Automatic case acquisition from texts for process-oriented case-based reasoning

This paper introduces a method for the automatic acquisition of a rich case representation from free text for process-oriented case-based reasoning. Case engineering is among the most complicated and costly tasks in implementing a case-based reasoning system. This is especially so for process-oriented case-based reasoning, where more expressive case representations are generally used and, in our opinion, actually required for satisfactory case adaptation. In this context, the ability to acquire cases automatically from procedural texts is a major step forward in order to reason on processes. We therefore detail a methodology that makes case acquisition from processes described as free text possible, with special attention given to assembly instruction texts. This methodology extends the techniques we used to extract actions from cooking recipes. We argue that techniques taken from natural language processing are required for this task, and that they give satisfactory results. An evaluation based on our implemented prototype extracting workflows from recipe texts is provided.Comment: Sous presse, publication pr\'evue en 201

Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.Comment: 6 pages, accepted by IEEE BIBM 2018 as regular pape

A Formal Framework for Linguistic Annotation

`Linguistic annotation' covers any descriptive or analytic notations applied to raw language data. The basic data may be in the form of time functions -- audio, video and/or physiological recordings -- or it may be textual. The added notations may include transcriptions of all sorts (from phonetic features to discourse structures), part-of-speech and sense tagging, syntactic analysis, `named entity' identification, co-reference annotation, and so on. While there are several ongoing efforts to provide formats and tools for such annotations and to publish annotated linguistic databases, the lack of widely accepted standards is becoming a critical problem. Proposed standards, to the extent they exist, have focussed on file formats. This paper focuses instead on the logical structure of linguistic annotations. We survey a wide variety of existing annotation formats and demonstrate a common conceptual core, the annotation graph. This provides a formal framework for constructing, maintaining and searching linguistic annotations, while remaining consistent with many alternative data structures and file formats.Comment: 49 page

CH-Bench: a user-oriented benchmark for systems for efficient distant reading (design, performance, and insights)

Data science deals with the discovery of information from large volumes of data. The data studied by scientists in the humanities include large textual corpora. An important objective is to study the ideas and expectations of a society regarding specific concepts, like “freedom” or “democracy,” both for today’s society and even more for societies of the past. Studying the meaning of words using large corpora requires efficient systems for text analysis, so-called distant reading systems. Making such systems efficient calls for a specification of the necessary functionality and clear expectations regarding typical work loads. But this currently is unclear, and there is no benchmark to evaluate distant reading systems. In this article, we propose such a benchmark, with the following innovations: As a first step, we collect and structure various information needs of the target users. We then formalize the notion of word context to facilitate the analysis of specific concepts. Using this notion, we formulate queries in line with the information needs of users. Finally, based on this, we propose concrete benchmark queries. To demonstrate the benefit of our benchmark, we conduct an evaluation, with two objectives. First, we aim at insights regarding the content of different corpora, i.e., whether and how their size and nature (e.g., popular and broad literature or specific expert literature) affect results. Second, we benchmark different data management technologies. This has allowed us to identify performance bottlenecks

Towards a query language for annotation graphs

The multidimensional, heterogeneous, and temporal nature of speech databases raises interesting challenges for representation and query. Recently, annotation graphs have been proposed as a general-purpose representational framework for speech databases. Typical queries on annotation graphs require path expressions similar to those used in semistructured query languages. However, the underlying model is rather different from the customary graph models for semistructured data: the graph is acyclic and unrooted, and both temporal and inclusion relationships are important. We develop a query language and describe optimization techniques for an underlying relational representation.Comment: 8 pages, 10 figure

Unsupervised, Efficient and Semantic Expertise Retrieval

We introduce an unsupervised discriminative model for the task of retrieving experts in online document collections. We exclusively employ textual evidence and avoid explicit feature engineering by learning distributed word representations in an unsupervised way. We compare our model to state-of-the-art unsupervised statistical vector space and probabilistic generative approaches. Our proposed log-linear model achieves the retrieval performance levels of state-of-the-art document-centric methods with the low inference cost of so-called profile-centric approaches. It yields a statistically significant improved ranking over vector space and generative models in most cases, matching the performance of supervised methods on various benchmarks. That is, by using solely text we can do as well as methods that work with external evidence and/or relevance feedback. A contrastive analysis of rankings produced by discriminative and generative approaches shows that they have complementary strengths due to the ability of the unsupervised discriminative model to perform semantic matching.Comment: WWW2016, Proceedings of the 25th International Conference on World Wide Web. 201

Temporal Information Processing: A Survey

Temporal Information Processing is a subfield of Natural Language Processing, valuable in many tasks like Question Answering and Summarization. Temporal Information Processing is broadened, ranging from classical theories of time and language to current computational approaches for Temporal Information Extraction. This later trend consists on the automatic extraction of events and temporal expressions. Such issues have attracted great attention especially with the development of annotated corpora and annotations schemes mainly TimeBank and TimeML. In this paper, we give a survey of Temporal Information Extraction from Natural Language texts