Researcher

Keywords

Fields of Research (FoR)

Quantitative Genetics, Bioinformatics, Pattern Recognition and Data Mining, Biostatistics, Genomics, Nervous system and disorders, Neurogenetics, Cancer Genetics, Biomedical Engineering, Artificial Intelligence and Image Processing, Knowledge Representation and Machine Learning

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Biography

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Dr Rokny (PhD, UNSW Sydney, 2018) is the Director of UNSW 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. He supervises 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 [5,250+, h-index 40 Google 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, UNSW 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 UNSW 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.


My Grants

Dr Rokny received extensive research funding support relative to career stage (total of $3.5M 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 2025, $499K).
  • UNSW-Mahidol Joint Seed Grant, (CIA, Nov 2025, $20K).
  • Australia's Economic Accelerator, (CIB, March 2025, $200K).
  • GESA Paediatric Research Grant (CIB, Nov, 2024)
  • UNSW GRIP Award (CIA, Nov, 2024)
  • UNSW-SJTU Collaborative Research Grant, (CIA, Nov, 2024)
  • Trustworthy Digital Society Grant, (CIA, Oct, 2024)
  • Garvan Cellular Genomics Futures Institute Award (CIA, Sep, 2024).
  • UNSW Scientia Program Fellowship (variation award) (sole CI), ($800K, Sep 2023).
  • CCFA LITWIN IBD Pioneers Program Grant (leading CIB), ($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), UNSW 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 UNSW
  • UNSW Cellular Genomics Futures Institute grant (CIB), in collab with Garvan Institute, May 2020, ($50K)
  • UNSW Cellular Genomics Futures Institute grant (CIC), in collab with UNSW BABS, May 2020, ($50K)
  • Highly competitive tenure-track UNSW Scientia Fellowship Program (sole CI), UNSW, Oct 2019, ($680k)
  • Academic Start-up Funding (sole CI), Faculty of Engineering, UNSW, 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)

 

Dr. Rokny has been named on several industry funding in collaboration with Macquarie University), These 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).

My Qualifications

  • Bachelor: Software Engineering, 2004-2009
  • Master: Artificial Intelligence, 2009-2012.
  • Industry: Data Scientist, 2012-2014.
  • Ph.D: BioMedical Machine Learning, UNSW Sydney, 2014-2018.
  • Post-Doctoral: Harry Perkins Institute of Medical Research, UWA Australia, 2017-2019.
  • Director of UNSW BioMedical Machine Learning Laboratory (BML), 2019-present.
     

My Awards

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:

  • ·     Millennium Prize for Outstanding EMCR, Lorne Genome, Feb 2025.
  • ·     Adjunct Research Scientist, CSIRO, Aug 2022-2023
  • ·     Honorary Lecturer Fellow, University of Macquarie, Oct 2020-2023
  • ·     Travel support award from Institute for Research in Fundamental Sciences, Iran, invited speaker, ($1.9K), Feb 2020
  • ·     Health Data Analytics Program Leader, AI-enabled Processes (AIP) Research Centre, Dec 2019-curent
  • ·     MBSJ2019 (42nd Annual Meeting of the Molecular Biology) Travel support award, Japan, ($1K), Dec 2019
  • ·     RIKEN-HUGO award for best oral presentation in Human Genome Meeting 2019, South Korea, ($0.2K), Oct 2019
  • ·     Highly competitive tenure-track UNSW Scientia Fellowship Program award in Aug 2019 ($680K)
  • ·     Vice-chancellor fellowship award from RMIT, ($350K), May 2019 (declined in favour of UNSW Scientia Program).
  • ·     HDR conference support award from UNSW Sydney, ($3K), Jul 2015
  • ·     Travel support award from University of Tehran as invited speaker, Tehran, ($2K), Feb 2015
  • ·     Ph.D scholarship from UNSW Sydney, ($87.5K for 3.5 years), Mar 2013
  • ·     Top-up scholarship from the faculty of medicine, UNSW Sydney, ($30K for 3 years), Mar 2013
  • ·     Ph.D Scholarship award from The University of Newcastle, Australia, Jul 2012
  • ·     Travel award from Faculty of Engineering, The University Newcastle, Australia, ($1K), Jul 2012
  • ·     Government scholarships for Bachelor and Master degrees, (tuition fee waived)
  • ·     Dean’s award as ranked 1 student (out of 700 Master students), Science and Research University of Tehran, Sep 2010


My Research Activities

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, classification, 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). The move to UNSW Biomedical Engineering school has allowed him to translate his engineering and medical research 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
  • UNSW Post-Graduate Research Scholarship for international students,
  • UNSW 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: https://www.unsw.edu.au/english-requirements-policy 

My Research Supervision


Supervision keywords


Areas of supervision

  • Statistical Machine Learning
  • Biostatistics
  • Data Science
  • Medical Artificial Intelligence
  • Deep Learning
  • Digital Medicine & Digital Biology
  • Bioinformatics
  • Systems Biology
  • Genomics
  • Health Data Analytics

There are multiple open Ph.D/Master/Honours positions in my Lab. Also Ph.D scholarships are available for outstanding applicants to study one of the following topics:

  • Enhancing chromosome conformation capture resolution with deep convolutional neural network.
  • A novel integrative approach to build up transcriptional regulatory networks in neurodevelopmental disorders.
  • Analysis of associations between genetic and transcriptomic variations in different populations.
  • Deep convolutional neural network in the classification of Single-cell data.
  • Using advanced data analytics techniques to get new insight into gene expression profiling in cancers.

