By Dr Hamid Alinejad-Rokny

Journal articles

Rokny HA; Pedram MM; Shirgahi H, 2011, 'Discovered motifs with using parallel Mprefixspan method', Scientific Research and Essays, 6, pp. 4220 - 4226, http://dx.doi.org/10.5897/sre11.212

Parvin H; Alinejad-Rokny H; Asadi M, 2011, 'An ensemble based approach for feature selection', Australian Journal of Basic and Applied Sciences, 5, pp. 1153 - 1163

Parvin H; Helmi H; Minaei B; Rokny HA; Shirgahi H, 2011, 'Linkage learning based on differences in local optimums of building blocks with one optima', International Journal of Physical Sciences, 6, pp. 3419 - 3425

Minaei-Bidgoli B; Parvin H; Alizadeh H; Alinejad-Rokny H; Punch WF, 2011, 'Effects of resampling method and adaptation on clustering ensemble efficacy', Artificial Intelligence Review, pp. 1 - 22, http://dx.doi.org/10.1007/s10462-011-9295-x

Conference Papers

Wang T; Yao Y; Wei Y; Zhu J; Alinejad-Rokny H; Chen L, 2026, 'FairTraj: Density-Aware Generative Data Augmentation for Fairness in Downstream Trajectory Learning Tasks', in Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 5035 - 5044, http://dx.doi.org/10.1145/3770855.3817841

Xu A; Yang Z; Li J; Yuan G; Chen L; Yan L; Zhou J; Qin Z; Chang H; Chen Y; Alinejad-Rokny H; Yang M, 2026, 'EVADE-Bench: Multimodal Benchmark for Evaluating and Enhancing Evasive Content Detection', in SIGIR 2026 Proceedings of the 49th International ACM SIGIR Conference on Research and Development in Information Retrieval, pp. 3506 - 3513, http://dx.doi.org/10.1145/3805712.3808579

Baghgolshani M; Beheshti A; Newton MAH; Alinejad-Rokny H, 2026, 'GRN-GEARS: Interpretable Gene Regulatory Modelling for Single-Cell Perturbation Response Prediction in Precision Oncology', Institute of Electrical and Electronics Engineers (IEEE), pp. 294 - 304, presented at 2026 IEEE International Conference on Digital Health (ICDH), http://dx.doi.org/10.1109/icdh72779.2026.00041

Chen G; Sun C; Fu C; Wang Q; Huang Z; Wei C; Chen G; Fang F; Argha A; Zhao B; Xu X; Han Q; Alinejad-Rokny H; Qu Q; Li B; Ni S; Yang M; Wei H; Li Y, 2026, 'Beyond Quantity: Trajectory Diversity Scaling for Code Agents', Association for Computational Linguistics (ACL), pp. 15676 - 15691, presented at Findings of the Association for Computational Linguistics: ACL 2026, http://dx.doi.org/10.18653/v1/2026.findings-acl.768

Li S; Shi J; Ni S; Zhang G; Li S; Wang S; Wen Z; LI Y; Alinejad-Rokny H; Liu J; Yang M; Huang W, 2026, 'CoTJudger: A Graph-Driven Framework for Automatic Evaluation of Chain-of-Thought Efficiency and Redundancy in LRMs', Association for Computational Linguistics (ACL), pp. 41837 - 41863, presented at Findings of the Association for Computational Linguistics: ACL 2026, http://dx.doi.org/10.18653/v1/2026.findings-acl.2077

Li S; Fan L; li Z; Wan Z; Lin Y; Ni S; Fang F; Alinejad-Rokny H; Song Y; Jing K; Zhang CJ; Yang M, 2026, 'SrDetection: A Self-Referential Framework for Data Leakage Detection in Code Large Language Models', Association for Computational Linguistics (ACL), pp. 5117 - 5129, presented at Findings of the Association for Computational Linguistics: ACL 2026, http://dx.doi.org/10.18653/v1/2026.findings-acl.252

