Machine Learning & Bioinformatics Lab

• 主持人受邀擔任 International Journal of Molecular Sciences (IJMS,SCI Q1, IF: 5.6) special issue 客座編輯，主題為：Machine Learning for Peptide and Protein Function Prediction. Deadline: 2027/1/31. 歡迎投稿原創性研究或相關review. 請參考此連結.

I am pleased to share that I will be serving as a Guest Editor for a Special Issue titled "Machine Learning for Peptide and Protein Function Prediction" in the International Journal of Molecular Sciences (IJMS, SCI Q1, IF: 5.6). We invite researchers and experts in the field to submit their high-quality original research or review articles. The submission deadline is January 31, 2027. For more details, please check the special issue webpage. 

• 恭禧專題生黃瑞麟榮獲「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.

Congratulations to Ruei-Lin Huang for being awarded funding from the "NSTC Undergraduate Research Project" program, for the project titled "Development of a High-Precision Neuropeptide Recognition System Based on Heterogeneous Model Ensemble Learning and Automated Hyperparameter Optimization." 

• 恭禧專題生朱苡綾、劉柏妘參加「2026智創未來- 生成式AI創意競賽」榮獲金牌獎，今年第三屆舉辦、共計450+隊參賽，已成為國內人工智慧主題之熱門競賽，我們參賽主題為「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」，團隊結合生成式AI技術擴增胜肽序列資料集、並利用蛋白質詞嵌入(word embeddings)與物理化學特性混合之特徵，以建構最佳化機器學習模型，此方法於獨立測試集 MCC 達到 0.913, F1-score 達到 0.93，為現今最準確的功能性胜肽預測模型. 期刊論文正撰寫中. 2026/6. 

We are thrilled to announce that lab members Yi-Ling Chu and Bo-Yun Liu have been awarded the Gold Medal in the Logical Thinking Design Category at the 2026 Generative AI Creative Design Competition. Facing competition from over 450+ teams, we secured the top spot with the project, "A Functional Peptide Prediction Platform Utilizing Intelligent Data Augmentation and Protein Language Models."

• 實驗室與國立台北大學資管所戴敏育所長合作的ESG資料標註成果已發表於IEEE EM-RITE 2026會議 (15th IEEE International Workshop on Empirical Methods for Recognizing Inference in Text )，題目為 VeriPromiseESG4K: A Traditional Chinese ESG Promise Verification Dataset for AI CUP 2026. 感謝參與計劃之亞大、北市大、北大同學進行ESG資料標註與驗證，成果作為AICup 2026春季賽「ESG 永續承諾驗證競賽」資料集. 2026/6. 

Our lab collaborated with Director Min-Yuh Day from Graduate Institute of Information Management at National Taipei University on ESG data annotation. The results were published in IEEE EM-RITE 2026 and used as the dataset for AICup 2026 competition.

• 實驗室主持人受邀加入 Scientific Reports (SCI Q1期刊) 編輯委員會成員. 2026/4. 

The lab PI was invited to serve as an Editorial Board Member of Scientific Reports (SCI Q1 journal).

• 實驗室主持人加入 BMC Bioinformatics (SCI Q1期刊) 編輯委員會成員. 2026/4. 

The lab PI has joined the Editorial Board of BMC Bioinformatics (SCI Q1 journal).

• 恭禧專題生王睿孺、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：以大語言模型進行兒童敘事句法能力檢測與分析. 2026/3. 

Congratulations to Rue-Ru Wang, Ya-Sin Li, TY Chen, and YS Yin for winning the First Place Award in the 114th Academic Year Senior Project Competition of BIME, Asia University. Title: MINAS: Mandarin Intelligent Narrative Assessment of Syntax for Children.

• 恭禧專題生陳立凱、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：結合蛋白質大型語言模型與機器學習以預測抗老化胜肽. 2026/3. 

Congratulations to Li-Kai Chen, Chih-Hsien Chen, and Yu-Hsiang Fu for winning the Second Place Award in the 114th Academic Year Senior Project Competition of BIME, Asia University. Title: Predicting anti-aging peptides through integrated protein language model embeddings and sequence features.

• 恭禧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：基於序列的抗發炎胜肽機器學習預測方法. 2026/3. 

Congratulations to Chi-Chi Tseng for winning the Third Place Award in the 114th Academic Year Senior Project Competition of BIME, Asia University. Title: Sequence-based predictions of anti-inlammatory peptides using machine learning approaches.

