Aayush Shah

Aayush Shah, Chakradhar Guntuboina, Amir Barati Farimani

In recent years, natural language processing (NLP) models have demonstrated remarkable capabilities in various domains beyond traditional text generation. In this work, we introduce PeptideGPT, a protein language model tailored to generate protein sequences with distinct properties: hemolytic activity, solubility, and non-fouling characteristics. To facilitate a rigorous evaluation of these generated sequences, we established a comprehensive evaluation pipeline consisting of ideas from bioinformatics to retain valid proteins with ordered structures. First, we rank the generated sequences based on their perplexity scores, then we filter out those lying outside the permissible convex hull of proteins. Finally, we predict the structure using ESMFold and select the proteins with pLDDT values greater than 70 to ensure ordered structure. The properties of generated sequences are evaluated using task-specific classifiers - PeptideBERT and HAPPENN. We achieved an accuracy of 76.26% in hemolytic, 72.46% in non-hemolytic, 78.84% in non-fouling, and 68.06% in solubility protein generation. Our experimental results demonstrate the effectiveness of PeptideGPT in de novo protein design and underscore the potential of leveraging NLP-based approaches for paving the way for future innovations and breakthroughs in synthetic biology and bioinformatics. Codes, models, and data used in this study are freely available at: https://github.com/aayush-shah14/PeptideGPT.

Yilei Zeng, Aayush Shah, Jameson Thai et al.

The game industry is moving into an era where old-style game engines are being replaced by re-engineered systems with embedded machine learning technologies for the operation, analysis and understanding of game play. In this paper, we describe our machine learning course designed for graduate students interested in applying recent advances of deep learning and reinforcement learning towards gaming. This course serves as a bridge to foster interdisciplinary collaboration among graduate schools and does not require prior experience designing or building games. Graduate students enrolled in this course apply different fields of machine learning techniques such as computer vision, natural language processing, computer graphics, human computer interaction, robotics and data analysis to solve open challenges in gaming. Student projects cover use-cases such as training AI-bots in gaming benchmark environments and competitions, understanding human decision patterns in gaming, and creating intelligent non-playable characters or environments to foster engaging gameplay. Projects demos can help students open doors for an industry career, aim for publications, or lay the foundations of a future product. Our students gained hands-on experience in applying state of the art machine learning techniques to solve real-life problems in gaming.