Breakthrough Research: New Applications of Machine Learning in Biosciences

02 May 2024

In a significant academic achievement, Assistant Professor Zhen Wei and his PhD student, Mr. Haokai Ye from the Department of Biological Sciences, School of Science (SCI) at Xi'an Jiaotong-Liverpool University (XJTLU) have published a groundbreaking Computational Biology research paper in the highly respected Nucleic Acids Research, a leading journal in biology known for its high impact factor of 16.191 (real time). Their research introduces a novel machine learning framework that effectively eliminates antibody non-specific binding artifacts in MeRIP-Seq omics data, which is essential for detecting m6A modifications on RNA.

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This innovative approach is especially important in Bioinformatics, where the quality of "ground truth" data is often compromised by biological experimental artifacts. In the more familiar domains of machine learning (such as natural language processing and image recognition), models are typically trained on large volumes of high-quality, well-labeled data, allowing for clear distinctions between accurate and inaccurate interpretations. However, in Bioinformatics, the inherent variability and frequent presence of experimental artifacts present unique challenges. Dr. Wei’s team addresses this issue by developing sophisticated computational methods aimed at reducing noise and enhancing signal detection. This advancement is pivotal for the field as it enables researchers to distinguish true biological signals from widespread variability and errors, a common obstacle in omics data analysis.

The journey to publication was intensive, spanning 18 months. Dr. Wei and Mr. Ye spent a year drafting the manuscript and a further six months on revisions following initial feedback. During revision, they collected and analyzed independent data from multiple perspectives to convincingly demonstrate the efficacy of their machine learning model. The results of these efforts have effectively demonstrated their approach can lead to more accurate biological discoveries across various datasets and applications.

Dr. Wei uses this opportunity to share insights into the research publication process. He encourages all undergraduate and especially Master’s and PhD research students to strive to publish their research work, emphasizing the importance of making solid, innovative contributions to scientific knowledge. He notes, "Publishing is a rigorous process that involves plotting many high-quality figures to defend the empirical validity of your idea from different angles. In addition, it is necessary to refine every aspect of your presentation, from graphs and tables to the writing of each sentence. It's about optimizing the way you convey complex information clearly and compellingly to a wider audience."

Reflecting on the talent at SCI and XJTLU, Dr. Wei is confident in the capability of the university's students to achieve remarkable research outcomes. Both of the first author and corresponding author completed their undergraduate studies at the department of biological science before advancing in their academic careers. Moreover, Dr. Wei highlights the importance of fostering a supportive and motivating environment for PhD students. "At our SCI and XJTLU, we prioritize a growth mindset and believe that a student's intellectual curiosity and passion for their field often predict research success more accurately than traditional metrics like GPA," he states.

As the first author of the article, student Haokai Ye made a crucial contribution to the publication of this work. Haokai is the first PhD student of Dr.Wei. He is diligent in his work and full of curiosity, devoting great effort to the presentation of scientific results, and pays meticulous attention to every detail. In addition, Haokai Ye has excellent communication skills and always maintains an optimistic attitude, which greatly facilitates the smooth progress of the research project.

The Dean of the School of Science, Professor John Moraros said that this publication is a testament to SCI and XJTLU’s commitment to fostering high-impact scientific research and demonstrates the university's role in nurturing the next generation of scientists and researchers. Through such achievements, SCI and XJTLU continue to contribute profoundly to the global scientific community, emphasizing the importance of meticulous research and academic perseverance.


Materials and proofreading: Dr. Zhen Wei

02 May 2024