Luo R; Li Y; Chen L; He W; Lin TE; Liu Z; Zhang L; Song Z; Alinejad-Rokny H; Xia X; Liu T; Hui B; Yang M, 2025, 'DEEM: DIFFUSION MODELS SERVE AS THE EYES OF LARGE LANGUAGE MODELS FOR IMAGE PERCEPTION', in 13th International Conference on Learning Representations Iclr 2025, Singapore, pp. 72484 - 72511, presented at The Thirteenth International Conference on Learning Representations, Singapore, 24 April 2025 - 28 April 2025, chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://proceedings.iclr.cc/paper_files/paper/2025/file/a8399aace3dfa6dfb8b635117748c561-Paper-Conference.pdf

Doan BG; Shamsi A; Guo XY; Mohammadi A; Alinejad-Rokny H; Sejdinovic D; Teney D; Ranasinghe DC; Abbasnejad E, 2025, 'Bayesian Low-Rank Learning (Bella): A Practical Approach to Bayesian Neural Networks', in Proceedings of the Aaai Conference on Artificial Intelligence, pp. 16298 - 16307, http://dx.doi.org/10.1609/aaai.v39i15.33790

Chen G; Fan L; Gong Z; Xie N; Li Z; Liu Z; Li C; Qu Q; Alinejad-Rokny H; Ni S; Yang M, 2025, 'AgentCourt: Simulating Court with Adversarial Evolvable Lawyer Agents', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 5850 - 5865, http://dx.doi.org/10.18653/v1/2025.findings-acl.304

Chen L; Shan R; Wang H; Wang L; Liu Z; Luo R; Wang J; Alinejad-Rokny H; Yang M, 2025, 'CLaSp: In-Context Layer Skip for Self-Speculative Decoding', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 31608 - 31618, http://dx.doi.org/10.18653/v1/2025.acl-long.1525

Zhu J; Tan M; Yang M; Li R; Alinejad-Rokny H, 2025, 'CollectiveSFT: Scaling Large Language Models for Chinese Medical Benchmark with Collective Instructions in Healthcare', in Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics, pp. 51 - 60, http://dx.doi.org/10.1007/978-981-96-1151-5_6

Shamsi A; Becirovic R; Argha A; Abbasnejad E; Alinejad-Rokny H; Mohammadi A, 2025, 'ETAGE: Enhanced Test Time Adaptation with Integrated Entropy and Gradient Norms for Robust Model Performance', in Conference Proceedings IEEE International Conference on Systems Man and Cybernetics, pp. 5907 - 5911, http://dx.doi.org/10.1109/SMC58881.2025.11342706

Chen D; Liu Z; Fang F; Leong CT; Ni S; Argha A; Alinejad-Rokny H; Yang M; Li C, 2025, 'Expanding before Inferring: Enhancing Factuality in Large Language Models through Premature Layers Interpolation', in Emnlp 2025 2025 Conference on Empirical Methods in Natural Language Processing Proceedings of the Conference, pp. 12770 - 12785, http://dx.doi.org/10.18653/v1/2025.emnlp-main.645

Sun Y; Chen G; Alinejad-Rokny H; Bao J; Huang Y; Liang B; Wong KF; Yang M; Xu R, 2025, 'Learning First-Order Logic Rules for Argumentation Mining', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 14133 - 14148, http://dx.doi.org/10.18653/v1/2025.acl-long.691

Zhu K; Zang Q; Jia S; Wu S; Fang F; Li Y; Guo S; Zheng T; Li B; Wu H; Qu X; Yang J; Liu Z; Yue X; Liu J; Lin C; Yang M; Alinejad-Rokny H; Ni S; Huang W; Zhang G, 2025, 'LIME: Less Is More for MLLM Evaluation', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 9086 - 9121, http://dx.doi.org/10.18653/v1/2025.findings-acl.474

Luo R; Zhang H; Chen L; Lin TE; Liu X; Wu Y; Yang M; Li Y; Wang M; Zeng P; Gao L; Shen HT; Li Y; Alinejad-Rokny H; Xia X; Huang F; Song J, 2025, 'MMEvol: Empowering Multimodal Large Language Models with Evol-Instruct', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 19655 - 19682, http://dx.doi.org/10.18653/v1/2025.findings-acl.1009

