Yung Chun Chang

TEMPTING system: A hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries

Patient discharge summaries provide detailed medical information about individuals who have been hospitalized. To make a precise and legitimate assessment of the abundant data, a proper time layout of the sequence of relevant events should be compiled and used to drive a patient-specific timeline, which could further assist medical personnel in making clinical decisions. The process of identifying the chronological order of entities is called temporal relation extraction. In this paper, we propose a hybrid method to identify appropriate temporal links between a pair of entities. The method combines two approaches: one is rule-based and the other is based on the maximum entropy model. We develop an integration algorithm to fuse the results of the two approaches. All rules and the integration algorithm are formally stated so that one can easily reproduce the system and results. To optimize the systems configuration, we used the 2012 i2b2 challenge TLINK track dataset and applied threefold cross validation to the training set. Then, we evaluated its performance on the training and test datasets. The experiment results show that the proposed TEMPTING (TEMPoral relaTion extractING) system (ranked seventh) achieved an F-score of 0.563, which was at least 30% better than that of the baseline system, which randomly selects TLINK candidates from all pairs and assigns the TLINK types. The TEMPTING system using the hybrid method also outperformed the stage-based TEMPTING system. Its F-scores were 3.51% and 0.97% better than those of the stage-based system on the training set and test set, respectively.

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID

BioC is a simple XML format for text, annotations and relations, and was developed to achieve interoperability for biomedical text processing. Following the success of BioC in BioCreative IV, the BioCreative V BioC track addressed a collaborative task to build an assistant system for BioGRID curation. In this paper, we describe the framework of the collaborative BioC task and discuss our findings based on the user survey. This track consisted of eight subtasks including gene/protein/organism named entity recognition, protein–protein/genetic interaction passage identification and annotation visualization. Using BioC as their data-sharing and communication medium, nine teams, world-wide, participated and contributed either new methods or improvements of existing tools to address different subtasks of the BioC track. Results from different teams were shared in BioC and made available to other teams as they addressed different subtasks of the track. In the end, all submitted runs were merged using a machine learning classifier to produce an optimized output. The biocurator assistant system was evaluated by four BioGRID curators in terms of practical usability. The curators’ feedback was overall positive and highlighted the user-friendly design and the convenient gene/protein curation tool based on text mining. Database URL: http://www.biocreative.org/tasks/biocreative-v/track-1-bioc/

A graphene-based microelectrode for recording neural signals

We designed, fabricated and tested a novel prototype neural interface using two-dimensional single-atom-thick graphene as microelectrode for neural applications. The cytotoxicity indicated a satisfactory biocompatibility and non-toxicity. The treatment graphene with steam plasma improved the biological properties. The action potentials of lateral giant (LG) nerve fiber of the escape circuit of an American crayfish had a ratio of signal to noise (SNR) as great as 30.2±2.45 dB.

Linguistic Template Extraction for Recognizing Reader-Emotion and Emotional Resonance Writing Assistance

In this paper, we propose a flexible principle-based approach (PBA) for reader-emotion classification and writing assistance. PBA is a highly automated process that learns emotion templates from raw texts to characterize an emotion and is comprehensible for humans. These templates are adopted to predict reader-emotion, and may further assist in emotional resonance writing. Results demonstrate that PBA can effectively detect reader-emotions by exploiting the syntactic structures and semantic associations in the context, thus outperforming wellknown statistical text classification methods and the state-of-the-art reader-emotion classification method. Moreover, writers are able to create more emotional resonance in articles under the assistance of the generated emotion templates. These templates have been proven to be highly interpretable, which is an attribute that is difficult to accomplish in traditional statistical methods.

A semantic frame-based intelligent agent for topic detection

Detecting the topic of documents can help readers construct the background of the topic and facilitate document comprehension. In this paper, we propose a semantic frame-based topic detection (SFTD) that simulates such process in human perception. We take advantage of multiple knowledge sources and extracted discriminative patterns from documents through a highly automated, knowledge-supported frame generation and matching mechanisms. Using a Chinese news corpus containing over 111,000 news articles, we provide a comprehensive performance evaluation which demonstrates that our novel approach can effectively detect the topic of a document by exploiting the syntactic structures, semantic association, and the context within the text. Experimental results show that SFTD is comparable to other well-known topic detection methods.

