Award & Honor

• 指導專題生黃瑞麟榮獲「科技部大專學生研究計劃」經費補助，題目：基於異質模型Ensemble Learning與自動化超參數優化之高精度神經胜肽識別系統開發. 2026/7.

• 指導實驗室專題生朱苡綾、劉柏妘榮獲「2026智創未來- 生成式AI創意競賽」邏輯思維設計組金牌獎 (共計450+隊參賽)，主題：運用智能型資料擴增與蛋白質語言模型的功能性胜肽預測平台. 2026/6. 

Gold Medal Award in the Logical Thinking Design Category at the 2026 Generative AI Creative Design Competition (In total 450+ participating teams). Project title: A Functional Peptide Prediction Platform Utilizing Intelligent Data Augmentation and Protein Language Models.

• 指導專題生王睿孺、李亞欣、陳韜宇、尹懌碩榮獲亞大生醫系「114學年度畢業專題競賽」第一名，題目：MINAS: Mandarin Intelligent Narrative Assessment of Syntax for Children. 2026/3. 

First Place Award in the 114th Academic Year Senior Project Competition of BIME, Asia University. 

• 指導專題生陳立凱、陳芷嫻、傅宥翔榮獲亞大生醫系「114學年度畢業專題競賽」第二名，題目：Predicting anti-aging peptides through integrated protein language model embeddings and sequence features. 2026/3. 

Second Place Award in the 114th Academic Year Senior Project Competition of BIME, Asia University.

• 指導專題生曾琪淇榮獲亞大生醫系「114學年度畢業專題競賽」第三名，題目：Sequence-based predictions of anti-inlammatory peptides using machine learning approaches. 2026/3. 

Third Place Award in the 114th Academic Year Senior Project Competition of BIME, Asia University. 

• 指導專題生鄭筠蓁、王婷萱榮獲亞大生醫系「114學年度畢業專題競賽」佳作，題目：Computational Method for IL-6-inducing Peptide Prediction. 2026/3. 

Merit Award in the 114th Academic Year Senior Project Competition of BIME, Asia University. 

• 指導外籍碩士生Tadeo Pontjoharyo參加「2025生成式人工智慧創新應用國際競賽」獲得佳作. Title: From Language to Biology: Protein Language Model-Generated Synthetic Data Enables Accurate Blood-Brain Barrier Penetrating Peptide Prediction. 2025/12. 

Merit Award in the 2025 International Generative Artificial Intelligence Innovation Application Competition.

• 指導學生王睿孺、李亞欣、陳韜宇、尹懌碩參加「2025 全國 AI 專題創意競賽」榮獲跨領域組第三名 (共112隊參與競賽). 題目：CARA -- Children's Assisted Real-time Narrative Assessment. 2025/12. 

Third Place in the Interdisciplinary Category at the 2025 National AI Project Creativity Competition (112 participating teams).

• 指導學生朱苡綾、鄭筠蓁參加「2025 全國 AI 專題創意競賽」榮獲跨領域組佳作 (共112隊參與競賽). 題目：基於蛋白質語言模型的功能性胜肽預測方法. 2025/12. 

Merit Award in the Interdisciplinary Category at the 2025 National AI Project Creativity Competition (112 participating teams). Project title: Functional Peptide Prediction Method Based on Protein Language Model.

• 榮獲臺北市立大學114年度教師研究成果獎勵. 2025/12. 

Faculty Research Award from the University of Taipei.

• 指導學生鄭筠蓁、尹懌碩、林浚瑋參加中央研究院統計所舉辦「2025資料科學漫步」榮獲優選獎. 題目：以機器學習方法與多元特徵預測幼兒社會與情緒能力. 2025/11. 

Excellence Award of the "2025 Data Science Odyssey" hosted by the Institute of Statistical Science, Academia Sinica. Title: Predicting Early Childhood Social and Emotional Competence Using Machine Learning Methods and Diverse Features.

• 指導學生王睿孺、李亞欣、陳韜宇參加「中技社AI創意競賽」榮獲佳作. (共54 隊伍/教師69人/學生189人參賽) 題目：MINA -- 兒童敘事能力評估與臨床建議系統. 2025/11. 

Merit Award for the CTCI Foundation AI Innovation Competition (54 participating teams). Project title:"MINA -- Mandarin Intelligent Narrative Assessment for Children. 

