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1. Tung-Hung Su, Sheng-Shun Yang, Mei-Hsuan Lee, Wei-Yu Kao, Shang-Chin Huang, Fen-Fang Chen, Francis SK Poon, Lung-Wen Tsai, Yi-Ting Chen, Che Lin, Weichung Wang, W Ray Kim, Jia-Horng Kao* , “High SAFE scores predict hepatocellular carcinoma in viral and non-viral hepatitis and metabolic dysfunction associated steatotic liver disease,” Clinical and Molecular Hepatology, 06 Jan 2025. https://doi.org/10.3350/cmh.2024.0822 

2. B.-R. Wu, S. Ormazabal Arriagada, T.-C. Hsu, T.-W. Lin, and C. Lin*, “Exploiting Common Patterns in Diverse Cancer Types via Multi-Task Learning”. npj Precision Oncology 8, 245, Oct. 2024. https://doi.org/10.1038/s41698-024-00700-z.

3. Hsinhan Tsai, Ta-Wei Yang, Kai-Hao Ou, Tung-Hung Su, Che Lin, Cheng-Fu Chou, "Multimodal Attention Network for Dementia Prediction," IEEE Journal of Biomedical and Health Informatics, doi: 10.1109/JBHI.2024.3438885, pp. 1-14, Aug. 2024.

4. Te-Cheng Hsu, Che Lin*, “Learning from Small Medical Data - Robust Semi-supervised Cancer Prognosis Classifier with Bayesian Variational Autoencoder,” Bioinformatics Advances, vol. 3, issue 1, Jan. 2023.

5. Sagaya Louis Gracy Thomas, Che Lin*, "Top-K ranking of drug-target interactions based on transfer learning and listwise loss," International Journal of Electrical Engineering (IJEE), vol. 29, no. 1, pp. 13-24, Feb. 2022. (Best paper award in signal processing) 

6. Y. -C. Wu, C. Lin*, and T. Q. S. Quek, "A Robust Distributed Hierarchical Online Learning Approach for Dynamic MEC Networks," IEEE Journal on Selected Areas in Communications, vol. 40, no. 2, pp. 641-656, Feb. 2022. 

7. Li-Hsin Cheng, Te-Cheng Hsu, Che Lin*, “Integrating ensemble systems biology feature selection and bimodal deep neural network for breast cancer prognosis prediction,” Scientific Reports, Sci Rep 11, 14914 (2021), 21 Jul. 2021

8. Y.-C Wu, T. Q. Dinh, Y. Fu, C. Lin* and T. Q. S. Quek, "A Hybrid DQN and Optimization Approach for Strategy and Resource Allocation in MEC Networks," IEEE Transactions on Wireless Communications, vol. 20, no. 7, pp. 4282-4295, Jul. 2021.

9. Wei-Hsin Lin, Yi-Wen Chang, Min-Xiang Hong, Te-Cheng Hsu, Ko-Chuan Lee, Che Lin*, and Jia-Lin Lee*, “STAT3 phosphorylation at Ser727 and Tyr705 differentially regulates the EMT–MET switch and cancer metastasis,” Oncogene, ONC-2020-01309R, 40:791-805, 1 Dec. 2020. 

10. Semon Wu, I-Chieh Tseng, Wen-Cheng Huang, Cheng-Wen Su, Yu-Heng Lai, Che Lin, Alan Yueh-Luen Lee, Chan-Yen Kuo, Li-Yu Su, Ming-Cheng Lee, Te-Cheng Hsu, Chun-Hsien Yu, “Establishment of an Immunocompetent Metastasis Rat Model with Hepatocyte Cancer Stem Cells,” Cancers, 12(12), 3721-3734, 11 Dec. 2020. 

