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1. dxpr: an R package for generating analysis-ready data from electronic health records—diagnoses and procedures

Author

Yi-Ju Tseng, Hsiang-Ju Chiu, and Chun Ju Chen

Subjects
Electronic health records, Analysis-ready data, Exploratory data analysis, R package, Electronic computers. Computer science, QA75.5-76.95
Abstract

Background Enriched electronic health records (EHRs) contain crucial information related to disease progression, and this information can help with decision-making in the health care field. Data analytics in health care is deemed as one of the essential processes that help accelerate the progress of clinical research. However, processing and analyzing EHR data are common bottlenecks in health care data analytics. Methods The dxpr R package provides mechanisms for integration, wrangling, and visualization of clinical data, including diagnosis and procedure records. First, the dxpr package helps users transform International Classification of Diseases (ICD) codes to a uniform format. After code format transformation, the dxpr package supports four strategies for grouping clinical diagnostic data. For clinical procedure data, two grouping methods can be chosen. After EHRs are integrated, users can employ a set of flexible built-in querying functions for dividing data into case and control groups by using specified criteria and splitting the data into before and after an event based on the record date. Subsequently, the structure of integrated long data can be converted into wide, analysis-ready data that are suitable for statistical analysis and visualization. Results We conducted comorbidity data processes based on a cohort of newborns from Medical Information Mart for Intensive Care-III (n = 7,833) by using the dxpr package. We first defined patent ductus arteriosus (PDA) cases as patients who had at least one PDA diagnosis (ICD, Ninth Revision, Clinical Modification [ICD-9-CM] 7470*). Controls were defined as patients who never had PDA diagnosis. In total, 381 and 7,452 patients with and without PDA, respectively, were included in our study population. Then, we grouped the diagnoses into defined comorbidities. Finally, we observed a statistically significant difference in 8 of the 16 comorbidities among patients with and without PDA, including fluid and electrolyte disorders, valvular disease, and others. Conclusions This dxpr package helps clinical data analysts address the common bottleneck caused by clinical data characteristics such as heterogeneity and sparseness.

Published
2021
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2. Abstracts from the 8th International Congress of the Asia Pacific Society of Infection Control (APSIC)