Luo R; Lin TE; Zhang H; Wu Y; Liu X; Li Y; Chen L; Li J; Zhang L; Xia X; Alinejad-Rokny H; Huang F; Yang M, 2025, 'OpenOmni: Advancing Open-Source Omnimodal Large Language Models with Progressive Multimodal Alignment and Real-time Emotional Speech Synthesis', in Advances in Neural Information Processing Systems, pp. 176413 - 176441

Lee S; Zhou J; Ao C; Li K; Du X; He S; Wu H; Liu T; Liu J; Alinejad-Rokny H; Yang M; Liang Y; Wen Z; Ni S, 2025, 'Quantification of Large Language Model Distillation', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 4985 - 5004, http://dx.doi.org/10.18653/v1/2025.acl-long.248

Zhao J; Xu L; Tan M; Zhang L; Argha A; Alinejad-Rokny H; Yang M, 2025, 'RxSafeBench: Identifying Medication Safety Issues of Large Language Models in Simulated Consultation', in Proceedings 2025 IEEE International Conference on Bioinformatics and Biomedicine Bibm 2025, pp. 4491 - 4496, http://dx.doi.org/10.1109/BIBM66473.2025.11356353

Li J; Chen Y; Liu Z; Tan M; Zhang L; Li Y; Luo R; Chen L; Luo J; Argha A; Alinejad-Rokny H; Zhou W; Yang M, 2025, 'STORYTELLER: An Enhanced Plot-planning Framework for Coherent and Cohesive Story Generation', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 20818 - 20846, http://dx.doi.org/10.18653/v1/2025.findings-acl.1071

Hansun S; Argha A; Alinejad-Rokny H; Liaw ST; Celler BG; Marks GB, 2024, 'Pulmonary Tuberculosis Detection Using an Ensemble of ConvNeXts', in Ibiomed 2024 Proceedings of the 5th International Conference on Biomedical Engineering 2024, pp. 29 - 33, http://dx.doi.org/10.1109/iBioMed62485.2024.10875706

Argha A; Li J; Magdy J; Alinejad-Rokny H; Celler BG; Butcher K; Ooi SY; Lovell NH, 2023, 'Assessing the Generalizability of a Deep Learning-based Automated Atrial Fibrillation Algorithm', in Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society EMBS, Institute of Electrical and Electronics Engineers (IEEE), AUSTRALIA, Sydney, pp. 1 - 6, presented at 2023 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), AUSTRALIA, Sydney, 24 July 2023 - 27 July 2023, http://dx.doi.org/10.1109/EMBC40787.2023.10341108

Montazerin M; Rahimian E; Naderkhani F; Atashzar SF; Alinejad-Rokny H; Mohammadi A, 2023, 'HYDRA-HGR: A Hybrid Transformer-Based Architecture for Fusion of Macroscopic and Microscopic Neural Drive Information', in ICASSP IEEE International Conference on Acoustics Speech and Signal Processing Proceedings, http://dx.doi.org/10.1109/ICASSP49357.2023.10096192

Asgharnezhad H; Shamsi A; Bakhshayeshi I; Alizadehsani R; Chamaani S; Alinejad-Rokny H, 2023, 'Improving PPG Signal Classification with Machine Learning: The Power of a Second Opinion', in International Conference on Digital Signal Processing DSP, http://dx.doi.org/10.1109/DSP58604.2023.10167869

Shahabikargar M; Beheshti A; Khatami A; Nguyen R; Zhang X; Alinejad-Rokny H, 2022, 'Domain Knowledge Enhanced Text Mining for Identifying Mental Disorder Patterns', in Proceedings 2022 IEEE 9th International Conference on Data Science and Advanced Analytics Dsaa 2022, http://dx.doi.org/10.1109/DSAA54385.2022.10032346