• 恭禧專題生鄭筠蓁、王婷萱榮獲亞大生醫系「114學年度畢業專題競賽」佳作，題目：IL-6 誘導胜肽預測的計算方法. 2026/3. 

Congratulations to Yun-Chen Cheng and Ting-Xuan Wang for winning the Merit Award in the 114th Academic Year Senior Project Competition of BIME, Asia University. Title: Computational Method for IL-6-inducing Peptide Prediction.

• 恭禧傅宥翔同學研究所甄試上榜：陽明交通大學分子醫學與生物研究所(正取)、陽明交通大學智慧醫電工程研究所(備取，已錄取). 2026/3.

• ​恭禧碩士生Tadeo Pontjoharyo參加「2025生成式人工智慧創新應用國際競賽」獲得佳作. 這是我們參加的第一個國際競賽 (由台灣、越南、印尼三地大學共同主辦), Tadeo使用蛋白質語言模型進行血腦屏障穿透胜肽的資料擴增, 讓機器學習準確率提升至比現今方法提高10%. Title: From Language to Biology: Protein Language Model-Generated Synthetic Data Enables Accurate Blood-Brain Barrier Penetrating Peptide Prediction. 2025/12. 

We congratulate our master student Tadeo Pontjoharyo on receiving a Merit Award in the 2025 International Generative Artificial Intelligence Innovation Application Competition.

• 恭禧王睿孺、李亞欣、陳韜宇、尹懌碩同學參加「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. 

Congratulations to our lab members, Rui-Ru Wang, Ya-Xin Li, Tao-Yu Chen, and Yi-Shuo Yin, for receiving the Third Place in the Interdisciplinary Category at the 2025 National AI Project Creativity Competition (in total 112 participating teams).  

• 恭禧朱苡綾、鄭筠蓁同學參加「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. 

Congratulations to our lab members, Yi-Ling Chu and Yun-Chen Cheng, for receiving the Merit Award in the Interdisciplinary Category at the 2025 National AI Project Creativity Competition (in total 112 participating teams). Project title: Functional Peptide Prediction Method Based on Protein Language Model.

• [賀!] 實驗室主持人榮獲臺北市立大學114年度教師研究成果獎. 2025/12. 

Congratuations to the lab director for receiving the 2025 Faculty Research Award from University of Taipei.

• 恭禧王睿孺同學研究所甄試上榜：師範大學資訊工程系(正取)、台北大學資訊工程系(正取)、陽明交通大學生物醫學資訊研究所(備9，已錄取)、清華大學醫學資訊碩士學位學程(備6，已錄取). 2025/11.

• 恭禧李亞欣同學研究所甄試上榜：陽明交通大學生物醫學資訊研究所(備1，已錄取)、高雄科技大學電機系(正取)、高雄大學資管系(備1). 2025/11.

• 恭禧曾琪淇同學研究所甄試上榜：中山大學精準醫學研究所(備取，已錄取)、台北醫學大學醫學資訊研究所(正取)、臺北市立大學資訊科學系碩士班(正取). 2025/11.

• 恭禧陳芷嫻同學研究所甄試上榜：陽明交通大學工程生物科學學院-甲組聯招(正取)、中央大學生醫科學與工程學系碩士班 (正取). 2025/11.

• 恭禧陳立凱同學研究所甄試上榜：陽明交通大學智慧醫電工程研究所(備6，已錄取)、陽明交通大學生物資訊與系統生物學研究所(備13).  2025/11.

• 恭禧鄭筠蓁同學研究所甄試上榜：中山大學精準醫學研究所(備1)、陽明交通大學生物醫學資訊所(備8，已錄取). 2025/11.

• 恭禧王婷萱同學研究所甄試上榜：中興大學基因體暨生物資訊研究所(備6)、彰化師範大學人工智慧科技應用碩士學位學程(備5)、元智大學生物與醫學資訊碩士學位學程(正取1). 2025/11.

• 恭禧劉維任同學研究所甄試上榜：彰化師範大學人工智慧科技與應用碩士學位學程(正取)、宜蘭大學資訊工程系碩士班(正取)資訊工程系碩士班(正取)、台中科技大學資訊工程系碩士班(備27)、逢甲大學人工智慧科技與管理碩士學位學程(備5)、逢甲大學資訊工程系(備34). 2026/3.