11. Yu-Heng Lai, Wei-Ning Chen, Te-Cheng Hsu, Che Lin*, Yu Tsao, Semon Wu, "Overall survival prediction of non-small cell lung cancer by integrating microarray and clinical data with deep learning," Scientific Reports, Sci Rep 10, 4679, 13 Mar. 2020. (Top 100 in Cancer paper)

12. Y.-C. Hsiao, Y.-C. Wu, and C. Lin*, “Energy-Efficient Beamforming Design for MU-MISO Mixed RF/VLC Heterogeneous Wireless Networks,” IEEE Trans. on Signal Processing, 67(14): 3770 - 3784, 15 Jul. 2019. 

13. C.-L. Chen, J.-T. Liu, Y.-C. Hsiao, C.-M. Chen, H.-C. Tsao, and C. Lin*, “Robust Beamforming Design for MISO Bursty Interference Channels under Traffic Uncertainties,” IEEE Trans. on Signal Processing, 67(6): 1477 - 1492, 15 Mar. 2019. 

14. F.-Y. Liu, T.-C. Hsu, P. Choong, M.-H. Lin, Y.-J. Chuang, B.-S. Chen and C. Lin*, “Uncovering the regeneration strategies of zebrafish organs: a comprehensive systems biology study on heart, cerebellum, fin, and retina regeneration,” BMC systems biology, 12(Suppl 2):33-46, 19 Mar. 2018. 

15. W. Liao, B. Liu, C.-C. Chang, L.-J. Lin, C. Lin, B.-S. Chen, and Z. Xie, "Functional characterization of insulation effect for synthetic gene circuits in mammalian cells," ACS Synthetic Biology 2018 7 (2), 412-418, 1 Dec. 2017. 

16. J.-W. Li and C. Lin*, “On the Optimal Power Allocation for Two-Way Full-Duplex AF Relay Networks,” IEEE Trans. Signal Processing, 65 (21): 5702-5715, Nov. 2017.

17. C.-L. Chen and C. Lin*, “Utility Maximization for Two-Way AF Relaying Under Rate Outage Constraints,” IEEE Trans. Wireless Communications, 16 (9), 5762-5778, Sept. 2017. 

18. M.-T. Lin, C.-Y. Wang, H.-J. Xie, C. H. Y. Cheung, C.-H. Hsieh, H.-F. Juan, B.-S. Chen, C. Lin*, “Novel utilization of terminators in the design of biologically adjustable synthetic filters,” ACS Synthetic Biology, vol. 5, no. 5, pp. 365–374, 25 Feb. 2016.

19. W.-H. Chen, W.-R. Lin, H.-C. Tsao, C. Lin*, “Probabilistic power allocation for cognitive radio networks with outage constraints and one-bit side information,” IEEE Trans. Signal Process., 64(4): 867–881, 15 Feb. 2016. 

20. C.-Y. Hsu, Z.-M. Pan, R.-H. Hu, C.-C. Chang, H.-C. Cheng, C. Lin, B.-S. Chen, “Systematic biological filter design with a desired I/O filtering response based on promoter-RBS libraries,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12 (3): 712-725, May 2015. 

21. C.-C. Wu, C. Lin, B.-S. Chen, “Dynamic Network-Based Relevance Score Reveals Essential Proteins and Functional Modules in Directed Differentiation,” in Stem Cells International, vol. 2015, Article ID 792843, 14 pages, Apr. 2015.

22. C. Lin*, C.-N. Lin, Y.-C. Wang, F.-Y. Liu, Y.-W. Chien, Y.-J. Chuang, C.-Y. Lan, W.-P. Hsieh, B.-S. Chen, “Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection,” BMC Systems Biology, 8(Suppl 5):S6, 12 Dec. 2014.  (Best Paper Award for 2014 GIW-ISCB-ASIA conference)

23. C. Lin*, C.-N. Lin, Y.-C. Wang, F.-Y. Liu, Y.-J. Chuang, C.-Y. Lan, W.-P. Hsieh, B.-S. Chen, “The role of TGF-β signaling and apoptosis in innate and adaptive immunity in zebrafish: a systems biology approach,” BMC Systems Biology, 8:116, 24 Oct. 2014. 

