Search

Discriminative neural networks offer little or no performance guarantees when deployed on data not generated by the same process as the training distribution. On such out-of-distribution (OOD) inputs, the prediction may not only be erroneous, but confidently so, limiting the safe deployment of classifiers in real-world applications. One such challenging application is bacteria identification based on genomic sequences, which holds the promise of early detection of diseases, but requires a model that can output low confidence predictions on OOD genomic sequences from new bacteria that were not present in the training data. We introduce a genomics dataset for OOD detection that allows other researchers to benchmark progress on this important problem. We investigate deep generative model based approaches for OOD detection and observe that the likelihood score is heavily affected by population level background statistics. We propose a likelihood ratio method for deep generative models which effectively corrects for these confounding background statistics. We benchmark the OOD detection performance of the proposed method against existing approaches on the genomics dataset and show that our method achieves state-of-the-art performance. We demonstrate the generality of the proposed method by showing that it significantly improves OOD detection when applied to deep generative models of images., Comment: Accepted to NeurIPS 2019

We propose a model-based metric to estimate the factual accuracy of generated text that is complementary to typical scoring schemes like ROUGE (Recall-Oriented Understudy for Gisting Evaluation) and BLEU (Bilingual Evaluation Understudy). We introduce and release a new large-scale dataset based on Wikipedia and Wikidata to train relation classifiers and end-to-end fact extraction models. The end-to-end models are shown to be able to extract complete sets of facts from datasets with full pages of text. We then analyse multiple models that estimate factual accuracy on a Wikipedia text summarization task, and show their efficacy compared to ROUGE and other model-free variants by conducting a human evaluation study.

Massively multi-label prediction/classification problems arise in environments like health-care or biology where very precise predictions are useful. One challenge with massively multi-label problems is that there is often a long-tailed frequency distribution for the labels, which results in few positive examples for the rare labels. We propose a solution to this problem by modifying the output layer of a neural network to create a Bayesian network of sigmoids which takes advantage of ontology relationships between the labels to help share information between the rare and the more common labels. We apply this method to the two massively multi-label tasks of disease prediction (ICD-9 codes) and protein function prediction (Gene Ontology terms) and obtain significant improvements in per-label AUROC and average precision for less common labels.

Abstractive summarization has been studied using neural sequence transduction methods with datasets of large, paired document-summary examples. However, such datasets are rare and the models trained from them do not generalize to other domains. Recently, some progress has been made in learning sequence-to-sequence mappings with only unpaired examples. In our work, we consider the setting where there are only documents (product or business reviews) with no summaries provided, and propose an end-to-end, neural model architecture to perform unsupervised abstractive summarization. Our proposed model consists of an auto-encoder where the mean of the representations of the input reviews decodes to a reasonable summary-review while not relying on any review-specific features. We consider variants of the proposed architecture and perform an ablation study to show the importance of specific components. We show through automated metrics and human evaluation that the generated summaries are highly abstractive, fluent, relevant, and representative of the average sentiment of the input reviews. Finally, we collect a reference evaluation dataset and show that our model outperforms a strong extractive baseline., Comment: Accepted to ICML 2019

Clinicians spend a significant amount of time inputting free-form textual notes into Electronic Health Records (EHR) systems. Much of this documentation work is seen as a burden, reducing time spent with patients and contributing to clinician burnout. With the aspiration of AI-assisted note-writing, we propose a new language modeling task predicting the content of notes conditioned on past data from a patient's medical record, including patient demographics, labs, medications, and past notes. We train generative models using the public, de-identified MIMIC-III dataset and compare generated notes with those in the dataset on multiple measures. We find that much of the content can be predicted, and that many common templates found in notes can be learned. We discuss how such models can be useful in supporting assistive note-writing features such as error-detection and auto-complete., Comment: preprint