• 恭禧鄭筠蓁、尹懌碩、林浚瑋同學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. 

Congratulations to lab members Yun-Chen Cheng, Yi-Shuo Yin, and Chun-Wei Lin on winning the Excellence Award of the "2025 Data Science Odyssey" hosted by the Institute of Statistical Science, Academia Sinica.

• 恭禧王睿孺、李亞欣、陳韜宇同學參加「中技社AI創意競賽」榮獲佳作獎 (比賽僅取前3名 + 佳作獎3名). 題目：MINA -- 兒童敘事能力評估與臨床建議系統. 2025/11. 

Congratulations to lab members Wang Rui-Ru, Li Ya-Sin, and Chen Tao-Yu for winning the Merit Award in the CTCI Foundation AI Innovation Competition! Our work is titled "MINA -- Mandarin Intelligent Narrative Assessment for Children".

• 恭禧實驗室成員王睿孺、李亞欣、尹懌碩、陳韜宇投稿論文 MINAS: Mandarin Intelligent Narrative Assessment of Syntax for Children 至「第三十七屆自然語言與語音處理研討會 (ROCLING 2025)」被接受為口頭發表論文，本年度會議將於台灣大學舉辦. 

• 實驗室發表研究成果HEPAD於SCI Q1國際期刊BMC Bioinformatics, 此為一套使用適性化特徵工程以預測具溶血毒性peptide的工具，由陳思涵、游荏捷等人完成. 2025/10. 

Our paper titled "HEPAD: enhancing hemolytic peptide prediction with adaptive feature engineering and diverse sequence descriptors" is now published in BMC Bioinformatics (IF = 3.3, rank = 15/67 in the category of MATHEMATICAL & COMPUTATIONAL BIOLOGY)

• IQUP文章發表於SCI Q1國際期刊Scientific Reports，恭禧周羿妘等同學完成以人工智慧模型篩選蛋白質標記化定量準確率差的圖譜，以提升整體定量準確性，此為現今唯一同類型工具，為人工智慧在蛋白質定量領域開創新的研究方向. 2025/8. 

Our paper titled "IQUP identifies quantitatively unreliable spectra with machine learning for isobaric labeling-based proteomics" is now published in Scientific Reports (IF = 3.9, rank = 24/135 (IF), 22/200 (CiteScore) in the Multidisciplinary category).

• [狂賀] 實驗室與高雄科技大學、澳洲UNSW合作的論文刊登於頂級國際期刊 npj Digital Medicine. 參與同學：周羿妘、廖威翔、林育全、鄧羽芹. 2025/8.

Our journal paper titled "Leveraging large language models for the deidentification and temporal normalization of sensitive health information in electronic health records" is now published in npj Digital Medicine (IF = 15.1, rank = 1/102 (IF) in the category of Health Care Sciences & Services). The paper is a collaborative effort between Asia University, National Kauhsiung University of Technology, and University of New South Wales.

• AAGP文章發表於SCI Q1期刊Scientific Reports，恭禧研究生Saptashwa Datta建構並發表當今第一套抗老化胜肽預測人工智慧模型! 

Our paper titled "AAGP integrates physicochemical and compositional features for machine learning-based prediction of anti-aging peptides" is now published in Scientific Reports (IF = 3.9, rank = 24/135 (IF), 22/200 (CiteScore) in the Multidisciplinary category) 2025/8.

• ​恭禧實驗室同學李亞欣、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 (共200+支隊伍參賽)，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. 

Congratulations to lab members Ya-Hsin Li, Rui-Ru Wang, and Tao-Yu Chen for winning the Corporate Innovation Award at the "Smart Innovation Future: 2025 Generative AI Creative Design Competition" hosted by Asia University (with over 200 participating teams). Project title: (MAIN-AI) Detection and Analysis of Children's Narrative Abilities Using Large Language Models.

• 恭禧實驗室同學陳立凱、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. 

Congratulations to lab members Li-Kai Chen, You-Xiang Fu, Zhi-Xian Chen, and Wei-Ren Liu for winning the 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 (with over 200 participating teams). Project title: Using Protein Language Models to Assist in the Development of Anti-inflammatory Peptide Drugs - Sequence Generation, Prediction, and Analysis.

• 恭禧實驗室同學陳立凱、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)，作品於世貿一館現場展覽，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. 