• 指導學生李亞欣、王睿孺、陳韜宇參與「智創未來 : 2025 生成式AI創意設計競賽」榮獲企業創新獎 (200+ 隊伍參賽)，題目：(MAIN-AI) 以大語言模型進行兒童敘事能力檢測與分析 (與亞洲大學聽力暨語言治療學系張顯達講座教授合作). 2025/6. 

Corporate Innovation Award at the "Smart Innovation Future: 2025 Generative AI Creative Design Competition" hosted by Asia University (200+ participating teams).

• 指導學生陳立凱、傅宥翔、陳芷嫻、劉維任、朱苡綾參與「智創未來 : 2025 生成式AI創意設計競賽」榮獲企業創新獎、與邏輯思維設計組第三名 (共200+支隊伍參賽)，題目：使用蛋白質語言模型輔助開發抗發炎胜肽藥物 -- 序列生成、預測、以及分析. 2025/6. 

Corporate Innovation Award and Third Place in the Logic Design Category at the "Smart Innovation Future: 2025 Generative AI Creative Design Competition" hosted by Asia University (200+ participating teams).

• 指導學生陳立凱、傅宥翔、陳芷嫻、劉維任參與經濟部舉辦「2025 Best AI Awards 智慧創新大賞」入圍決賽 (共1000+支隊伍參賽, <10%隊伍進入決賽)，題目：使用蛋白質語言模型輔助開發抗發炎胜肽藥物 -- 序列生成、預測、以及分析. 2025/4. 

Finalist in the 2025 Best AI Awards hosted by the Ministry of Economic Affairs. (1000+ participating teams, less than 10% become finalists)

• 指導學生周羿妘、李亞欣獲得亞大生醫系「113年畢業專題競賽」第一名. 題目：IQUP--使用機器學習識別定量高誤差圖譜以改善標記化蛋白質體實驗. 2025/02.  

First Place in the 113th Academic Year Senior Project Competition of BIME, Asia University. Project title: IQUP-- Machine Learning Approach to Identify Quantitative High-Error Spectra for Improving Isobaric Labeling Proteomics.

• 指導學生林億祥、侯韻淇、鄧羽芹獲得亞大生醫系「113年畢業專題競賽」第二名. 題目：使用生成式AI合成蛋白質片段以提升IL-13誘導胜肽機器學習預測準確性. 2025/02. 

Second Place in the  113th Academic Year Senior Project Competition of BIME, Asia University. Project title: Using Generative AI to Produce Peptides for Improving Machine Learning Prediction Accuracy of IL-13 Inducing Peptides.

• 指導學生林億祥、傅宥翔、陳芷嫻獲得國科會舉辦「2024 GenAI Stars生成式AI 百工百業應用選拔」創意創客組優選獎，題目：使用生成式AI以提升醫療用胜肽機器學習預測準確性. 2024/10. (500+ 隊伍參賽). 

Excellence Award in the "Creative Maker Category" of the 2024 GenAI Stars-- Generative AI Applications Competition (500+ participating teams) hosted by the National Science and Technology Council. Project title: Using Generative AI to Improve Machine Learning Prediction Accuracy for Therapeutic Peptides.

• 指導學生林億祥獲得「智創未來 : 2024 生成式AI創意設計競賽」邏輯思維設計組金牌獎 & 企業創意獎，題目：使用生成式AI合成蛋白質片段以提升醫療用胜肽機器學習預測準確性--以白介素(IL-13) inducing peptide為例. 2024/6. (200+ 隊伍參賽). 

Gold Medal Award & Corporate Creativity Award in the "Logic Design Category" of the Smart Innovation Future: 2024 Generative AI Creative Design Competition (200+ participating teams). Project title: Using Generative AI to Produce Peptides for Improving Machine Learning Prediction Accuracy of Therapeutic Peptides--Taking Interleukin (IL-13) Inducing Peptides as an Example.

• 指導學生周羿妘、陳立凱、劉維任獲得「智創未來 : 2024 生成式AI創意設計競賽」問題解決組金牌獎 & 企業創意獎，題目：例用生成式AI建構生醫關係網路--以蛋白質交互作用為例. 2024/6. (200+ 隊伍參賽). 