We show that generating English Wikipedia articles can be approached as a multi- document summarization of source documents. We use extractive summarization to coarsely identify salient information and a neural abstractive model to generate the article. For the abstractive model, we introduce a decoder-only architecture that can scalably attend to very long sequences, much longer than typical encoder- decoder architectures used in sequence transduction. We show that this model can generate fluent, coherent multi-sentence paragraphs and even whole Wikipedia articles. When given reference documents, we show it can extract relevant factual information as reflected in perplexity, ROUGE scores and human evaluations., Comment: Published as a conference paper at ICLR 2018

Predictive modeling with electronic health record (EHR) data is anticipated to drive personalized medicine and improve healthcare quality. Constructing predictive statistical models typically requires extraction of curated predictor variables from normalized EHR data, a labor-intensive process that discards the vast majority of information in each patient's record. We propose a representation of patients' entire, raw EHR records based on the Fast Healthcare Interoperability Resources (FHIR) format. We demonstrate that deep learning methods using this representation are capable of accurately predicting multiple medical events from multiple centers without site-specific data harmonization. We validated our approach using de-identified EHR data from two U.S. academic medical centers with 216,221 adult patients hospitalized for at least 24 hours. In the sequential format we propose, this volume of EHR data unrolled into a total of 46,864,534,945 data points, including clinical notes. Deep learning models achieved high accuracy for tasks such as predicting in-hospital mortality (AUROC across sites 0.93-0.94), 30-day unplanned readmission (AUROC 0.75-0.76), prolonged length of stay (AUROC 0.85-0.86), and all of a patient's final discharge diagnoses (frequency-weighted AUROC 0.90). These models outperformed state-of-the-art traditional predictive models in all cases. We also present a case-study of a neural-network attribution system, which illustrates how clinicians can gain some transparency into the predictions. We believe that this approach can be used to create accurate and scalable predictions for a variety of clinical scenarios, complete with explanations that directly highlight evidence in the patient's chart., Comment: Published version from https://www.nature.com/articles/s41746-018-0029-1

The driving force behind the recent success of LSTMs has been their ability to learn complex and non-linear relationships. Consequently, our inability to describe these relationships has led to LSTMs being characterized as black boxes. To this end, we introduce contextual decomposition (CD), an interpretation algorithm for analysing individual predictions made by standard LSTMs, without any changes to the underlying model. By decomposing the output of a LSTM, CD captures the contributions of combinations of words or variables to the final prediction of an LSTM. On the task of sentiment analysis with the Yelp and SST data sets, we show that CD is able to reliably identify words and phrases of contrasting sentiment, and how they are combined to yield the LSTM's final prediction. Using the phrase-level labels in SST, we also demonstrate that CD is able to successfully extract positive and negative negations from an LSTM, something which has not previously been done., Comment: Oral presentation at ICLR 2018

Faraday rotation is a fundamental property present in all non-reciprocal optical elements. In the THz range, graphene displays strong Faraday rotation; unfortunately, it is limited to frequencies below the cyclotron resonance. Here we show experimentally that in specifically design metasurfaces, magneto-plasmons can be used to circumvent this limitation. We find excellent agreement between theory and experiment and provide new physical insights and predictions on these phenomena. Finally, we demonstrate strong tuneability in these metasurfaces using electric and magnetic field biasing., Comment: 5 pages, 3 figures

Neural sequence-to-sequence models have provided a viable new approach for abstractive text summarization (meaning they are not restricted to simply selecting and rearranging passages from the original text). However, these models have two shortcomings: they are liable to reproduce factual details inaccurately, and they tend to repeat themselves. In this work we propose a novel architecture that augments the standard sequence-to-sequence attentional model in two orthogonal ways. First, we use a hybrid pointer-generator network that can copy words from the source text via pointing, which aids accurate reproduction of information, while retaining the ability to produce novel words through the generator. Second, we use coverage to keep track of what has been summarized, which discourages repetition. We apply our model to the CNN / Daily Mail summarization task, outperforming the current abstractive state-of-the-art by at least 2 ROUGE points., Comment: Add METEOR evaluation results, add some citations, fix some equations (what are now equations 1, 8 and 11 were missing a bias term), fix url to pyrouge package, add acknowledgments