Congratulations to LK Chen, YH Fu, and ZH Chen for advancing to the Finals of the 2025 Best AI Awards Innovation Competition organized by the Ministry of Economic Affairs (in total 1000+ participating teams). Project title: "Using Protein Language Models to Assist in the Development of Anti-inflammatory Peptide Drugs - Sequence Generation, Prediction, and Analysis."

• 恭禧實驗室專題生周羿妘、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. 

Congratulations to YY Chou and YH Lih for winning the First place in the 113th Academic Year Senior Project Competition of BIME, Asia University. Title: IQUP--Identification of quantitatively unreliable spectra with machine learning for isobaric labeling-based proteomics.

• 恭禧實驗室專題生林億祥、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. 

Congratulations to YH Lin, YC Hou, and YC Deng for winning the Second Place in the 113th Academic Year Senior Project Competition of BIME, Asia University. Title: Improving the prediction of IL-13 inducing peptide with sequences produced by generative AI.

• A book chapter titled  "Deidentification and Temporal Normalization of the Electronic Health Record Notes Using Large Language Models: The 2023 SREDH/AI-Cup Competition for Deidentification of Sensitive Health Information." was published in Large Language Models for Automatic Deidentification of Electronic Health Record Notes, 1–16. Singapore: Springer Nature, 2025.

• A book chapter titled "Utilizing Large Language Models for Privacy Protection and Advancing Medical Digitization." was published in Large Language Models for Automatic Deidentification of Electronic Health Record Notes, 177–88. Singapore: Springer Nature, 2025.

• 恭禧實驗室成員林億祥研究所甄試正取交通大學-生物資訊及系統生物學研究所, 正取中興大學-基因體暨生物資訊研究所, 備取(備2，已獲錄取)清華大學-醫學資訊碩士學位學程, 備取(備1, 已獲錄取), 中央大學-生醫科學與工程學系碩士班. 2024/12. 

• 恭禧實驗室成員周羿妘正取台灣大學-精準健康碩士學位學程, 正取中興大學-基因體暨生物資訊研究所, 備取交通大學-生物資訊及系統生物學研究所. 2024/12. 

• 恭禧實驗室成員侯韻淇備取(備1，已獲錄取)雲林科技大學-資訊工程系碩士班, 備取中興大學-基因體暨生物資訊研究所, 備取台中教育大學資訊工程系碩士班. 2025/01. 

• 恭禧實驗室專題生林億祥、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.  (共計500+組參與團隊) 2024/10. 

Congratulations to Yi-Xiang Lin, You-Hsiang Fu, and Jhih-Sian Chen for winning the "Creative Innovators" category of the 2024 GenAI Stars Competition, hosted by the National Science and Technology Council. Their project, "Improving the Accuracy of Machine Learning Predictions for Therapeutic Peptides Using Generative AI," was awarded a Excellence Award. (in total 500+ participating groups).

• 恭禧實驗室成員周羿妘、陳立凱、劉維任投稿論文至「第三十六屆自然語言與語音處理研討會 (ROCLING 2024)」被接受為口頭發表論文，本年度會議將於中央研究院舉辦. 2024/9. 

Congratulations to the lab members Yi-Yun Chou, Li-Kai Chen, and Wei-Jen Liu for having their paper accepted for oral presentation at the 36th Conference on Computational Linguistics and Speech Processing (ROCLING 2024). This year’s conference will be held at Academia Sinica. Title: Enhancing Protein-Protein Interaction Recognition Accuracy in Large Language Models through Sentence Reduction and Few-Shot Learning.

• 實驗室發表腫瘤T細胞抗原預測的機器學習方法於PLoS ONE期刊，我們開發的ENCAP為現今最準確的預測方法，由專題生游荏捷、倪寬合作完成. 

Our paper titled "ENCAP: Computational Prediction of Tumor T Cell Antigens with Ensemble Classifiers and Diverse Sequence Features" was published in PLOS ONE (IF=3.7, rank = 15/120). 2024/7

• 實驗室發表抗血管增生胜肽預測的機器學習方法於Scientific Reports期刊，我們開發的AAPL為現今最準確的預測方法，由專題生李昀蓁、游荏捷、倪寬合作完成. 

Our paper titled "Improved prediction of anti-angiogenic peptides based on machine learning models and comprehensive features from peptide sequences" was published in Scientific Reports (IF=4.6, rank = 11/120). 2024/6

• ​A big welcome to Tadeo Pontjoharyo for joining our lab. 2024/6.

