We present a method to automatically generate a concise summary by identifying and synthesizing similar elements across related text from a set of multiple documents. Our approach is unique in its usage of language generation to reformulate the wording of the summary.
BackgroundThe increasing availability of Electronic Health Record (EHR) data and specifically free-text patient notes presents opportunities for phenotype extraction. Text-mining methods in particular can help disease modeling by mapping named-entities mentions to terminologies and clustering semantically related terms. EHR corpora, however, exhibit specific statistical and linguistic characteristics when compared with corpora in the biomedical literature domain. We focus on copy-and-paste redundancy: clinicians typically copy and paste information from previous notes when documenting a current patient encounter. Thus, within a longitudinal patient record, one expects to observe heavy redundancy. In this paper, we ask three research questions: (i) How can redundancy be quantified in large-scale text corpora? (ii) Conventional wisdom is that larger corpora yield better results in text mining. But how does the observed EHR redundancy affect text mining? Does such redundancy introduce a bias that distorts learned models? Or does the redundancy introduce benefits by highlighting stable and important subsets of the corpus? (iii) How can one mitigate the impact of redundancy on text mining?ResultsWe analyze a large-scale EHR corpus and quantify redundancy both in terms of word and semantic concept repetition. We observe redundancy levels of about 30% and non-standard distribution of both words and concepts. We measure the impact of redundancy on two standard text-mining applications: collocation identification and topic modeling. We compare the results of these methods on synthetic data with controlled levels of redundancy and observe significant performance variation. Finally, we compare two mitigation strategies to avoid redundancy-induced bias: (i) a baseline strategy, keeping only the last note for each patient in the corpus; (ii) removing redundant notes with an efficient fingerprinting-based algorithm. aFor text mining, preprocessing the EHR corpus with fingerprinting yields significantly better results.ConclusionsBefore applying text-mining techniques, one must pay careful attention to the structure of the analyzed corpora. While the importance of data cleaning has been known for low-level text characteristics (e.g., encoding and spelling), high-level and difficult-to-quantify corpus characteristics, such as naturally occurring redundancy, can also hurt text mining. Fingerprinting enables text-mining techniques to leverage available data in the EHR corpus, while avoiding the bias introduced by redundancy.
Recent work in the field of automatic summarization and headline generation focuses on maximizing ROUGE scores for various news datasets. We present an alternative, extrinsic, evaluation metric for this task, Answering Performance for Evaluation of Summaries. APES utilizes recent progress in the field of reading-comprehension to quantify the ability of a summary to answer a set of manually created questions regarding central entities in the source article. We first analyze the strength of this metric by comparing it to known manual evaluation metrics. We then present an end-to-end neural abstractive model that maximizes APES, while increasing ROUGE scores to competitive results.
Query Focused Summarization (QFS) has been addressed mostly using extractive methods. Such methods, however, produce text which suffers from low coherence. We investigate how abstractive methods can be applied to QFS, to overcome such limitations. Recent developments in neural-attention based sequence-to-sequence models have led to state-of-the-art results on the task of abstractive generic single document summarization. Such models are trained in an end to end method on large amounts of training data. We address three aspects to make abstractive summarization applicable to QFS: (a) since there is no training data, we incorporate query relevance into a pre-trained abstractive model; (b) since existing abstractive models are trained in a single-document setting, we design an iterated method to embed abstractive models within the multi-document requirement of QFS; (c) the abstractive models we adapt are trained to generate text of specific length (about 100 words), while we aim at generating output of a different size (about 250 words); we design a way to adapt the target size of the generated summaries to a given size ratio. We compare our method (Relevance Sensitive Attention for QFS) to extractive baselines and with various ways to combine abstractive models on the DUC QFS datasets and demonstrate solid improvements on ROUGE performance.
Morphological disambiguation is the process of assigning one set of morphological features to each individual word in a text. When the word is ambiguous (there are several possible analyses for the word), a disambiguation procedure based on the word context must be applied. This paper deals with morphological disambiguation of the Hebrew language, which combines morphemes into a word in both agglutinative and fusional ways. We present an unsupervised stochastic model-the only resource we use is a morphological analyzerwhich deals with the data sparseness problem caused by the affixational morphology of the Hebrew language. We present a text encoding method for languages with affixational morphology in which the knowledge of word formation rules (which are quite restricted in Hebrew) helps in the disambiguation. We adapt HMM algorithms for learning and searching this text representation, in such a way that segmentation and tagging can be learned in parallel in one step. Results on a large scale evaluation indicate that this learning improves disambiguation for complex tag sets. Our method is applicable to other languages with affix morphology.
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