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

Learning Domain-Specific Word Embeddings from Sparse Cybersecurity Texts

Word embedding is a Natural Language Processing (NLP) technique that automatically maps words from a vocabulary to vectors of real numbers in an embedding space. It has been widely used in recent years to boost the performance of a vari-ety of NLP tasks such as Named Entity Recognition, Syntac-tic Parsing and Sentiment Analysis. Classic word embedding methods such as Word2Vec and GloVe work well when they are given a large text corpus. When the input texts are sparse as in many specialized domains (e.g., cybersecurity), these methods often fail to produce high-quality vectors. In this pa-per, we describe a novel method to train domain-specificword embeddings from sparse texts. In addition to domain texts, our method also leverages diverse types of domain knowledge such as domain vocabulary and semantic relations. Specifi-cally, we first propose a general framework to encode diverse types of domain knowledge as text annotations. Then we de-velop a novel Word Annotation Embedding (WAE) algorithm to incorporate diverse types of text annotations in word em-bedding. We have evaluated our method on two cybersecurity text corpora: a malware description corpus and a Common Vulnerability and Exposure (CVE) corpus. Our evaluation re-sults have demonstrated the effectiveness of our method in learning domain-specific word embeddings

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

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Background. 
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.

Description. 
SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies