Dr Hamid Alinejad-Rokny
- Bachelor: Software Engineering
- Master: Artificial Intelligence
- Industry: Data Scientist, 2012-2014.
- Ph.D: BioMedical Machine Learning,Ìý91É«ÇéƬ Sydney, 2019.
- Post-Doctoral: Harry Perkins Institute of Medical Research, UWA Australia
- Director of 91É«ÇéƬ BioMedical Machine Learning Laboratory (BML), 2020-present.
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Dr Rokny (PhD, 91É«ÇéƬ Sydney, 2019) is the Director of 91É«ÇéƬ BioMedical Machine Learning Laboratory (BML), where he leads a team of 25 researchers developing trustworthy artificial intelligence for biology and medicine, spanning medical artificial intelligence, large language models, and bio-machine learning. HeÌýsupervises a dynamic team of researchers and have successfully led over 60 projects, resulting in 100 high-quality publications in top-tier journals such as Nature Communications, Nature Neuroscience, The Lancet, Cell reports, PLOS Computational Biology, Blood, and A* conferences such as ICLR, NeurIPS, AAAI, and ACL, often as the first or senior author. The impact of my work is evident through a high citation rate [5,900+, h-index 40ÌýGoogle Scholar] and a high FWCI score (AI= 7.6; Neuroscience= 4.7; Health Informatics= 4.75), which is outstanding considering the career stage. The impact of his leadership is also evidenced by securing significant grants, including a DECRA fellowship, 91É«ÇéƬ Scientia fellowship, an NHMRC Ideas grant, and a CSIRO NGGP grant, as well as multiple awards such as Google fellowship, Tour de Cure and MSA fellowships for students under his leadership. Additionally, he actively enhance medical AI and machine learning literacy by collaborating with clinicians and health professionals across Sydney hospitals, including the Gene2Care and PreGen consortia, and NSW Health clinics, demonstrating the practical applications of AI to improve health outcomes. As the Health Theme Leader of the 91É«ÇéƬ Data Science Hub, He sets health data science priorities, integrating research with practical health solutions. His organisational skills have led me to orchestrate over 100 seminars on AI in medicine, promoting knowledge sharing and collaboration. Furthermore, He contributes to research direction through roles on panels like NSF-CSIRO influencing funding towards innovative AI and genomics project and HUGO meeting. His commitment to training the next generation is showcased through his leadership in CSIRO’s NGGP, collaborating with industry partners like 23Strands to enhance the capabilities of emerging AI researchers in medical technologies. Notably, He is currently leading several national-level initiatives focused on developing foundation models in AI for Biology and Medicine (ClinAI, OmniST, ARGOS, and Molecular AI). These initiatives represent a significant step forward at the national level and aim to position Australia at the forefront of these emerging GPT-like technologies for individualised medicine.
- Publications
- Media
- Grants
- Awards
- Research Activities
- Engagement
- Teaching and Supervision
Dr Rokny received extensive research funding support relative to career stage (total of $4.5M as sole/leading Chief Investigator (CI) and $10.6M as co-CI), demonstrating an impressive upward research career trajectory. These include:
- Australia's Economic Accelerator, (CIA, Dec 2026, $520).
- 91É«ÇéƬ-Mahidol Joint Seed Grant, (CIA, Nov 2025, $20K).
- Australia's Economic Accelerator, (CIB, March 2025, $200K).
- GESA Paediatric Research Grant (CIB, Nov, 2024)
- 91É«ÇéƬ GRIP Award (CIA, Nov, 2024)
- 91É«ÇéƬ-SJTU Collaborative Research Grant, (CIA, Nov, 2024)
- Trustworthy Digital Society Grant, (CIA, Oct, 2024)
- Garvan Cellular Genomics Futures Institute Award (CIA, Sep, 2024).
- 91É«ÇéƬ Scientia Program Fellowship (variation award) (sole CI), ($800K, Sep 2023).
