulting model by encouraging the encoder to map similar texts to similar latent representations. In empirical comparisons with various types of autoencoders, our model provides the best trade-off between generation quality and reconstruction capacity. Moreover, the improved geometry of the DAAE latent space enables zero-shot text style transfer via simple latent vector arithmetic.

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arXiv2020

Multi-Objective Molecule Generation using Interpretable Substructures

Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes increasingly challenging when there are many property constraints. We propose to offset this complexity by composing molecules from a vocabulary of substructures that we call molecular rationales. These rationales are identified from molecules as substructures that are likely responsible for each property of interest. We then learn to expand rationales into a full molecule using graph generative models. Our final generative model composes molecules as mixtures of multiple rationale completions, and this mixture is fine-tuned to preserve the properties of interest. We evaluate our model on various drug design tasks and demonstrate significant improvements over state-of-the-art baselines in terms of accuracy, diversity, and novelty of generated compounds.

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arXiv2020

Improved Conditional Flow Models for Molecule to Image Synthesis

In this paper, we aim to synthesize cell microscopy images under different molecular interventions, motivated by practical applications to drug development. Building on the recent success of graph neural networks for learning molecular embeddings and flow-based models for image generation, we propose Mol2Image: a flow-based generative model for molecule to cell image synthesis. To generate cell features at different resolutions and scale to high-resolution images, we develop a novel multi-scale flow architecture based on a Haar wavelet image pyramid. To maximize the mutual information between the generated images and the molecular interventions, we devise a training strategy based on contrastive learning. To evaluate our model, we propose a new set of metrics for biological image generation that are robust, interpretable, and relevant to practitioners. We show quantitatively that our method learns a meaningful embedding of the molecular intervention, which is translated into an image representation reflecting the biological effects of the intervention.

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arXiv2020

Uncertainty Quantification Using Neural Networks for Molecular Property Prediction

Uncertainty quantification (UQ) is an important component of molecular property prediction, particularly for drug discovery applications where model predictions direct experimental design and where unanticipated imprecision wastes valuable time and resources. The need for UQ is especially acute for neural models, which are becoming increasingly standard yet are challenging to interpret. While several approaches to UQ have been proposed in the literature, there is no clear consensus on the comparative performance of these models. In this paper, we study this question in the context of regression tasks. We systematically evaluate several methods on five benchmark datasets using multiple complementary performance metrics. Our experiments show that none of the methods we tested is unequivocally superior to all others, and none produces a particularly reliable ranking of errors across multiple datasets. While we believe these results show that existing UQ methods are not sufficient for all common use-cases and demonstrate the benefits of further research, we conclude with a practical recommendation as to which existing techniques seem to perform well relative to others.

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arXiv2020

Adaptive Invariance for Molecule Property Prediction

Effective property prediction methods can help accelerate the search for COVID-19 antivirals either through accurate in-silico screens or by effectively guiding on-going at-scale experimental efforts. However, existing prediction tools have limited ability to accommodate scarce or fragmented training data currently available. In this paper, we introduce a novel approach to learn predictors that can generalize or extrapolate beyond the heterogeneous data. Our method builds on and extends recently proposed invariant risk minimization, adaptively forcing the predictor to avoid nuisance variation. We achieve this by continually exercising and manipulating latent representations of molecules to highlight undesirable variation to the predictor. To test the method we use a combination of three data sources: SARS-CoV-2 antiviral screening data, molecular fragments that bind to SARS-CoV-2 main protease and large screening data for SARS-CoV-1. Our predictor outperforms state-of-the-art transfer learning methods by significant margin. We also report the top 20 predictions of our model on Broad drug repurposing hub.

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arXiv2020

Hierarchical Generation of Molecular Graphs using Structural Motifs

Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to smaller molecules. Indeed, as we demonstrate, their performance degrades significantly for larger molecules. In this paper, we propose a new hierarchical graph encoder-decoder that employs significantly larger and more flexible graph motifs as basic building blocks. Our encoder produces a multi-resolution representation for each molecule in a fine-to-coarse fashion, from atoms to connected motifs. Each level integrates the encoding of constituents below with the graph at that level. Our autoregressive coarse-to-fine decoder adds one motif at a time, interleaving the decision of selecting a new motif with the process of resolving its attachments to the emerging molecule. We evaluate our model on multiple molecule generation tasks, including polymers, and show that our model significantly outperforms previous state-of-the-art baselines.

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arXiv2020

The Limitations of Stylometry for Detecting Machine-Generated Fake News

Recent developments in neural language models (LMs) have raised concerns about their potential misuse for automatically spreading misinformation. In light of these concerns, several studies have proposed to detect machine-generated fake news by capturing their stylistic differences from human-written text. These approaches, broadly termed stylometry, have found success in source attribution and misinformation detection in human-written texts. However, in this work, we show that stylometry is limited against machine-generated misinformation. While humans speak differently when trying to deceive, LMs generate stylistically consistent text, regardless of underlying motive. Thus, though stylometry can successfully prevent impersonation by identifying text provenance, it fails to distinguish legitimate LM applications from those that introduce false information. We create two benchmarks demonstrating the stylistic similarity between malicious and legitimate uses of LMs, employed in auto-completion and editing-assistance settings. Our findings highlight the need for non-stylometry approaches in detecting machine-generated misinformation, and open up the discussion on the desired evaluation benchmarks.

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arXiv2020

Few-shot Text Classification with Distributional Signatures

In this paper, we explore meta-learning for few-shot text classification. Meta-learning has shown strong performance in computer vision, where low-level patterns are transferable across learning tasks. However, directly applying this approach to text is challenging--lexical features highly informative for one task may be insignificant for another. Thus, rather than learning solely from words, our model also leverages their distributional signatures, which encode pertinent word occurrence patterns. Our model is trained within a meta-learning framework to map these signatures into attention scores, which are then used to weight the lexical representations of words. We demonstrate that our model consistently outperforms prototypical networks learned on lexical knowledge (Snell et al., 2017) in both few-shot text classification and relation classification by a significant margin across six benchmark datasets (20.0% on average in 1-shot classification).

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arXiv2019

Automatic Fact-guided Sentence Modification

Online encyclopediae like Wikipedia contain large amounts of text that need frequent corrections and updates. The new information may contradict existing content in encyclopediae. In this paper, we focus on rewriting such dynamically changing articles. This is a challenging constrained generation task, as the output must be consistent with the new information and fit into the rest of the existing document. To this end, we propose a two-step solution: (1) We identify and remove the contradicting components in a target text for a given claim, using a neutralizing stance model; (2) We expand the remaining text to be consistent with the given claim, using a novel two-encoder sequence-to-sequence model with copy attention. Applied to a Wikipedia fact update dataset, our method successfully generates updated sentences for new claims, achieving the highest SARI score. Furthermore, we demonstrate that generating synthetic data through such rewritten sentences can successfully augment the FEVER fact-checking training dataset, leading to a relative error reduction of 13%.

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