Gold Medal Award & Corporate Creativity Award in the "Problem Solving Category" of the Smart Innovation Future: 2024 Generative AI Creative Design Competition (200+ participating teams). Project title: Using Generative AI to Construct Biomedical Networks--Taking Protein-Protein Interaction as an Example.

• 指導學生游荏捷獲得亞大生醫系「112年畢業專題競賽」第二名 2024/03. 題目：Constructing a VHH paratope predictor using optimized machine learning models. 

Second Place in the 112th Academic Year Senior Project Competition of Department of Bioinformatics and Medical Engineering, Asia University. Title: Constructing a VHH paratope predictor using optimized machine learning models.

• 指導學生蔡敦竹、楊景臣獲得亞大生醫系「112年畢業專題競賽」產業委員獎 (僅取一名) 2024/03. 題目：Constructing hybrid quantitation algorithms for isobaric labeling proteomics. 

Industry Committee Award in the 112th Academic Year Senior Project Competition of Department of Bioinformatics and Medical Engineering, Asia University. Title: Constructing hybrid quantitation algorithms for isobaric labeling proteomics.

• 指導學生「陳思涵、郭邵淳」獲得亞大生醫系「111年畢業專題競賽」並列第一名, 題目：Sequence-based prediction of tumor T-cell antigen, 2023/02. 

First place in the 112th Academic Year Senior Project Competition of Department of Bioinformatics and Medical Engineering, Asia University. Title: Sequence-based prediction of tumor T-cell antigen.

• 指導學生「倪寬、游荏捷」獲得亞大生醫系「111年畢業專題競賽」並列第一名，題目：Using machine learning methods to develop a sequence-based prediction model for hemolytic peptides, 2023/02. 

First place in the 112th Academic Year Graduation Project Competition of Department of Bioinformatics and Medical Engineering, Asia University. 

• 指導學生榮獲亞洲大學 110學年度APP程式設計競賽，醫學暨健康學院第一名，題目：認識自己一下吧，學生姓名：黃詠郁(心理系)

• 指導學生榮獲亞洲大學 110學年度APP程式設計競賽，管理學院第二名，題目：酒的小知識，學生姓名：張雅絜(休憩系)

• 指導學生榮獲亞洲大學 110學年度APP程式設計競賽，管理學院第三名，題目：小酒館，學生姓名：劉育廷(休憩系)

Research Grant

• Integrating Protein Language Model Embeddings and Sequence Features for Blood-Brain Barrier Penetrating Peptide Prediction. 混合蛋白質語言模型詞嵌入及序列特徵以預測血腦屏障穿透胜肽. Principal investigator, NSTC 115-2221-E-845-002 (國科會/工程處). 

• Integration of protein large language models and machine learning for the prediction of anti-aging peptides. 結合蛋白質大型語言模型與機器學習以預測抗老化胜肽. Principal investigator, NSTC 114-2221-E-468-010 (國科會/工程處). 

• Nanobody paratope prediction based on large language models. 以大型語言模型預測奈米抗體互補位置. Principal investigator, ASIA-113-CMUH-14. (113學年度亞洲大學與中國醫藥大學附設醫院研究平台計畫). (核定/因職務異動未執行). 

• VHH paratope prediction using artificial intelligence approaches. 使用人工智慧方法預測單域抗體互補位. Principal investigator, NSTC 113-2221-E-468-006 (國科會/工程處).

• 建構智慧型溝通能力快速評估工具, Co-principal investigator, NSTC 113-2410-H-468-012 (國科會/人文處).

• Predicting hemolytic peptides using machine learning methods with two-stage optimization. 以兩階段最佳化機器學習方法預測溶血毒性胜肽. Principal investigator, NSTC 112-2221-E-468-019 (國科會/工程處).

• Clinical record deidentification and temporal normalization for AI Cup. 臨床病例去識別化與時間資訊正規化競賽暨標註資料蒐集計畫. Co-principal investigator, Artificial Intelligence Competition and labeled data acqUisition Project (AI Cup)/ Ministry of Education. 2023. (教育部).

• Construction of optimized machine learning predictor for VHH paratope prediction. 建構適用於VHH的最佳化paratope機器學習預測方法. Principal investigator, Industry-Academia Cooperative Research Program with AnTaimmu BioMed Corp. 2023. (產學計劃-- 安肽生醫).