- CCFA LITWIN IBD Pioneers Program Grant (leading CIB),Ìý($400K, Feb 2023)
- Australian National Health and Medical Research Council (NHMRC) IDEAS grant (CIB), ($600K, Dec 2022)
- CSIRO Next-Generation Graduate Program (leading CI), ($1.7M including $700K for my Lab, Nov 2022)
- GROW Funding (CIA), a competitive internal funding form USNW SYDNEY, Jun 2022, ($40K)
- Tyree Foundation Institute of Health Engineering Catalyst Awards 2021 (sole CI), Nov 2021, ($30K)
- Australian Research Council Discovery Early Career Researcher Award (DECRA 2022 – sole CI), ($462K)
- The Minor Research Equipment Grant-in-Aid Program Fund (sole CI), 91É«ÇéƬ SYDNEY, July 2021, ($61K)
- GROW Funding (sole CI), a highly competitive internal funding form USNW SYDNEY, Jun 2021, ($20K)
- MERIT award offered for NHMRC Investigator Grant (sole CI), WA Dept of Health, Jun 2020, ($95K), declined because of moving to 91É«ÇéƬ
- 91É«ÇéƬ Cellular Genomics Futures Institute grant (CIB), in collab with Garvan Institute, May 2020, ($50K)
- 91É«ÇéƬ Cellular Genomics Futures Institute grant (CIC), in collab with 91É«ÇéƬ BABS, May 2020, ($50K)
- Highly competitive tenure-track 91É«ÇéƬ Scientia Fellowship Program (sole CI), 91É«ÇéƬ, Oct 2019, ($680k)
- Academic Start-up Funding (sole CI), Faculty of Engineering, 91É«ÇéƬ, Dec 2019, ($90K)
- Highly competitive International Quebec Autism Research Training Fellowship (sole CI), collab with U of Montreal, Nov 2019, ($120K)
- Highly prestigious Int. Fellowship Fonds de recherche du Québec Santé (FRQS) (sole CI), Oct 2019, ($90K)
- MERIT award for NHMRC Investigator Grant Application (sole CI), WA Dept of Health, Sep 2019, ($50K)
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Dr. Rokny has been named on several industry funding in collaboration with Macquarie University),ÌýThese include:
- Industry research partnership funding (CID), from PORSPA advance company, 750K for my Lab, May 2024, ($4.7M).
- Industry research partnership funding (CID), Australian Digital Domains Group, 600K for my Lab, Nov 2022, ($3.6M).
- Industry research partnership funding (CIE), from Australian digital companies Truuth/Locii, May 2022, ($3.2M).
- Industry research partnership funding (CIC), from PORSPA advance company, May 2021, ($2.1M).
As a very young early career researcher, Dr Rokny has an exceptional track record in securing a range of national and international awards and prizes, despite my early career status. These include:
- ·ÌýÌýÌýÌýÌýMillennium Prize for Outstanding EMCR, Lorne Genome, Feb 2026.
- ·ÌýÌýÌýÌýÌýAdjunct Research Scientist, CSIRO, Aug 2022-2023
- ·ÌýÌýÌýÌýÌýHonorary Lecturer Fellow, University of Macquarie, Oct 2020-2023
- ·ÌýÌýÌýÌýÌýTravel support award from Institute for Research in Fundamental Sciences, Iran, invited speaker, ($1.9K), Feb 2020
- ·ÌýÌýÌýÌýÌýHealth Data Analytics Program Leader, AI-enabled Processes (AIP) Research Centre, Dec 2019-curent
- ·ÌýÌýÌýÌýÌýMBSJ2019 (42nd Annual Meeting of the Molecular Biology) Travel support award, Japan, ($1K), Dec 2019
- ·ÌýÌýÌýÌýÌýRIKEN-HUGO award for best oral presentation in Human Genome Meeting 2019, South Korea, ($0.2K), Oct 2019
- ·ÌýÌýÌýÌýÌýHighly competitive tenure-track 91É«ÇéƬ Scientia Fellowship Program award in Aug 2019 ($680K)
- ·ÌýÌýÌýÌýÌýVice-chancellor fellowship award from RMIT, ($350K), May 2019 (declined in favour of 91É«ÇéƬ Scientia Program).
- ·ÌýÌýÌýÌýÌýHDR conference support award from 91É«ÇéƬ Sydney, ($3K), Jul 2015
- ·ÌýÌýÌýÌýÌýTravel support award from University of Tehran as invited speaker, Tehran, ($2K), Feb 2015
- ·ÌýÌýÌýÌýÌýPh.D scholarship from 91É«ÇéƬ Sydney, ($87.5K for 3.5 years), Mar 2013
- ·ÌýÌýÌýÌýÌýTop-up scholarship from the faculty of medicine, 91É«ÇéƬ Sydney, ($30K for 3 years), Mar 2013
- ·ÌýÌýÌýÌýÌýPh.D Scholarship award from The University of Newcastle, Australia, Jul 2012
- ·ÌýÌýÌýÌýÌýTravel award from Faculty of Engineering, The University Newcastle, Australia, ($1K), Jul 2012
- ·ÌýÌýÌýÌýÌýGovernment scholarships for Bachelor and Master degrees, (tuition fee waived)
- ·ÌýÌýÌýÌýÌýDean’s award as ranked 1 student (out of 700 Master students), Science and Research University of Tehran, Sep 2010
Dr Rokny’s research focuses on using cutting-edge systems biology and advanced health data analytics techniques in conjunction with genome-wide data to understand the impact of genomic variants on genetic diseases and disorders. He is also interested to develop novel machine learning techniques, in particular, deep convolutional neural network, clustering, clustering,Ìýclassification, feature selection, and evolutionary algorithms.