Khozeimeh F; Roshanzamir M; Shoeibi A; Darbandy MT; Alizadehsani R; Alinejad-Rokny H; Ahmadian D; Khosravi A; Nahavandi S, 2022, 'Importance of Wearable Health Monitoring Systems Using IoMT; Requirements, Advantages, Disadvantages and Challenges', in IEEE Joint 22nd International Symposium on Computational Intelligence and Informatics and 8th International Conference on Recent Achievements in Mechatronics Automation Computer Science and Robotics Cinti Macro 2022 Proceedings, pp. 245 - 250, http://dx.doi.org/10.1109/CINTI-MACRo57952.2022.10029528

Danaei S; Bostani A; Moravvej SV; Mohammadi F; Alizadehsani R; Shoeibi A; Alinejad-Rokny H; Nahavandi S, 2022, 'Myocarditis Diagnosis: A Method using Mutual Learning-Based ABC and Reinforcement Learning', in IEEE Joint 22nd International Symposium on Computational Intelligence and Informatics and 8th International Conference on Recent Achievements in Mechatronics Automation Computer Science and Robotics Cinti Macro 2022 Proceedings, pp. 265 - 270, http://dx.doi.org/10.1109/CINTI-MACRo57952.2022.10029403

Conference Abstracts

Buthpitiya Lekamlage Don U; Becirovic R; van Dorst J; Coffey M; Halim J; Beheshti, B; Argha R; Alinejad-Rokny H; Ooi KC, 2025, 'Artificial intelligence integrating gut microbiome multi-omics to predict clinical outcomes in children with cystic fibrosis', in 16 Artificial intelligence integrating gut microbiome multi-omics to predict clinical outcomes in children with cystic fibrosis, presented at North American Cystic Fibrosis Conference

Taylor R; Taylor J; Denisenko E; Jones M; Clayton J; Laing N; Forrest A; Alinejad-Rokny H; Ravenscroft G, 2024, 'Mapping human skeletal muscle enhancers to increase rates of genetic diagnosis', in NEUROMUSCULAR DISORDERS, PERGAMON-ELSEVIER SCIENCE LTD, CZECH REPUBLIC, Prague, Vol. 43, presented at 29th International Congress of the World-Muscle-Society (WMS), CZECH REPUBLIC, Prague, 08 October 2024 - 12 October 2024, http://dx.doi.org/10.1016/j.nmd.2024.07.096

Truong P; Shen S; Joshi S; Afrasiabi A; Zhong L; Raftery MJ; Larsson J; Lock RB; Walkley CR; Rokny HA; Thoms JAI; Jolly CJ; Pimanda JE, 2022, 'Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and Sumoylation Blockade in Myelodysplastic Syndromes and Acute Myeloid Leukemia', in Blood, American Society of Hematology, Vol. 140, pp. 220 - 221, http://dx.doi.org/10.1182/blood-2022-165713

Gooneratne S; Alinejad-Rokny H; Mohammadi D; Bohn P; Wiseman R; O'Connor D; Davenport M; Kent S, 2015, 'LINKING PIGTAIL MACAQUE MHC I HAPLOTYPES AND CTL ESCAPE MUTATIONS IN SIV INFECTION', in JOURNAL OF MEDICAL PRIMATOLOGY, WILEY-BLACKWELL, Vol. 44, pp. 335 - 335, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000361966000094&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Preprints

Chen S; Zahedi R; Chhuo L; Nguyen R; BaghGolshani M; Beheshti A; Grosser M; Yang M; Farbehi N; Lovell N; Argha A; Porntaveetusm T; Vafaee F; Ye Y; Alinejad-Rokny H, 2026, Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation, http://dx.doi.org/10.48550/arxiv.2607.17227

Liang Y; Chhuo L; Argha A; Farbehi N; Chen L; Alizadehsani R; Hosseinzadeh M; Yang M; Porntaveetusm T; Ye Y; Alinejad-Rokny H, 2026, Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability, http://dx.doi.org/10.48550/arxiv.2604.05478

Shamsi A; Guo X-Y; Alinejad-Rokny H; Mohammadi A; Teney D; Abbasnejad E, 2026, Multi-Hypothesis Test-Time Adaptation to Mitigate Underspecification, http://dx.doi.org/10.48550/arxiv.2607.00259