SPIRIT: A Tree Kernel-Based Method for Topic Person Interaction Detection

The development of a topic in a set of topic documents is constituted by a series of person interactions at a specific time and place. Knowing the interactions of the persons mentioned in these documents is helpful for readers to better comprehend the documents. In this paper, we propose a topic person interaction detection method called SPIRIT, which classifies the text segments in a set of topic documents that convey person interactions. We design the rich interactive tree structure to represent syntactic, context, and semantic information of text, and this structure is incorporated into a tree-based convolution kernel to identify interactive segments. Experiment results based on real world topics demonstrate that the proposed rich interactive tree structure effectively detects the topic person interactions and that our method outperforms many well-known relation extraction and protein-protein interaction methods.

PIPE: a protein–protein interaction passage extraction module for BioCreative challenge

Identifying the interactions between proteins mentioned in biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this article, we propose PIPE, an interaction pattern generation module used in the Collaborative Biocurator Assistant Task at BioCreative V (http://www.biocreative.org/) to capture frequent protein-protein interaction (PPI) patterns within text. We also present an interaction pattern tree (IPT) kernel method that integrates the PPI patterns with convolution tree kernel (CTK) to extract PPIs. Methods were evaluated on LLL, IEPA, HPRD50, AIMed and BioInfer corpora using cross-validation, cross-learning and cross-corpus evaluation. Empirical evaluations demonstrate that our method is effective and outperforms several well-known PPI extraction methods. Database URL:

Ontology-Based Intelligent Web Mining Agent for Taiwan Travel

Due to the gradual increase in travel, the travel agent plays an important role in providing travel information conform to tourist’s requirements. Taiwan, also known as Formosa, its society is known throughout the world for its sincere hospitality and diverse cultural cuisine, and it has been one of the top tourist attractions in East Asia for years. In this paper, we propose an ontology-based intelligent web mining agent for Taiwan travel. The core technologies of the agent contain the ontology model, fuzzy inference mechanism, particle swarm optimization and ant colony optimization. The proposed agent can help tourist to collect Taiwan travel information form World Wide Web automatically by using tourist’s natural language description or documents. In this way, it will reduce travel agency’s workload and to accelerate the speed of tourist’s getting the travel information.

Intelligent healthcare agent for food recommendation at Tainan City

Nowadays, people sometimes eat too much and exercise too little, causing their weight more than their healthy weight range and even developing a disease such as diabetes. In this paper, an intelligent healthcare agent, including an ontology construction mechanism and a food route recommendation mechanism, is proposed for food recommendation at Tainan City. The proposed agent combines the ontology with the fuzzy inference mechanism and the intelligent search mechanism not only to make a guide to Tainan City gourmet but also to display how many calories this gourmet has on the Google map. In this way, the user can enjoy delicious food while he can stay healthy. The experimental results show that the proposed agent can effectively recommend a personalized schedule of enjoying Tainan City gourmet.

Section Heading Recognition in Electronic Health Records Using Conditional Random Fields

Electronic health records (EHRs) contain a wealth of information, such as discharge diagnoses, laboratory results, and pharmacy orders, which can be used to support clinical decision support systems and enable clinical and translational research. Unfortunately, the information is represented in a highly heterogeneous semi-structured or unstructured format with author- and domain-specific idiosyncrasies, acronyms and abbreviations. To take full advantage of health data, text-mining techniques have been applied by researchers to recognize named entities (NEs) mentioned in EHRs. However, the judgment of clinical data cannot be known solely from the NE level. For instance, a disease mention in the section of past medical history has different clinical significance when mentioned in the family medical history section. To obtain high-quality information and improve the understanding of clinical records, this work developed a machine learning-based section heading recognition system and evaluated its performance on a manually annotated corpus. The experiment results showed that the machine learning-based system achieved a satisfactory F-score of 0.939, which outperformed a dictionary-based system by 0.321.