• Improving isobaric labeling quantitation accuracy with artificial intelligence and data-driven approaches 使用人工智慧以及資料導向方法以提升標記化蛋白質體定量準確性. Principal investigator, MOST 110-2222-E-468-003 (科計部).

Academic Service & Leadership

• Guest Editor for Special Issue titled "Machine Learning for Peptide and Protein Function Prediction" in the International Journal of Molecular Sciences (IJMS, SCI Q1, IF: 5.6). 

• Program Committee member, The 24th Asia Pacific Bioinformatics Conference (APBC 2026).

• Session chair, 2025 International workshop on Deidentification of Electronic Medical Record Notes (IW-DMRN, in collaboration with MedInfo), Taipei International Convention Center, Taipei, 2025.

• Session chair, Intelligent Computing Symposium, Taipei, 2025.

• Program Committee member, IEEE AIxMHC, Taichung, 2025. 

• Poster judge, 2023 Annual Symposium of Taiwanese Society of Biomedical Engineering (TSBME), Taoyuan, 2023. 

• Program Committee member and session chair, The 22nd IEEE International Conference on BioInformatics and BioEngineering (BIBE 2022)

Invited Talks and Seminars

• Title: Teaching Machines to Speak Protein: AI for Therapeutic Peptide Discovery. TIGP Social Network and Human-Centric Computing program, Academia Sinica. Nov, 2025. (中央研究院資訊所/國際研究生學程)

• Title: Identification of quantitatively unreliable spectra with machine learning for isobaric labeling-based proteomics. The 21th Taiwan Society for Mass Spectrometry Annual Conference (台灣質譜學會第21屆學術研討會). Chang Gung University. July, 2025. 

• 講題：人工智慧科技發展與應用. 台灣石油工會113年度各委員會聯席會議. 台中永豐棧酒店. Sep, 2024.

• Title: Improving accuracy of isobaric labeling-based protein quantitation with peptide-spectrum-match filter and spectral library searching. The 19th Taiwan Society for Mass Spectrometry Annual Conference (台灣質譜學會20週年年會暨第19屆學術研討會). 台中金典酒店. July, 2023.

• ​Title: Computational proteomics and its application to cancer tissue data analysis, Taiwan Joint Commission of Precision Medicine (台灣精準醫療品質策進會), Aug. 26, 2022.

• Title: Bioinformatics and data science for cancer proteomics research, Department of Computer Science and Information Engineering, Asia University, Apr. 8, 2021.

• Title: Automatic proteomics data analysis and isobaric labeling quantitation using WinProphet and Multi-Q 2, Bioinformatics Training Courses of Life Science Library, Academia Sinica, Apr. 7, 2021. (including hands-on training)

• Title: Computational proteomics and its application to cancer tissue data analysis, Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Feb. 27, 2020.

• Title: iTop-Q-- an intelligent top-down proteomics quantitation tool using DYAMOND algorithm for charge state deconvolution, Bioinformatics Program, Taiwan Internation Graduate Program, Academia Sinica. Mar. 22, 2018.

• Title: User-friendly tools for proteomics: WinProphet for identification and Multi-Q for isobaric labeling quantitation, Fall Seminar, Taiwan Society of Mass Spectrometry, Academia Sinica. Oct. 20, 2017. (including hands-on training)

• Title: Structure-based protein-protein interaction site predictions, Department of Mathematics, Fu-Jen Catholic University, Jun. 1, 2016.

• Title: Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces, Computational Bioinformatics Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan, Feb. 28, 2014.

• Title: Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces, Graduate Institute of Biomedical Informatics, Taipei Medical University, Nov. 28, 2013.

Reviewer

• 2026: Genome Biology, BMJ Health and Care Inormatics, npj Drug Discovery.

• 2025: Computers in Biology and Medicine, Heliyon.

• 2024: Database, Heliyon, npj Digital Medicine, International Journal of Molecular Sciences.

• IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2024).