Author

Nantanit Sutthiruk, Mari Botti, Julie Considine, Andrea Driscoll, Ana Hutchinson, Kumthorn Malathum, Cucunawangsih Cucunawangsih, Veronica Wiwing, Vivien Puspitasari, Rathina Kumar Shanmugakani, Yukihiro Akeda, Takuya Kodera, Pitak Santanirand, Kazunori Tomono, Takayuki Yamanaka, Hiroyuki Moriuchi, Hiroyuki Kitajima, Yuho Horikoshi, Alyona Lavrinenko, Ilya Azizov, Nurlan Tabriz, Margulan Kozhamuratov, Yekatherine Serbo, Dahae Yang, Woonhyoung Lee, Il Kwon Bae, Jae Hyun Lee, Hyukmin Lee, Jung Ok Kim, Seok Hoon Jeong, Kyungwon Lee, Thiba Peremalo, Priya Madhavan, Sharina Hamzah, Leslie Than, Eng Hwa Wong, Mohd Nasir Mohd Desa, Kee Peng Ng, Marionne Geronimo, Maria Fe Tayzon, Maria Jesusa Maño, Angela Chow, Pei-Yun Hon, Mar-Kyaw Win, Brenda Ang, Yee-Sin Leo, Tina See, Rocio Alvarez Marin, Marta Aires de Sousa, Nicolas Kieffer, Patrice Nordmann, Laurent Poirel, Wison Laochareonsuk, Sireekul Petyu, Pawin Wanasitchaiwat, Sutasinee Thana, Chollathip Bunyaphongphan, Woranan Boonsomsuk, Pakpoom Maneepongpermpoon, Silom Jamulitrat, Dorairajan Sureshkumar, Kalyanaraman Supraja, Soundararajan Sharmila, Benny Setiawan, Nicolaski Lumbuun, Haruo Nakayama, Toshiko Ota, Naoko Shirane, Chikako Matuoka, Kentaro Kodama, Masanobu Ohtsuka, Silverose Ann Andales Bacolcol, Melecia Velmonte, Allan Alde, Keithleen Chavez, Arlene Joy Esteban, Aisa Jensen Lee, Tai-Chin Hsieh, Shio-ShinJean, Huey-Jen Huang, Shu-Ju Huang, Yu-Huan Huang, Pei-Chen Cheng, Su-Fang Yu, Shih-Ming Tsao, Yuan-Ti Lee, Chien-Feng Li, Min-Chi Lu, Nattapol Pruetpongpun, Thana Khawcharoenporn, Pansachee Damronglerd, Nuntra Suwantarat, Anucha Apisarnthanarak, Sasinuch Rutjanawech, Lisa Cushinotto, Patty McBride, Harding Williams, Hans Liu, Phan Thi Hang, Dinh Pham Phuong Anh, Ngai Le, Dung Khu, Lam Nguyen, Roel Beltran Castillo, Ram Gopalakrishnan, Venkatasubramanian Ramasubramanian, Subramanian Sreevidya, Ranganathan Jayapradha, Atsushi Umetsu, Tetsuhiro Noda, Kenyuu Hashimoto, Akihiro Hayashi, Mikie Kabashima, Ursula Jadczak, Knut Elvelund, Marit Johnsen, Bente Borgen, Egil Lingaas, Chia-Hua Mao, Fu-Chieh Chang, Chang-Pan Liu, Ru-Hui Chao, Fu-chieh Chang, Chang-pan Liu, Junpen Pawapotako, Chadanan Prasertpan, Wantanee Malaihuan, Phisit Uirungroj, Chalermpong Saenjum, Teerapat Ouirungrog, Sue Borrell, Pauline Bass, Leon Worth, Zhao Xian-li, Li Xiao-long, Yao Xue-hua, Ren Wei, Zhang Xia Zeng, Man Ying Kong, Christopher Koon Chi Lai, Suet Yi Lee, Ngai Chong Tsang, M. M. O’Donoghue, M. V. Boost, L. K. P. Suen, G. K. Siu, K. W. Mui, C. K. C. Lai, D. N. C. Tsang, Yuka Sato, Mariko Tateishi, Mutsuko Mihashi, Jose Paulo Flor, Marko Bautista, V. Jay De Roxas, Justine Vergara, Nicolo Andrei Añonuevo, Marion Kwek, Jose Acuin, Anna Josea Sanchez, Avel Bathan, Jamilah Binte Jantan, Chua Chor Guek, Eu Chiow Kian, Pampe Anak Pirido, Nur Fadilah Binte Mohd Aron, Leah May Estacio, Francis Alvarez Palana, Michelle Gracia, Nur Syafiqah Binte Shamsuddin, Kersten Timbad Castro, Madonna Baloria, Faezah Binte Adam, Zhang Wei, Poh Bee Fong, Marimuthu Kalisvar, I-Ju Chuang, Yi-ChunCho, Yu-Fen Chiu, Lung-Chih Chen, Yi-Chun Lin, Shao-Xing Dong, Yi-Chieh Lee, Hui-Chen Kuan, Hsin-Hua