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

WISER: A Semantic Approach for Expert Finding in Academia based on Entity Linking

We present WISER, a new semantic search engine for expert finding in academia. Our system is unsupervised and it jointly combines classical language modeling techniques, based on text evidences, with the Wikipedia Knowledge Graph, via entity linking. WISER indexes each academic author through a novel profiling technique which models her expertise with a small, labeled and weighted graph drawn from Wikipedia. Nodes in this graph are the Wikipedia entities mentioned in the author's publications, whereas the weighted edges express the semantic relatedness among these entities computed via textual and graph-based relatedness functions. Every node is also labeled with a relevance score which models the pertinence of the corresponding entity to author's expertise, and is computed by means of a proper random-walk calculation over that graph; and with a latent vector representation which is learned via entity and other kinds of structural embeddings derived from Wikipedia. At query time, experts are retrieved by combining classic document-centric approaches, which exploit the occurrences of query terms in the author's documents, with a novel set of profile-centric scoring strategies, which compute the semantic relatedness between the author's expertise and the query topic via the above graph-based profiles. The effectiveness of our system is established over a large-scale experimental test on a standard dataset for this task. We show that WISER achieves better performance than all the other competitors, thus proving the effectiveness of modelling author's profile via our "semantic" graph of entities. Finally, we comment on the use of WISER for indexing and profiling the whole research community within the University of Pisa, and its application to technology transfer in our University

Word-Entity Duet Representations for Document Ranking

This paper presents a word-entity duet framework for utilizing knowledge bases in ad-hoc retrieval. In this work, the query and documents are modeled by word-based representations and entity-based representations. Ranking features are generated by the interactions between the two representations, incorporating information from the word space, the entity space, and the cross-space connections through the knowledge graph. To handle the uncertainties from the automatically constructed entity representations, an attention-based ranking model AttR-Duet is developed. With back-propagation from ranking labels, the model learns simultaneously how to demote noisy entities and how to rank documents with the word-entity duet. Evaluation results on TREC Web Track ad-hoc task demonstrate that all of the four-way interactions in the duet are useful, the attention mechanism successfully steers the model away from noisy entities, and together they significantly outperform both word-based and entity-based learning to rank systems

On the Effect of Semantically Enriched Context Models on Software Modularization

Many of the existing approaches for program comprehension rely on the linguistic information found in source code, such as identifier names and comments. Semantic clustering is one such technique for modularization of the system that relies on the informal semantics of the program, encoded in the vocabulary used in the source code. Treating the source code as a collection of tokens loses the semantic information embedded within the identifiers. We try to overcome this problem by introducing context models for source code identifiers to obtain a semantic kernel, which can be used for both deriving the topics that run through the system as well as their clustering. In the first model, we abstract an identifier to its type representation and build on this notion of context to construct contextual vector representation of the source code. The second notion of context is defined based on the flow of data between identifiers to represent a module as a dependency graph where the nodes correspond to identifiers and the edges represent the data dependencies between pairs of identifiers. We have applied our approach to 10 medium-sized open source Java projects, and show that by introducing contexts for identifiers, the quality of the modularization of the software systems is improved. Both of the context models give results that are superior to the plain vector representation of documents. In some cases, the authoritativeness of decompositions is improved by 67%. Furthermore, a more detailed evaluation of our approach on JEdit, an open source editor, demonstrates that inferred topics through performing topic analysis on the contextual representations are more meaningful compared to the plain representation of the documents. The proposed approach in introducing a context model for source code identifiers paves the way for building tools that support developers in program comprehension tasks such as application and domain concept location, software modularization and topic analysis