• Molecules (2022)

• Asia Pacific Bioinformatics Conference (APBC 2017)

• IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016)

• Asia Pacific Bioinformatics Conference (APBC 2015)

• IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015)

• PLoS ONE (2014)

• Research in Computational Molecular Biology (RECOMB 2014)

• Asia Pacific Bioinformatics Conference (APBC 2014)

• Research in Computational Molecular Biology (RECOMB 2013)

• Asia Pacific Bioinformatics Conference (APBC 2013)

• IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013)

Photography

• 講師, 基礎攝影--理論與實務, 台北市原住民部落大學(2012) 

Lecturer, "Photography: Theory and Practice", Taipei Indigenous Community College (2012)

• 專案攝影講師, 屏東縣春日鄉歸祟村「回歸祟前，請記得我」社區營造專案 (本專案獲得信義房屋 2011年社區一家幸福行動計畫個人獎首獎) 

Lecturer, "Basic Photography" (Workshop) — Guey-Chung Community Development Association, Pingtung (2012)

• 婚禮攝影師 (場次：10+)

Wedding photographer for 10+ wedding events

• 副社長, 中央研究院攝影社 (2011)

Vice president, Photo Club, Academia Sinica (2011)

• 資訊長, 中央研究院攝影社 (2010)

Information officer, Photo Club, Academia Sinica (2010)

Creative Awards & Distinctions 

• 2013 天下雜誌主辦「觸動．感動 國際攝影大賽」，作品入圍決選 (參賽作品共10,376張)

• 2013 法鼓山世界青年會「無悔的步履」攝影比賽，作品榮獲優選

• 2012 台北旅遊網「旅行台北．發現最美」圖文競賽，「都市人物浮世繪」類別榮獲優勝及入選獎，「城市設計狂想曲」類別榮獲佳作及入選獎。

• 2012 台北市政府觀光傳播局「我心目中的台北」照片入選（入選照片將製作為「台北探索館」十周年館慶特別活動影片）

• 2012 待磨工作室「徵相．寶藏巖」影像徵選活動榮獲第一名

• 2011 聯合報「兩岸大交流，你我共參與」競賽「城市印象．隨手拍」類別榮獲佳作獎

• 2011 原住民文化事業基金會「按．照你」圖文競賽「部落寫真」類別榮獲特優獎，作品於西門町紅樓展出 

• 2011 教育部「閱遊台灣．百聞一見」圖文競賽榮獲第二名，作品出版為筆計書

• 2011 台北市政府觀光傳播局「台北．一遊未盡」網路圖文競賽，作品入選

攝影個展

• 2011.5  慢活．輕旅遊 @ 台北市原住民部落大學

• 2011.10  鏡頭下的原住民 @ 台北市原住民部落大學 

Sport

• Taroko Gorge Marathon (2006), 5 KM

• Shihmen Reservoir Swimming Carnival (2004), freestyle swimming for 3 KM

• Inline skating instructor, Hsin-Chu (2002)

• 銀牌, 男子400公尺自由式接力, 國立交通大學 游泳錦標賽 (2001).

Silver Medal, Men's 4 x 100m freestyle relay, NCTU Swimming Tournament (2001)

• 金牌, 男子400公尺自由式接力, 國立交通大學 游泳錦標賽 (2000).

Gold Medal, Men's 4 x 100m freestyle relay, NCTU Swimming Tournament (2000)

• 金牌, 男子400公尺混合接力, 國立交通大學 游泳錦標賽 (2000).

Gold Medal, Men's 4 x 100m Medley relay, NCTU Swimming Tournament (2000)

• 金牌, 男子400公尺自由式接力, 國立交通大學 游泳錦標賽 (1999).

Gold Medal, Men's 4 x 100m freestyle relay, NCTU Swimming Tournament (1999)

• 金牌, 男子400公尺混合接力, 國立交通大學 游泳錦標賽 (1999).

Gold Medal, Men's 4 x 100m Medley relay, NCTU Swimming Tournament (1999)

• 金牌, 男子100公尺蛙式, 國立交通大學 新生游泳競賽 (1997)

Gold Medal, Men's 100m Breaststroke, NCTU Freshman Swimming Tournament (1997)

• 救生員執照, 中華民國紅十字會 (1997)

Lifeguard Certification, The Red Cross Society of Republic of China, (1997)

• 銅牌, 國立交通大學 新生盃籃球競賽 (1998), 先發控球後衛

Bronze Medal, NCTU Freshman Basketball Tournament, 1998 (served as starting point guard)