Lin, Chia-Chun Chi, Chin-Te Lu, Tang Ya-Fen, Su Li-Hsiang, Liu Jien-Wei, Hsuehlan Chao, PinRu ChangChien, WeiFang Chen, ChungHsu Lai, Lutfe Ara, Syed Mohammad Niaz Mowla, Shaikh Mahmud Kamal Vashkar, Wai Fong Chan, Mabel Yin ChunYau, Karen Kam LingChong, Tze OnLi, Rajwinder Kaur, Ng Po Yan, Gloria Chor Shan Chiu, Christina W. Y. Cheung, Patricia T. Y. Ching, Radley H. C. Ching, Conita H. S. Lam, C. H. Kan, Shirley S. Y. Lee, C. P. Chen, Regina F. Y. Chan, Annie F. Y. Leung, Isadora L. C. Wong, S. S. Lam, Queenie W. L. Chan, Cecilia Chan, Seyed Sadeq Seyed Nematian, Charles John Palenik, Mehrdad Askarian, Nahid Hatam, Itaru Nakamura, Hiroaki Fujita, Ayaka Tsukimori, Takehito Kobayashi, Akihiro Sato, Shinji Fukushima, Tetsuya Matsumoto, V. James De Roxas, V James De Roxas, Nicolo AndreiAñonuevo, Yeng May Ho, Jia Qi Kum, Bee Fong Poh, Kalisvar Marimuthu, Tzu-Yin Liu, Sin-Man Chu, Hui-Zhu Chen, Tun-chieh Chen, Yichun Chen, Ya-Ching Tsao, Sumawadee Skuntaniyom, Pirawadee Tipluy, Sangwan Paengta, Ratchanee wongsaen, Sutthiphun thanomphan, Samettanet Tariyo, Buachan Thongchuea, Pattama Khamfu, Sutthiphan Thanomphan, Wipaporn Natalie Songtaweesin, Suvaporn Anugulruengkit, Rujipat Samransamruajkit, Darintr Sosothikul, Ornanong Tansrijitdee, Anry Nakphunsung, Patchareeyawan Srimuan, Jirachaya Sophonphan, ThanyaweePuthanakit, Kunyanut Payuk, Wilawan Picheansathian, Nongkran Viseskul, Elizabeth DeNardo, Rachel Leslie, Todd Cartner, Luciana Barbosa, Heinz-Peter Werner, Florian H. H. Brill, Julia Yaeko Kawagoe, Elizabeth De Nardo, Sarah Edmonds- Wilson, David Macinga, Patricia Mays-Suko, Collette Duley, Tran Thi Thuy Hang, Tran Thi My Hanh, Christopher Gordon, Roopa Durairaj, Anusha Rohit, Saujanya Saravanakumar, Jothymani Hemalatha, Ryuichi Hirano, Yuichi Sakamoto, Shoji Yamamoto, Naoki Tachibana, Miho Miura, Fumiyo Hieda, Yoshiro Sakai, Hiroshi Watanabe, Silverose Ann Bacolcol, Keitleen Chavez, Jia-Wei Lim, Aung-Aung Hein, Grace Tin, Vanessa Lim, Huwi-chun Chao, Chiu-Yin Yeh, Mei-feng Lo, Chonlada Piwpong, Songyos Rajborirug, Ploypailin Preechawetchakul, Yada Pruekrattananapa, Tharntip Sangsuwan, Ratchanee Wongsaen, Sungwan Paengta, Napatnun Nilchon, Sutthipun Thanompan, Samattanet Tariyo, Svetlana Kolesnichenko, Yerbol Tishkambayev, Asylkhan Alibecov, Yekaterina Serbo, Youngwon Nam, Jae Hyeon Park, Yun Ji Hong, Taek Soo Kim, Jeong Su Park, Kyoung Un Park, Eui-Chong Kim, Samuel Abumhere Aziegbemhin, Onaiwu Enabulele, Yao-Shen Tung, An-Chi Chen, Shen-Min Huang, Yui-Yein Yang, Li-Hung Wu, Chin-cheng Lin, Tzu Hao Lien, Jia Hao Chang, Yu Shan Huang, Yi Shun Chen, Sasithorn Sirilun, Phisit Ouirungroj, Suwanna Trakulsomboon, Patcharee Prasajak, Maryanne W. N. Kwok, Lady S. H. Ng, Lindy M. T. Wong, Lenina S. L. Poon, Mary K. L. Lai, Holly H. S. Cheng, S. K. Fong, Cindy F. Y. Leung, Jumpei Hasegawa, Hiroki Shirakawa, Sachiko Wakai, Makiko Mieno, Shuji Hatakeyama, Manu Deeudom, Prasit Tharavichitkul, Terrence Chinniah, Jackson Tan, Kavitha Prabu, Sartaj Alam, Aung Kyaw Wynn, Rashidah Ahmad, Amalina Sidek, Dg Azizah Samsuddin, Noraini Ajis, Aliyah Ahmad, Susylawathi Magon, Boon Chu, Jiqiu Kuang, Yan Gao, Shoujun Wang, Yunxiao