24. C. Lin*, C.-J. Lu, and W.-H. Chen, “Outage-constrained coordinated beamforming with opportunistic interference cancellation,” IEEE Trans. on Signal Processing, 62(16): 4311 - 4326, 15 Aug. 2014. 

25. C.-C. Chen, C.-S. Tseng, J. Denis, and C. Lin*, “Adaptive distributed beamforming for amplify-and-forward relay networks: convergence analysis,” IEEE Trans. Wireless Communications, 13(8): 4167-4178, 8 Aug. 2014. 

26. C.-S. Tseng, J. Denis, and C. Lin*, “On the robust design of adaptive distributed beamforming for wireless sensor/relay networks,” IEEE Trans. Signal Processing, 62(13): 3429-3441, Jul. 2014.

27. C.-C. Wu, T.-H. Tsai, T.-T. Lee, C. Lin, I. H.-J. Cheng, M.-C. Sun, Y.-J. Chuang, B.-S. Chen, “On the crucial cerebellar wound healing-related pathways after traumatic brain injury in Danio rerio,” PLoS ONE 9(6): e97902, June 2014.

28. Y.-C. Wang, I-C. Tsai, C. Lin, W.-P. Hsieh, C.-Y. Lan, Y.-J. Chuang and B.-S. Chen, “Essential functional modules for pathogenic and defensive mechanisms in candida albicans infections,” BioMed Research International, vol. 2014 (2014), Article ID 136130, 15 pages, Mar. 2014.

29. C. Lin and B.-S. Chen, “Achieving pareto optimal power tracking control for interference limited wireless systems via multi-objective H2/H∞ optimization,” in IEEE Trans. Wireless Communications, vol.12, no.12, pp.6154-6165, Dec. 2013.

30. Y.-Y. Lee, C.-Y. Hsu, L.-J. Lin, C.-C. Chang, H.-C. Cheng, T.-H. Yeh, R.-H. Hu, C. Lin, Z. Xie, and B.-S. Chen, “Systematic design methodology for robust genetic transistors based on I/O specifications via promoter-RBS libraries,” in BMC Systems Biology, 7:109, Oct. 2013.

31. Y.-C. Wang, C. Lin, M.-T. Chuang, W.-P. Hsieh, C.-Y. Lan, Y.-J. Chuang, B.-S. Chen, “Interspecies protein-protein interaction network construction for characterization of host- pathogen interactions: a candida albicans-zebrafish interaction study,” in BMC Systems Biology, 7:79, Aug. 2013.

32. W.-C. Li, T.-H. Chang, C. Lin and C.-Y. Chi, “Coordinated beamforming for multiuser MISO interference channel under rate outage constraints,” in IEEE Trans. Signal Processing, 61(5): 1087– 1103, Mar. 2013.

33. C. Lin, V. Veeravalli, and S. Meyn, “A random search framework for convergence analysis of distributed beamforming with feedback,” in IEEE Trans. Information Theory, 56(12): 6133-6141, Dec. 2010.

34. C. Lin, V. Raghavan, and V. Veeravalli, “To code or not to code across time: space-time coding with feedback,” IEEE JSAC, 26(8): 1588-1598, Oct. 2008.

35. C. Lin and V. Veeravalli, “Optimal linear dispersion codes for correlated MIMO channels,” in IEEE Trans. Wireless Communication, 7(2): 657-666, Feb. 2008.

1. Chien-Fu Liu, Che Lin, and Liang-Ming Chiu*, “LM-DTA: Integrating Large Language Model Embedding for Enhanced Drug Target Affinity Prediction,” the 6th Multiomics and Precision Medicine Joint Conference, Taipei, Taiwan, November 2024. 

2. Shun-Cheng Chang, Hsin-Pei Yu*, Yi-Hsien Hsieh, Pochuan Wang, Weichung Wang, Tung-Hung Su, JH Kao, Che Lin, "ReViT: A Hybrid Approach for BCLC Staging of Hepatocellular Carcinoma Using 3D CT with Multiple Instance Learning," 2024 IEEE-EMBS International Conference on Biomedical and Health Informatics (IEEE BHI), Houston, Texas, United States, November 2024.