Li S; Fan L; Li Z; Wan Z; Lin Y; Ni S; Fang F; Alinejad-Rokny H; Song Y; Jing K; Zhang CJ; Yang M, 2026, SrDetection: A Self-Referential Framework for Data Leakage Detection in Code Large Language Models, http://dx.doi.org/10.48550/arxiv.2606.29815

Xu A; Yang Z; Li J; Yuan G; Chen L; Yan L; Zhou J; Qin Z; Chang H; Chen Y; Alinejad-Rokny H; Yang M, 2026, EVADE-Bench: Multimodal Benchmark for Evaluating and Enhancing Evasive Content Detection, http://dx.doi.org/10.48550/arxiv.2505.17654

Li S; Shi J; Ni S; Zhang G; Li S; Wang S; Wen Z; Li Y; Alinejad-Rokny H; Liu J; Yang M; Huang W, 2026, CoTJudger: A Graph-Driven Framework for Automatic Evaluation of Chain-of-Thought Efficiency and Redundancy in LRMs, http://dx.doi.org/10.48550/arxiv.2603.07078

Luo R; Lin T-E; Zhang H; Wu Y; Liu X; Yang M; Li Y; Chen L; Li J; Zhang L; Xia X; Alinejad-Rokny H; Huang F, 2025, OpenOmni: Advancing Open-Source Omnimodal Large Language Models with Progressive Multimodal Alignment and Real-Time Self-Aware Emotional Speech Synthesis, http://dx.doi.org/10.48550/arxiv.2501.04561

Zahedi R; Argha A; Farbehi N; Bakhshayeshi I; Ye Y; Lovell NH; Alinejad-Rokny H, 2025, SemanticST: Spatially Informed Semantic Graph Learning for Clustering, Integration, and Scalable Analysis of Spatial Transcriptomics, http://dx.doi.org/10.48550/arxiv.2506.11491

Doan BG; Shamsi A; Guo X-Y; Mohammadi A; Alinejad-Rokny H; Sejdinovic D; Teney D; Ranasinghe DC; Abbasnejad E, 2025, Bayesian Low-Rank LeArning (Bella): A Practical Approach to Bayesian Neural Networks, http://dx.doi.org/10.48550/arxiv.2407.20891

Lee S; Zhou J; Ao C; Li K; Du X; He S; Wu H; Liu T; Liu J; Alinejad-Rokny H; Yang M; Liang Y; Wen Z; Ni S, 2025, Quantification of Large Language Model Distillation, http://dx.doi.org/10.48550/arxiv.2501.12619

Lee S; Ni S; Wei C; Li S; Fan L; Argha A; Alinejad-Rokny H; Xu R; Gong Y; Yang M, 2025, xJailbreak: Representation Space Guided Reinforcement Learning for Interpretable LLM Jailbreaking, http://dx.doi.org/10.48550/arxiv.2501.16727

Wang Q; Ni S; Liu H; Lu S; Chen G; Feng X; Wei C; Qu Q; Alinejad-Rokny H; Lin Y; Yang M, 2024, AutoPatent: A Multi-Agent Framework for Automatic Patent Generation, http://dx.doi.org/10.48550/arxiv.2412.09796

Ni S; Wu H; Yang D; Qu Q; Alinejad-Rokny H; Yang M, 2024, Small Language Model as Data Prospector for Large Language Model, http://dx.doi.org/10.48550/arxiv.2412.09990

Liang Y; Abedini S; Farbehi N; Alinejad-Rokny H, 2024, How chromatin interactions shed light on interpreting non-coding genomic variants: opportunities and future direc-tions, http://dx.doi.org/10.48550/arxiv.2411.17956

Zhu J; Tan M; Yang M; Li R; Alinejad-Rokny H, 2024, CollectiveSFT: Scaling Large Language Models for Chinese Medical Benchmark with Collective Instructions in Healthcare, http://dx.doi.org/10.48550/arxiv.2407.19705

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