• 恭禧實驗室同學林億祥獲得「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. (共計200+組參與團隊) 2024/6. 

Congratulations to Lin, Yi-Xiang for winning the Gold Medal Award and Corporate Innovation Award in the "Logical Thinking Design" category of the Smart Innovation Future: 2024 Generative AI Creative Design Competition. His award-winning project title is "Generative AI-based Generation of Peptide Fragments to Improve Machine Learning Prediction Accuracy for Therapeutic Peptides - A Case Study on Interleukin-13 (IL-13) Inducing Peptides" (in total 200+ participating groups). 

• 恭禧實驗室同學周羿妘、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：利用生成式AI建構生醫關係網路--以蛋白質交互作用為例.  (共計200+組參與團隊) 2024/6. 

Congratulations to our lab members Chou, Yi-Yun, Chen, Li-Kai, and Liu, Wei-Ren for winning the Gold Medal Award and Corporate Innovation Award in the "Problem Solving" category of the Smart Innovation Future: 2024 Generative AI Creative Design Competition. Their award-winning project title is "Generative AI for the Construction of Biomedical Networks - A Case Study on Protein-Protein Interactions" (in total 200+ participating groups).

• 恭禧實驗室專題生蔡敦竹、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)，題目：建構混合式蛋白質體標記化定量演演算法. 2024/03. 

Congratulations to TC Tsai and CC Yang for winning the Industrial Committee Award of The 112th Academic Year Senior Project Competition of BIME, Asia University. Title: Construction of a hybrid isobaric-labeling proteomic quantitation algorithm.

• 恭禧實驗室專題生游荏捷獲得亞大生醫系「112年畢業專題競賽」第二名. 題目：使用最佳化機器學習模型以預測單域抗體互補位.  2024/03. 

Congratulations to JC Yu for winning the Second Place in The 112th Academic Year Senior Project Competition of BIME, Asia University. Title: Construction of a VHH paratope predictor using optimized machine learning models.

• The journal paper titled "Unlocking the Secrets Behind Advanced Artificial Intelligence Language Models in De-Identifying Chinese-English Mixed Clinical Text,” was published in  Journal of Medical Internet Research. (IF = 7.4, rank = 3/105) 2024/1

• 恭禧實驗室同學楊景臣錄取逢甲大學數據科學碩士學位學程 2024/1. 

• 恭禧實驗室同學李昀蓁錄取台灣科技大學資訊工程系碩士班 2023/12. 

• 恭禧實驗室同學游荏捷錄取中興大學基因體暨生物資訊學研究所 2023/11. 

• A big welcome to Mr. Saptashwa Datta as he becomes a part of our lab team!  2023/9

• [賀!] 我們開發世界上第一套使用spectral library searching以提升標記化蛋白質體定量準確率的方法，為計算蛋白質體學開創新的研究方向，論文發表於SCI Q1期刊Scientific Reports. 

The journal paper titled "Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter" was published in Scientific Reports (IF=4.996, rank = 8/110). 2023/8

• 恭禧實驗室專題生「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：基於序列的腫瘤T細胞抗原預測 2023/02. 

Congratulations to K Ni and JC You, for winning the joint First Place in The 111th Academic Year Senior Project Competition of BIME, Asia University. Title: Sequence-based prediction of tumor T-cell antigen.

• 恭禧實驗室專題生「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：利用機器學習方法開發基於胺基酸序列的溶血性胜肽預測模型. 2023/02.

Congratulations to SH Chen and SC Guo for winning the joint First Place in The 111th Academic Year Senior Project Competition of BIME, Asia University. Title: Development of a sequence-based hemolytic peptide predictor with machine learning models.

• 恭禧實驗室三位同學陳思涵、郭劭淳、倪寬錄取中興大學基因體暨生物資訊學研究所 2022/11. 

Congratulations to SH Chen, SC Kuo, and K Ni on admissions to the Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University.

• 實驗室發表文章 Sequence-based Prediction of Antimicrobial Peptides with CatBoost Classifier 於 IEEE International Conference on BioInformatics and BioEngineering (BIBE 2022) (游荏捷、倪寬為共同第一作者)

• The journal paper titled "Calibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics" was published in Scientific Reports (IF=4.996, rank = 8/110)