3. Jefferson Dionisio, Muhammad Rizwan*, Hidetaka Suzuki, Kazi Mahmudul Hassan, Ingon Chanpornpakdi, Lian-Yu Lin, Toshihisa Tanaka, Che Lin, "Is Attention All You Need for EEG to Predict Neurological Outcomes in Cardiac Arrest?," 2024 IEEE-EMBS International Conference on Biomedical and Health Informatics (IEEE BHI), Houston, Texas, United States, November 2024.

4. Yun-Chi Chen, Tung Chao, Wimaya Nitya Phandita, Tzu-Yu Sun, Huai-Zhi Wang, Yi-Hsien Hsieh, Le-Yin Hsu and Che Lin*, "Predicting Microsatellite Instability from Histology Images with Dilated Neighborhood Attention Transformer in Colorectal Cancer," 2024 24th The IEEE International Conference on Bioinformatics & Bioengineering (BIBE2024), Kragujevac, Serbia, November 2024.

5. Shun-Cheng Chang*, Pochuang Wang, Weichung Wang, Tung-Hung Su, Jia-Horng Kao, and Che Lin, "A BCLC Staging System for Hepatocellular Carcinoma using Swin Transformer and CT Imaging," 2024 46th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Orlando, USA, July 2024. 

6. Tsung-Wei Lin*, Sofia Ormazabal Arriagada, Che Lin, "Multi-task Learning Graph Neural Networks for Cancer Prognosis Prediction with Genomic Data," 2024 46th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Orlando, USA, July 2024. 

7. Ming-Che Cheng, Yi-Hsien Hsieh*, Te-Cheng Hsu, Tung-Hung Su, and Che Lin, "Deep STI: Deep Stochastic Time-series Imputation on Electronic Health Records," 2024 46th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Orlando, USA, July 2024. 

8. Chun-Kai Huang, Yi-Hsien Hsieh, Shao-Hua Sun, Tung-Hung Su, JH Kao, and Che Lin*, "Combating missing values in multivariate time series by learning to embed each value as a token," 2024 The Twelfth International Conference on Learning Representations (ICLR) (Workshop), Vienna, Austria, May 2024.

9. H. C. Hsu, T. -L. Lin, B. -J. Wu, M. -Y. Hong, C. Lin and C. -Y. Wang, "FincGAN: A Gan Framework of Imbalanced Node Classification on Heterogeneous Graph Neural Network," 2024 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Seoul, Korea, April 2024.

10. C. -C. Yu, M. -Y. Hong, C. -Y. Ho and C. Lin*, "Push4Rec: Temporal and Contextual Trend-Aware Transformer Push Notification Recommender," 2024 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Seoul, Korea, April 2024.

11. Jefferson Dionisio*, C. Lin, L. -Y. Lin and W. -C. Wu, "Predicting Neurological Outcomes of Comatose Cardiac Arrest Patients Using Transformer Neural Networks with EEG Data," 2023 Computing in Cardiology (CinC), Atlanta, GA, USA, Oct. 2023. 

12. Hsu-Hsiang Chang*, Te-Cheng Hsu, Yi-Hsien Hsieh, Che Lin, "Meta-EHR: A meta-learning approach for electronic health records with a high imbalanced ratio and missing rate," 2023 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Sydney, Australia, July 2023. 

13. Tzu-Chen Huang*, Te-Cheng Hsu, Yi-Hsien Hsieh and Che-Lin, "Utilizing Graph Neural Networks for Breast Cancer Prognosis Prediction with High-dimensional Genomic Data," 2023 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Sydney, Australia, July 2023. 

14. Lok-In Tsui*, Te-Cheng Hsu and Che Lin, "NG-DTA: Drug-target affinity prediction with n-gram molecular graphs," 2023 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Sydney, Australia, July 2023. 