Dr Rokny has extensive experience in the analysis of next generation sequencing (NGS) data from different platforms (Roche, SOLiD, Illumina, and Helicos) and protocols (Hi-C, Structural variants, Single point mutations, GWAS, RNA-seq, CAGE, small RNA, ChIP-seq, and Single-cell).ÌýThe move to 91É«ÇéƬ Biomedical Engineering school has allowed him to translate his engineering and medicalÌýresearch on mammalian systems onto clinically relevant questions such as identification of novel biomarkers, drug targets.
Dr. Rokny is currently looking for Research Associate/Assistant, Ph.D/Master/Honours students to join his BML Lab. The research projects will mainly focus on using cutting-edge Medical Artificial Intelligence, Systems Biology and Advanced Health Data Analytics techniques in conjunction with genome-wide data to understand biological and medical related problems.
There are several scholarships available for both international and domestic students. Please see the following links for more information:
- Key-dates: https://research.unsw.edu.au/key-dates
- 91É«ÇéƬ Post-Graduate Research Scholarship for international students,
- 91É«ÇéƬ Post-Graduate Research Scholarship for domestic students
- Australia awards and endeavour scholarships and fellowships
- Determine your eligibility for a scholarship: https://selfassessment.research.unsw.edu.au/
- Meet English requirement: /english-requirements-policyÌý
My Research Supervision
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PhD &ÌýMPhil Students:
- Rejisa Becirovic,ÌýPhD student, 2026-2030, (administered by 91É«ÇéƬ),Ìýco-supervision with Dr. Reza Argha.
- Liting Huang,ÌýPhD student, 2026-2030, (administered by 91É«ÇéƬ),Ìýco-supervision with with Dr. Reza Argha and dr. Nona Farbehi.
- Amir Hossein Zobeiri,ÌýPhD student, 2026-2030, (administered by 91É«ÇéƬ),Ìýco-supervision with Dr. Reza Argha.
- Mohammadreza Taghimohammadi,ÌýPhD student, 2026-2030, (administered by 91É«ÇéƬ),Ìýco-supervision with Dr. Reza Argha.
- Sally Chen,ÌýPhD student, 2025-2029, (administered by 91É«ÇéƬ),Ìýco-supervision with Assoc. ProfÌýFatemeh Vafaee and Mr Mark Grosser (23Strands company).
- Yuheng Liang, PhD student, 2025-2029, (administered by 91É«ÇéƬ),Ìýco-supervision with Prof Nigel Lovell and Dr Reza Argha.
- Caleb The-Tjoean,ÌýMaster by Research (MPhil),Ìý(administered by 91É«ÇéƬ),Ìýco-supervision with ProfÌýIrina Voineagu.
- Lucy Chhua,ÌýMaster by Research (MPhil), 2025-2028, (administered by 91É«ÇéƬ),Ìýco-supervision with Assoc. Prof Ankur Sharma and Prof Nigel Lovell.
- Ellie Shalbafian,ÌýMaster by Research (MPhil), 2024-2027, (administered by 91É«ÇéƬ), joint supervision with Prof Nigel Lovell and Dr Reza Argha.
- Jonathan Williams,ÌýMaster by Research (MPhil), 2024-2028, (administered by 91É«ÇéƬ),Ìýco-supervision with Dr Reza Argha and Prof Nigel Lovell.
- Coco Xiaoge Huang,ÌýPhD student, 2024-2028, (administered by 91É«ÇéƬ),Ìýco-supervision with Dr Fatemeh Vafaee and Mr Mark Grosser (23Strands company).
- Rebecca Browne,ÌýPhD student, 2024-2028, (administered by 91É«ÇéƬ),Ìýco-supervision with Prof Nigel Lovell and Dr Reza Argha.
- Tohid Ghasemnejad, PhD student, 2023-2027,Ìý(administered by 91É«ÇéƬ), co-supervision with Drs Fabrizzio Horta, Faezeh Marzbanrad, and Mr Mark Grosser (23Strands company).