Hao, Rong Liu, Dongmei Li, Hui Wang, Hisanori Nishio, Hitomi Mori, Yoshiko Morokuma, Takaaki Yamada, Makiko Kiyosuke, Sachie Yasunaga, Kazuhiro Toyoda, Nobuyuki Shimono, Dmitriy Babenko, Anar Turmuhambetova, Antonella Cheşcă, Mark A. Toleman, Lyudmila L. Akhmaltdinova, Mark Albert Magsakay, Angelo Macatibag, Jeannica Kriselle Lerios, Alyona Lavrineko, Dmitry Babenko, Eugene Sheck, Mikhail Edelstein, Lih-Yue Li, Chiung-Wen Chan, Hui-Chuan Pan, Wipa Vanishakije, Warisra Jaikampun, Su-Yin Li, Jian-Feng Li, Yu-Ping Wu, Chiao-Hui Lin, Ping-Chin Chang, Samatanet Tariyo, Suttsiphan Thanompan, Suchada Sukkra, Khalequ Zaman, Sheikh Farzana Zaman, Farzana Zaman, Asma Aziz, Sayeed-Bin Faisal, Magali Traskine, Javier Ruiz-Guiñazú, Dorota Borys, Wendy Wai Yee Lam, May Chow, Lucy Choy, Joseph Kam, Sharifah Azura Salleh, Razila Yacob, Siti Rokiah Yusof, Nordiah Awang Jalil, Maria Lourdes Millan, Jose Lito Acuin, Melecia A. Velmonte, Silverose Ann A. Bacolcol, Ching-I Ting, Sunisa Dissayasriroj, Terrence Rohan Chinniah, Jauharatud DiniSuhaimi, Aizzuddin Mirasin, Nurul Morni, Azizah Samsuddin, Amalina AbuBakar, Amanie Shafiee, Julaini Safar, Leung Annie, Fung Yuk Ling, Lau Edna, Luk Kristine, Satoshi Shinomiya, Kumiko Yamamoto, Kayoko Kjiwara, Mitsuhiro Yamaguchi, Wei Zhang, Bee-Fong Poh, Ming-Chin Chan, Chih-Chien Wang, Huan-Yu Huang, Chiung-Ling Lai, Sajeerat Kosol, Wantana Sakolwirat, Patchanee Paepong, Sawalee Jansanga, Pattarin Jaisamoot, Nuttha Thongnuanual, Chittima Srithong, Somporn Somsakul, Sutima Plongpunth, Mukkapon Punpop, Porntip Malathum, Kulada Peautiwat, Nattawipa boon kirdram, Pimpaporn Klunklin, Geetha Samethadka, Naoko Suzuki, Hitomi Asada, Masao Katayama, Atsushi Komano, Hidehiro Watanabe, Hye Kyung Seo, Joo-Hee Hwang, Myoung Jin Shin, Su Young Kim, Eu Suk Kim, Kyoung-Ho Song, Hong Bin Kim, Lai-Si Un, Choi-Ian Vong, Jocelyn Koh, Sherly Agustinus, Rozita Bte Abu Hassan, Yin Phyu Thinn, Benjamin Ng, Soe Pyae Tun, Su Mon Thi Ha, Xue Xiaoting, Lin Li, Leyland Chuang, Attanayaka Mudiyanselage Chulani Niroshika, Kaluarachchige Anoma Kaluarachchi Perera, Dimingo Kankanamalage Diana Grace Fernando, Bodhipakshage Rohini Hemamala, Chiu-yin Yeh, Hui-Chun Yang, Hsiang-Ju Chiu, Ya-Ling Shih, Yu-Shan Chien, Wan-Yi Lin, Chia-Yun Pan, Ying-Yun Chang, Chiu-Yuch Yea, Ming-Hsien Chu, Li-Chu Lee, Lin Yu-Hsiu, Guo Siao-Pei, Leung Pak-On, Sie Mei-Fe, Chen Jyh-Jou, Chang Yong-Yuan, Shu-Yuan Kuo, Yu-Hsiu Lin, Ji-Sheng Zhang, Pak-On Leung, Mei-Fe Sie, Jyh-Jou Chen, Yan-Ru Chen, Ying-Ling Chen, Chi-Fen Taou, Hsiao-Shan Chen, Hung-Jen Tang, Shin Yu Chen, Yin Yin Chen, Fu Der Wang, Tzu-Ping Shih, Chin-Yu Chen, Su-Jung Chen, Mei-chi Wu, Wan-ju Yang, Mei-ling Chou, Man-Ling Yu, Li-Chu Li, Cheng-Wei Chu, Wen-Hao Tsou, Wen-Chih Wu, Wen-Chi Cheng, Cho-Ching Sun, Shu-Hua Lu, Hsin-Ling Yang, Cheng-Yu Lu, Nitchawan Hirunprapakorn, Sirilux Apivanich, Ttipakorn Pornmee, Chonnikarnt Beowsomboon, Itthaporn Kumkoom, Nongyao Kasatpibal, Jittaporn Chitreecheur, JoAnne D. Whitney, Surasak Saokaew, Kirati Kengkla, Margaret M. Heitkemper, Thanomvong Muntajit, Siriluk Apivanich, Hang Thi Phan, Anh Pham Phuong Dinh, and Tuyet Thi Kim Nguyen