15. Yi-Hsien Hsieh*, Jung-Chi Hsu, Che Lin, and Lian-Yu Lin, "X-RIM: Extreme Recurrent Independent Mechanisms for Noise-resistant and Interpretable Stroke Risk Prediction," 2023 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Sydney, Australia, July 2023. 

16. Jia-Huei Ju, Yu-Shiang Huang, Cheng-Wei Lin, Che Lin and Chuan-Ju Wang, "A Compare-and-contrast Multistage Pipeline for Uncovering Financial Signals in Financial Reports," 2023 61st Annual Meeting of the Association for Computational Linguistics (ACL’23), Toronto, Canada, July 2023. 

17. Tanoj Langore, Te-Cheng Hsu, Yi Hsien Hsieh and Che Lin*, "LE-DTA: Local Extrema convolution for Drug Target Affinity Prediction," IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Rhodes Island, Greece, June 2023.

18. Ming-Yi Hong, Shih-Yen Chang, Hao-Wei Hsu, Yi-Hsiang Huang, Chih-Yu Wang and Che Lin*, "TREEXGNN: CAN GRADIENT-BOOSTED DECISION TREES HELP BOOST HETEROGENEOUS GRAPH NEURAL NETWORKS?" IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Rhodes Island, Greece, June 2023.

19. Tung-Hung Su, Ming-Zhe Zheng, Jia-Horng Kao, Che Lin,"Personalized risk scores for hepatocellular carcinoma using routine sequential laboratory tests and deep learning," AASLD, Washington, DC., U.S., Oct. 2022 (poster presentation)

20. Sagaya Louis Gracy Thomas and Che Lin*, "Top-k Ranking of Drug Target Interactions based on Transfer Learning and Listwise Loss," Taiwan telecommunications Annual Symposium, Taipei, Taiwan, Jan. 2022. (Best paper award in signal processing)

21. Te-Cheng Hsu*, and Che Lin. “Training with Small Medical Data: Robust Bayesian Neural Networks for Colon Cancer Overall Survival Prediction,” 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), pp. 2030-2033, Guadalajara, Mexico, Nov. 2021. (The 3rd place in student paper competition)

22. D. Daiya and C. Lin*, "Stock Movement Prediction and Portfolio Management via Multimodal Learning with Transformer," IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Toronto, Canada, Jun. 2021.

23. Y.-C. Wu, C. Lin*, and T. Q. S. Quek, “A Robust Hierarchical Learning Approach for dynamic MEC Networks,” IEEE Global Communications Conference (GLOBECOM), Taipei, Taiwan, Dec. 2020. 

24. Te-Cheng Hsu, and Che Lin*. “Generative Adversarial Networks for Robust Breast Cancer Prognosis Prediction with Limited Data Size,” Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Jul. 2020. 

25. Divyanshu Daiya, Min-Sheng Wu, Che Lin*, "Stock Movement Prediction that integrates heterogeneous data sources using Dilated Causal Convolution Networks with Attention," IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Barcelona, Spain, May 2020.

26. Y.-C. Wu, D. Q. Thinh, Yaru Fu, C. Lin*, Tony Q. S. Quek, “A Learning-based Expected Best Offloading Strategy in Wireless Edge Networks,” IEEE Global Communications Conference (GLOBECOM), Waikoloa, U.S., Dec. 2019.

27. Ta-Chun Kuan, Sz-Wei Wu, Cheng-Che Liao, Mahsa Ashouri, Galit Shmueli and Che Lin, “Forecasting Daily Accommodation Occupancy for Supply Preparation by a Sharing Economy Platform,” IEEE International Conference on Big Data Intelligence and Computing (IEEE DataCom), Kaohsiung, Taiwan, Nov. 2019.

28. T. Hsu, S. Liou, Y. Wang, Y. Huang and C. Lin*, “Enhanced Recurrent Neural Network for Combining Static and Dynamic Features for Credit Card Default Prediction,” IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Brighton, United Kingdom, May 2019.