Please send me the following documents when you are querying about the scholarships:

  • CV
  • Transcripts (undergraduate and postgraduate study)
  • English test result/plan for international applicants
  • Please note that UNSW offers scholarships for outstanding post-graduate students. However, if you have your own funding, it will simplify the process.

 


Currently supervising

 

PhD & MPhil Students:

  • Rejisa Becirovic, PhD student, 2026-2030, (administered by UNSW), co-supervision with Dr. Reza Argha.
  • Liting Huang, PhD student, 2026-2030, (administered by UNSW), co-supervision with with Dr. Reza Argha and dr. Nona Farbehi.
  • Amir Hossein Zobeiri, PhD student, 2026-2030, (administered by UNSW), co-supervision with Dr. Reza Argha.
  • Mohammadreza Taghimohammadi, PhD student, 2026-2030, (administered by UNSW), co-supervision with Dr. Reza Argha.
  • Sally Chen, PhD student, 2025-2029, (administered by UNSW), co-supervision with Assoc. Prof Fatemeh Vafaee and Mr Mark Grosser (23Strands company).
  • Yuheng Liang, PhD student, 2025-2029, (administered by UNSW), co-supervision with Prof Nigel Lovell and Dr Reza Argha.
  • Caleb The-Tjoean, Master by Research (MPhil), (administered by UNSW), co-supervision with Prof Irina Voineagu.
  • Lucy Chhua, Master by Research (MPhil), 2025-2028, (administered by UNSW), co-supervision with Assoc. Prof Ankur Sharma and Prof Nigel Lovell.
  • Ellie Shalbafian, Master by Research (MPhil), 2024-2027, (administered by UNSW), joint supervision with Prof Nigel Lovell and Dr Reza Argha.
  • Jonathan Williams, Master by Research (MPhil), 2024-2028, (administered by UNSW), co-supervision with Dr Reza Argha and Prof Nigel Lovell.
  • Coco Xiaoge Huang, PhD student, 2024-2028, (administered by UNSW), co-supervision with Dr Fatemeh Vafaee and Mr Mark Grosser (23Strands company).
  • Rebecca Browne, PhD student, 2024-2028, (administered by UNSW), co-supervision with Prof Nigel Lovell and Dr Reza Argha.
  • Tohid Ghasemnejad, PhD student, 2023-2027, (administered by UNSW), co-supervision with Drs Fabrizzio Horta, Faezeh Marzbanrad, and Mr Mark Grosser (23Strands company).
  • Roxana Zahedi Nasab, PhD student, 2023-2027, (administered by UNSW), co-supervision with Prof Nigel Lovell, Dr Reza Argha, and Dr Mo Lotfollahi.
  • Ivan Bakhshayeshi, PhD student, 2023-2027, (administered by UNSW), co-supervision with Prof Nigel Lovell and Dr Reza Argha.
  • Mona (Sedigheh) Abedini, 2023-2027, (administered by UNSW), co-supervision with Dr Fatemeh Vafaee and A/Prof Orazio Vittorio.
  • Md. Mushahidul Islam Shamim, Ph.D student, 2023-2027, (administered by UNSW), co-supervision with A/Prof Nadeem Kaakoush.
  • Reza Ghamsari, PhD student, 2022-2026, (administered by UNSW), co-supervision with Prof Nigel Lovell and Prof Matthew Ritchie (WEHI).
  • Afshar Shamsi, PhD student, 2023-2027, (administered by Concordia University), co-supervision with Assoc Prof Arash Mohammadi.

 

Master Students:

  • Morgan Wong, Master student, 2026-2027, (administered by UNSW).
  • Anish Sinha, Master student, 2026-2027, (administered by UNSW).
  • Evan Watson,  Master student, 2026-2027, (administered by UNSW).
  • Hannah Veitch, Master student, 2025-2026, (administered by UNSW)

 

Previous supervision and mentoring:

  • Mehran Piran, PhD student, 2020-2024, (administered by Monash University), co-supervision with Dr Alex Combes.
  • Mahdieh Labani, PhD student, 2021-2025, (administered by Macquarie University), co-supervision with Prof Amin Beheshti.
  • Ali Afrasiabi, PhD student, 2020-2024, (administered by UNSW).
  • 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, PhD student, 2019-2023, (administered by UNSW), co-supervision with Assoc Prof Irina Voineagu.
  • Yuheng Liang, Master by Research (MPhil), 2022-2024, (administered by UNSW).
  • Sally Chen, Master student, 2023-2024, (administered by UNSW).
  • Michael De Francesco, Master student, 2023-2024, (administered by UNSW).
  • Gabrielle Younes, Master student, 2023-2024, (administered by UNSW).
  • Aryan Bhatla, Master student, 2023-2024, (administered by UNSW).
  • Ivy Lan Liu, Master student, 2022-2023, (administered by UNSW).
  • Aravind Venkateswaran, Master student, 2022-2023, (administered by UNSW).
  • Sascha Graham, Master student, 2022-2023, (administered by UNSW).
  • Weilin Wu, Master student, 2021-2022, (administered by UNSW).
  • Anthony Xu, Master student, 2021-2022, (administered by UNSW).
  • Hanwen Liang, MS student, 2019-2020, (administered by UNSW).
  • 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)

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Location

Engineering
UNSW BioMedical Machine Learning Lab (BML),
Graduate School of Biomedical Engineering, Level 1, Room 1002, Biological Sciences Building (E26)

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Contact

+61 2 9385 1725

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ORCID as entered in ROS

orcid_icon https://orcid.org/0000-0002-2189-9153

UNSW Sydney NSW 2052 Australia Telephone +61 2 93851000
Authorised by Deputy Vice-Chancellor (Research)
UNSW CRICOS Provider Code: 00098G ABN: 57 195 873 179

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