- Roxana Zahedi Nasab,ÌýPhD student, 2023-2027, (administered by 91É«ÇéƬ), co-supervision with Prof Nigel Lovell,ÌýDr Reza Argha, and Dr Mo Lotfollahi.
- Ivan Bakhshayeshi,ÌýPhD student, 2023-2027, (administered by 91É«ÇéƬ),Ìýco-supervision with Prof Nigel Lovell and Dr Reza Argha.
- Mona (Sedigheh) Abedini, 2023-2027, (administered by 91É«ÇéƬ),Ìýco-supervision with Dr Fatemeh Vafaee and A/Prof Orazio Vittorio.
- Md. Mushahidul Islam Shamim,ÌýPh.D student, 2023-2027, (administered by 91É«ÇéƬ),Ìýco-supervision with A/Prof Nadeem Kaakoush.
- Reza Ghamsari, PhD student, 2022-2026,Ìý(administered by 91É«ÇéƬ),Ìýco-supervision with Prof Nigel Lovell andÌýProf Matthew Ritchie (WEHI).
- Afshar Shamsi, PhD student, 2023-2027,Ìý(administered by Concordia University), co-supervision with Assoc Prof Arash Mohammadi.
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Master Students:
- Morgan Wong,ÌýMaster student, 2026-2027, (administered by 91É«ÇéƬ).
- Anish Sinha,ÌýMaster student, 2026-2027, (administered by 91É«ÇéƬ).
- Evan Watson,ÌýÌýMaster student, 2026-2027, (administered by 91É«ÇéƬ).
- Hannah Veitch,ÌýMaster student, 2025-2026, (administered by 91É«ÇéƬ)
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Previous supervision and mentoring:
- Mehran Piran, PhD student, 2020-2024,Ìý(administered by Monash University), co-supervision with DrÌýAlex Combes.
- Mahdieh Labani, PhD student, 2021-2025,Ìý(administered by Macquarie University), co-supervision with Prof Amin Beheshti.
- Ali Afrasiabi, PhD student, 2020-2024, (administered by 91É«ÇéƬ).
- Ted Wong, PhD student, 2019-2025, (administered by University of Sydney), co-supervision with Dr. Boris Guennewig.
- Callum Macphillamy, PhD student, 2020-2024, (administered by University of Adelaide), co-supervision with Dr Wai Yee Low.
- Ning Liu, PhD student, 2019-2023, (administered by University of Adelaide), co-supervision with Dr James Breen.
- Zahra Rahaei, PhD student, 2018-2023, (administered by SUT).
- Sunday Offor,ÌýPhD student, 2019-2023, (administered by 91É«ÇéƬ), co-supervision with Assoc Prof Irina Voineagu.
- Yuheng Liang, Master by Research (MPhil), 2022-2024, (administered by 91É«ÇéƬ).
- Sally Chen,ÌýMaster student, 2023-2024, (administered by 91É«ÇéƬ).
- Michael De Francesco,ÌýMaster student, 2023-2024, (administered by 91É«ÇéƬ).
- Gabrielle Younes,ÌýMaster student, 2023-2024, (administered by 91É«ÇéƬ).
- Aryan Bhatla,ÌýMaster student, 2023-2024, (administered by 91É«ÇéƬ).
- Ivy Lan Liu,ÌýMaster student, 2022-2023, (administered by 91É«ÇéƬ).
- Aravind Venkateswaran,ÌýMaster student, 2022-2023, (administered by 91É«ÇéƬ).
- Sascha Graham,ÌýMaster student, 2022-2023, (administered by 91É«ÇéƬ).
- Weilin Wu, Master student, 2021-2022, (administered by 91É«ÇéƬ).
- Anthony Xu, Master student, 2021-2022, (administered by 91É«ÇéƬ).
- Hanwen Liang, MS student, 2019-2020, (administered by 91É«ÇéƬ).
- Rasaa Ghavami, Master student, 2017-2019. Scholarship awarded for PhD degree from SUT.
- Narges Rezaei, Honours student, 2018-2019. Scholarship awarded for Ph.D Degree from University of California, US.
- Masroor Bayati, Honours student, 2017-2018. Scholarship awarded for Ph.D Degree from University of Toronto.
- Hamed Dashti, Honours student, 2016-2018. Scholarship awarded for Master Degree from University of Zurich.
- Mahshid Khatami, Master student, 2018-2020, (administered by SUT).
- Fariba Raoufi, Master student, 2016-2017.
My Teaching
Biomedical Informatics (BIOM9540)
Biomedical Engineering (BIOM4951, BIOM4952, BIOM4953)