29. Ho-Chun Tsao and Che Lin, "Utility Maximization for MISO Bursty Interference Channels," in The Tenth International Conference on Wireless Communications and Signal Processing (WCSP), Hangzhou, China, Oct. 2018.

30. Te-Cheng Hsu, Jia-Siang Chen, Wei-Zhu Chen, Yu-Hsuan Chien, Sz Wei Wu, Mahsa Ashouri, Che Lin, and Galit Shmueli, "A Deep Learning Approach To Bank Direct Marketing," in 2018 Informs International Conference, Taipei, Taiwan, June 2018.

31. Yi Chun Hsiao, Chien Ming Chen, and Che Lin, “Energy Efficiency Maximization in Multi-user MISO Mixed RF/VLC Heterogeneous Cellular Networks,” in IEEE International Conference on Sensing, Communication, and Networking (SECON), Hong-Kong, June 2018. (acceptance ratio: 23.2%)

32. Chao Lin Chen, Li Yu Wang, and Che Lin, “Utility Maximization for MISO Bursty Interference Channel under traffic uncertainties,” in Signal Processing Advances in Wireless Communications (SPAWC), Sapporo, Japan, Jul. 2017.

33. Li-Yu Wang, Chao-Lin Chen, and Che Lin, “Energy Efficient Beamforming Design with SWIPT for Heterogeneous Cellular Networks,” in Signal Processing Advances in Wireless Communications (SPAWC), Sapporo, Japan, Jul. 2017.

34. Jyun-Wei Li and Che Lin, “On the Optimal Power Allocation for Two-Way Full-Duplex AF Relay Networks,” Proc. IEEE ICC, Paris, France, May 2017.

35. W.-C. Li, T.-H. Chang, C. Lin, and C.-Y. Chi, “Outage constrained weighted sum rate maximization for MISO interference channel by pricing-based optimization,” Proc. IEEE ICASSP, Vancouver, Canada, May. 2013.

36. J. Denis, C.-S. Tseng, C.-W. Lee, C.-Y. Tsai, and C. Lin, “Deterministic bisection search algorithm for distributed sensor/relay networks,” Proc. IEEE Globecom, Anaheim, California, USA, Dec. 2012.

37. W.-C. Li, T.-H. Chang, C. Lin, and C.-Y. Chi, “A convex approximation approach to weighted sum rate maximization of multiuser MISO interference channel under outage constraints,” Proc. IEEE ICASSP, Prague, Czech, May 2011.

38. C.-S. Tseng, C.-C. Chen, and C. Lin, “A bio-inspired robust adaptive random search algorithm for distributed beamforming,” Proc. IEEE ICC, Kyoto, Japan, June 2011.

39. C.-C. Chen, C.-S. Tseng, and C. Lin, “A general proof of convergence for adaptive distributed beamforming schemes,” Proc. IEEE ICASSP, Prague, Czech, May 2011.

40. C. Lin, V . Raghavan, and V . V eeravalli, “Limited feedback space-time coding in correlated MIMO channels,” Proc. IEEE CISS, Princeton, New Jersey, USA, Mar. 2008.

41. C. Lin, V . Raghavan, and V . V eeravalli, “Optimal power allocation for linear dispersion codes over correlated MIMO channels with channel state feedback,” Proc. IEEE Globecom, Washington D. C., USA, Nov. 2007.

42. C. Lin and V. Veeravalli, “A limited feedback scheme for linear dispersion codes over correlated MIMO channels,” Proc. IEEE ICASSP, Honolulu, Hawaii, USA, Apr. 2007.

43. C. Lin and V. Veeravalli, “Optimal linear dispersion codes for correlated MIMO channels,” Proc. IEEE CISS, Princeton, New Jersey, USA, Mar. 2006.

44. H. Y. Chao, C. Lin, K. Pirapaharan, and W. C. Chew, "Fast field calculation by a multilevel fast multipole algorithm for large complex radiators and scatterers," Proc. IEEE AP-S International Symposium, Columbus, Ohio, USA, Jun. 2003.