Subjects
Infectious and parasitic diseases, RC109-216
Published
2017
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5. dxpr: an R package for generating analysis-ready data from electronic health records—diagnoses and procedures

Author

Chun Ju Chen, Hsiang Ju Chiu, and Yi Ju Tseng

Subjects
General Computer Science, Computer science, Bioinformatics, Field (computer science), Set (abstract data type), 03 medical and health sciences, Databases, 0302 clinical medicine, Exploratory data analysis, Health care, medicine, Electronic health records, 030212 general & internal medicine, Medical diagnosis, 030304 developmental biology, Analysis-ready data, 0303 health sciences, business.industry, Data Science, R package, Software Engineering, QA75.5-76.95, medicine.disease, Comorbidity, Visualization, Electronic computers. Computer science, Data analysis, Medical emergency, business
Abstract

Background Enriched electronic health records (EHRs) contain crucial information related to disease progression, and this information can help with decision-making in the health care field. Data analytics in health care is deemed as one of the essential processes that help accelerate the progress of clinical research. However, processing and analyzing EHR data are common bottlenecks in health care data analytics. Methods The dxpr R package provides mechanisms for integration, wrangling, and visualization of clinical data, including diagnosis and procedure records. First, the dxpr package helps users transform International Classification of Diseases (ICD) codes to a uniform format. After code format transformation, the dxpr package supports four strategies for grouping clinical diagnostic data. For clinical procedure data, two grouping methods can be chosen. After EHRs are integrated, users can employ a set of flexible built-in querying functions for dividing data into case and control groups by using specified criteria and splitting the data into before and after an event based on the record date. Subsequently, the structure of integrated long data can be converted into wide, analysis-ready data that are suitable for statistical analysis and visualization. Results We conducted comorbidity data processes based on a cohort of newborns from Medical Information Mart for Intensive Care-III (n = 7,833) by using the dxpr package. We first defined patent ductus arteriosus (PDA) cases as patients who had at least one PDA diagnosis (ICD, Ninth Revision, Clinical Modification [ICD-9-CM] 7470*). Controls were defined as patients who never had PDA diagnosis. In total, 381 and 7,452 patients with and without PDA, respectively, were included in our study population. Then, we grouped the diagnoses into defined comorbidities. Finally, we observed a statistically significant difference in 8 of the 16 comorbidities among patients with and without PDA, including fluid and electrolyte disorders, valvular disease, and others. Conclusions This dxpr package helps clinical data analysts address the common bottleneck caused by clinical data characteristics such as heterogeneity and sparseness.

Published
2021

6. A multiple measurements case-based reasoning method for predicting recurrent status of liver cancer patients

Author

Pei Ming Yang, Yan Po Lin, Ja-Der Liang, Guan-Tarn Huang, Xiao Ou Ping, Feipei Lai, Yi Ju Tseng, and Hsiang Ju Chiu

Subjects
Matching (statistics), Similarity (geometry), General Computer Science, Computer science, Single measurement, General Engineering, Early detection, computer.software_genre, Improved performance, Case-based reasoning, Data mining, Time series, computer, Temporal information
Abstract

In general, the studies introducing the medical predictive models which frequently handle time series data by direct matching between pairs of features within sequences during calculation of similarity may have following limitations: (1) direct matching may not be a suitable matching because these paired cases by a fixed order may not be with the most similar temporal information, and (2) when two patients have different numbers of multiple cases, some cases may be ignored. For example, one patient with four cases and another one with five cases, only first four cases of these two patients are paired and the left one case may be ignored. In this paper, in order to dynamically determine matching pairs among cases and pair all cases between two patients, we propose a multiple measurements case-based reasoning (MMCBR) to be used for building liver cancer recurrence predictive models. MMCBR and single measurement case-based reasoning (SingleCBR) are evaluated and compared. According to experiment results in this study, the performance of MMCBR models is better than that of SingleCBR models. Multiple measurements accumulated during a period of time do have benefits for building predictive models with improved performance based on this proposed MMCBR method.

Published
2015
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7. Rule-based healthcare-associated bloodstream infection classification and surveillance system

Author

Yi-Ju, Tseng, Jung-Hsuan, Wu, Hui-Chi, Lin, Hsiang-Ju, Chiu, Bo-Chiang, Huang, Rung-Ji, Shang, Ming-Yuan, Chen, Wei-Hsin, Chen, Huai-Te, Chen, Feipei, Lai, and Yee-Chun, Chen

Subjects
Male, Cross Infection, Population Surveillance, Prevalence, Taiwan, Humans, Bacteremia, Female, Decision Support Systems, Clinical, Risk Assessment, Algorithms
Abstract

Healthcare-associated infections (HAIs) are a major patient safety issue. These adverse events add to the burden of resource use, promote resistance to antibiotics, and contribute to patient deaths and disability. A rule-based HAI classification and surveillance system was developed for automatic integration, analysis, and interpretation of HAIs and related pathogens. Rule-based classification system was design and implement to facilitate healthcare-associated bloodstream infection (HABSI) surveillance. Electronic medical records from a 2200-bed teaching hospital in Taiwan were classified according to predefined criteria of HABSI. The detailed information in each HABSI was presented systematically to support infection control personnel decision. The accuracy of HABSI classification was 0.94, and the square of the sample correlation coefficient was 0.99.

Published
2013

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