Neural Summarization of Electronic Health Records

Hospital discharge documentation is among the most essential, yet time-consuming documents written by medical practitioners. The objective of this study was to automatically generate hospital discharge summaries using neural network summarization models. We studied various data preparation and neural network training techniques that generate discharge summaries. Using nursing notes and discharge summaries from the MIMIC-III dataset, we studied the viability of the automatic generation of various sections of a discharge summary using four state-of-the-art neural network summarization models (BART, T5, Longformer and FLAN-T5). Our experiments indicated that training environments including nursing notes as the source, and discrete sections of the discharge summary as the target output (e.g. "History of Present Illness") improve language model efficiency and text quality. According to our findings, the fine-tuned BART model improved its ROUGE F1 score by 43.6% against its standard off-the-shelf version. We also found that fine-tuning the baseline BART model with other setups caused different degrees of improvement (up to 80% relative improvement). We also observed that a fine-tuned T5 generally achieves higher ROUGE F1 scores than other fine-tuned models and a fine-tuned FLAN-T5 achieves the highest ROUGE score overall, i.e., 45.6. For majority of the fine-tuned language models, summarizing discharge summary report sections separately outperformed the summarization the entire report quantitatively. On the other hand, fine-tuning language models that were previously instruction fine-tuned showed better performance in summarizing entire reports. This study concludes that a focused dataset designed for the automatic generation of discharge summaries by a language model can produce coherent Discharge Summary sections

A Graph-Based Approach for the Summarization of Scientific Articles

Automatic text summarization is one of the eminent applications in the field of Natural Language Processing. Text summarization is the process of generating a gist from text documents. The task is to produce a summary which contains important, diverse and coherent information, i.e., a summary should be self-contained. The approaches for text summarization are conventionally extractive. The extractive approaches select a subset of sentences from an input document for a summary. In this thesis, we introduce a novel graph-based extractive summarization approach. With the progressive advancement of research in the various fields of science, the summarization of scientific articles has become an essential requirement for researchers. This is our prime motivation in selecting scientific articles as our dataset. This newly formed dataset contains scientific articles from the PLOS Medicine journal, which is a high impact journal in the field of biomedicine. The summarization of scientific articles is a single-document summarization task. It is a complex task due to various reasons, one of it being, the important information in the scientific article is scattered all over it and another reason being, scientific articles contain numerous redundant information. In our approach, we deal with the three important factors of summarization: importance, non-redundancy and coherence. To deal with these factors, we use graphs as they solve data sparsity problems and are computationally less complex. We employ bipartite graphical representation for the summarization task, exclusively. We represent input documents through a bipartite graph that consists of sentence nodes and entity nodes. This bipartite graph representation contains entity transition information which is beneficial for selecting the relevant sentences for a summary. We use a graph-based ranking algorithm to rank the sentences in a document. The ranks are considered as relevance scores of the sentences which are further used in our approach. Scientific articles contain reasonable amount of redundant information, for example, Introduction and Methodology sections contain similar information regarding the motivation and approach. In our approach, we ensure that the summary contains sentences which are non-redundant. Though the summary should contain important and non-redundant information of the input document, its sentences should be connected to one another such that it becomes coherent, understandable and simple to read. If we do not ensure that a summary is coherent, its sentences may not be properly connected. This leads to an obscure summary. Until now, only few summarization approaches take care of coherence. In our approach, we take care of coherence in two different ways: by using the graph measure and by using the structural information. We employ outdegree as the graph measure and coherence patterns for the structural information, in our approach. We use integer programming as an optimization technique, to select the best subset of sentences for a summary. The sentences are selected on the basis of relevance, diversity and coherence measure. The computation of these measures is tightly integrated and taken care of simultaneously. We use human judgements to evaluate coherence of summaries. We compare ROUGE scores and human judgements of different systems on the PLOS Medicine dataset. Our approach performs considerably better than other systems on this dataset. Also, we apply our approach on the standard DUC 2002 dataset to compare the results with the recent state-of-the-art systems. The results show that our graph-based approach outperforms other systems on DUC 2002. In conclusion, our approach is robust, i.e., it works on both scientific and news articles. Our approach has the further advantage of being semi-supervised

Natural Language Processing for Technology Foresight Summarization and Simplification: the case of patents

Technology foresight aims to anticipate possible developments, understand trends, and identify technologies of high impact. To this end, monitoring emerging technologies is crucial. Patents -- the legal documents that protect novel inventions -- can be a valuable source for technology monitoring. Millions of patent applications are filed yearly, with 3.4 million applications in 2021 only. Patent documents are primarily textual documents and disclose innovative and potentially valuable inventions. However, their processing is currently underresearched. This is due to several reasons, including the high document complexity: patents are very lengthy and are written in an extremely hard-to-read language, which is a mix of technical and legal jargon. This thesis explores how Natural Language Processing -- the discipline that enables machines to process human language automatically -- can aid patent processing. Specifically, we focus on two tasks: patent summarization (i.e., we try to reduce the document length while preserving its core content) and patent simplification (i.e., we try to reduce the document's linguistic complexity while preserving its original core meaning). We found that older patent summarization approaches were not compared on shared benchmarks (making thus it hard to draw conclusions), and even the most recent abstractive dataset presents important issues that might make comparisons meaningless. We try to fill both gaps: we first document the issues related to the BigPatent dataset and then benchmark extractive, abstraction, and hybrid approaches in the patent domain. We also explore transferring summarization methods from the scientific paper domain with limited success. For the automatic text simplification task, we noticed a lack of simplified text and parallel corpora. We fill this gap by defining a method to generate a silver standard for patent simplification automatically. Lay human judges evaluated the simplified sentences in the corpus as grammatical, adequate, and simpler, and we show that it can be used to train a state-of-the-art simplification model. This thesis describes the first steps toward Natural Language Processing-aided patent summarization and simplification. We hope it will encourage more research on the topic, opening doors for a productive dialog between NLP researchers and domain experts.Technology foresight aims to anticipate possible developments, understand trends, and identify technologies of high impact. To this end, monitoring emerging technologies is crucial. Patents -- the legal documents that protect novel inventions -- can be a valuable source for technology monitoring. Millions of patent applications are filed yearly, with 3.4 million applications in 2021 only. Patent documents are primarily textual documents and disclose innovative and potentially valuable inventions. However, their processing is currently underresearched. This is due to several reasons, including the high document complexity: patents are very lengthy and are written in an extremely hard-to-read language, which is a mix of technical and legal jargon. This thesis explores how Natural Language Processing -- the discipline that enables machines to process human language automatically -- can aid patent processing. Specifically, we focus on two tasks: patent summarization (i.e., we try to reduce the document length while preserving its core content) and patent simplification (i.e., we try to reduce the document's linguistic complexity while preserving its original core meaning). We found that older patent summarization approaches were not compared on shared benchmarks (making thus it hard to draw conclusions), and even the most recent abstractive dataset presents important issues that might make comparisons meaningless. We try to fill both gaps: we first document the issues related to the BigPatent dataset and then benchmark extractive, abstraction, and hybrid approaches in the patent domain. We also explore transferring summarization methods from the scientific paper domain with limited success. For the automatic text simplification task, we noticed a lack of simplified text and parallel corpora. We fill this gap by defining a method to generate a silver standard for patent simplification automatically. Lay human judges evaluated the simplified sentences in the corpus as grammatical, adequate, and simpler, and we show that it can be used to train a state-of-the-art simplification model. This thesis describes the first steps toward Natural Language Processing-aided patent summarization and simplification. We hope it will encourage more research on the topic, opening doors for a productive dialog between NLP researchers and domain experts