Computational Biology: Recent submissions

  • Evaluating the quality of ontologies 
    Sammi, Daksh; Bhushan, Lakshay; Mutharaju, Raghava (Advisor); Shimizu, Cogan (Advisor) (IIIT-Delhi, 2024-11-27)
    Ontologies serve as fundamental tools for organizing and representing knowledge in various do mains. Evaluating ontology quality is crucial for ensuring their e!ectiveness and usability. This paper presents a comprehensive ...
  • Cryo-EM resolution improvement through enhanced deep learning methods. 
    Jain, Prem Kamal; Garg, Manan; Jain, Vivek; Kumar, Vibhor (Advisor) (IIIT-Delhi, 2024-11-27)
    Recent advancements in cryo-electron microscopy (cryo-EM) have transformed the study of biomolecular structures by enabling the determination of complex structures at near-atomic res olution. However, many cryo-EM maps ...
  • Function prediction of protein cavities using 3D shape descriptors and machine learning 
    Mittal, Pratham; Ray, Arjun (Advisor) (IIIT-Delhi, 2025-07-18)
    Understanding protein function at the structural level requires accurate representation of their biologically active forms. However, structures deposited in the Protein Data Bank (PDB) often include only the asymmetric ...
  • Embedding morality in AI systems 
    Goel, Rahul; Mutharaju, Raghava (Advisor) (IIIT-Delhi, 2025-07-18)
    The increasing integration of Artificial Intelligence into complex societal domains necessitates a deeper understanding of how to embed ethical reasoning into machines. This project addresses the challenge of quantifying ...
  • Epiglobe: unleashing the power of knowledge graphs for enhanced data analysis and insights 
    Singh, Ankit; Ahuja, Gaurav (Advisor) (IIIT-Delhi, 2024-04-29)
    This work shows an overall method of using more than one biomedical knowledge graph to improve learning with graphs in the field of biomedical study. We combined various knowledge graphs with entities like proteins, genes, ...
  • FMT hub phase II: comprehensive web infrastructure for the FMT center and the microbiome informatics lab at IIIT-Delhi 
    Bhaskar, Siddharth; Bali, Siddhant; Kumar, Rishabh; Ghosh, Tarini Shankar (Advisor) (IIIT-Delhi, 2025-07-17)
    We present FMT Hub - Phase II, We are developing the official website for the Microbiome Informatics Lab at IIIT Delhi as a digital extension of the FMT Hub. The platform is being built uscentralized 15, React 19, Node.js, ...
  • Unsupervised clustering of kinases based on sequence and structural features 
    Yadav, Karan; Singh, Manveet; Gautam, Mayank; Ray, Arjun (Advisor) (IIIT-Delhi, 2025-07-24)
    The way kinases interact with their substrates has been a longstanding problem in biology prediction and important to drug developing. This report is about a new computational system like Multimodal Siamese Graph Network ...
  • Allergen based classification of peptides 
    Jindal, Naman; Mehta, Neil; Saini, Saksham; Bagler, Ganesh (Advisor) (IIIT-Delhi, 2025-07-18)
    Peptides, as essential biological molecules, exhibit diverse structural and functional properties, some of which can trigger allergenic responses and pose significant challenges in biotherapeutic applications and drug ...
  • Fine-tuning language models for novel recipe generation 
    Gautam, Sambhav; Singh, Sambhav; Bagler, Ganesh (Advisor) (IIIT-Delhi, 2025-07)
    This project focuses on fine-tuning four lightweight language models—Phi-1, Phi-1.5, Phi-2, and TinyL- lama—for novel recipe generation using a recipe dataset sourced from MongoDB. The process involved data preprocessing, ...
  • Apply machine learning and optimization in optical networks 
    Sajin, Ashwin; Mitra, Abhijit (Advisor) (IIIT-Delhi, 2025-11-28)
    In the EONs, that is, Elastic Optical Networks, a sophisticated management and planning approach is employed to address the physical impairments and resource limitations inherent in high-capacity data transmission over ...
  • Development of a haptic device for surgical training in mixed reality 
    Dharmender; Parihar, Ritesh; Shankhwar, Kalpana (Advisor) (IIIT-Delhi, 2024-11-27)
    This project focuses on designing a haptic device integrated into a Virtual reality (VR) environment to enhance surgical training. Combining force feedback, sensor integration, and 3D modeling, the device offers a realistic ...
  • Predicting lipid-binding proteins using structural biology and ML approaches 
    Singh, Kumar Aryan; Saini, Kartikeya; Ray, Arjun (Advisor) (IIIT-Delhi, 2024-11-26)
    Predicting lipid-binding proteins is essential for understanding their roles in cellular functions and disease mechanisms. This research aims to develop a machine learning (ML) model to accurately identify lipid-binding ...
  • Predicting allostery in proteins 
    Virdi, Mandeep Singh; Verma, Lovleen K; Gupta, Arnav; Ray, Arjun (Advisor) (IIIT-Delhi, 2024-11-29)
    Allosteric site prediction has emerged as a pivotal approach in drug discovery, offering enhanced selectivity and reduced side effects compared to traditional orthosteric targeting. This report explores multiple computational ...
  • Large language model in bio-medical domain 
    Gupta, Bhavya; Gupta, Shruti; Sengupta, Debarka (Advisor) (IIIT-Delhi, 2024-12-13)
    The rapid advancement of biomedical research has led to an overwhelming influx of scholarly articles, making efficient retrieval and comprehension of domain-specific knowledge a significant challenge. This project presents ...
  • Development of AI-based tools for functional annotation of lncRNA and its applications 
    Choudhury, Shubham; Raghava, Gajendra Pal Singh (Advisor) (IIIT-Delhi, 2026-07)
    Long non-coding RNAs (lncRNAs) are a significant component of the human transcriptome and are well known for their ability to regulate gene expression. They have been implicated in a variety of disease-associated pathways. ...
  • Development of AI-based tools for designing subunit vaccines 
    Kumar, Nishant; Raghava, Gajendra Pal Singh (Advisor) (IIIT-Delhi, 2026-03)
    Immunization continues to be a cornerstone of global public health, drastically reducing mortality rates worldwide. Over time, the field of vaccinology has progressively shifted from utilizing whole-pathogen preparations ...
  • Evaluating positional analog scanning as a method for lead optimization 
    Mothukuri, Vishnu; Ray, Arjun (Advisor) (IIIT-Delhi, 2024-11-27)
    Understanding how molecular modifications influence biological activity is a cornerstone of drug discovery and development. This project leverages Positional Analog Scanning, a powerful technique in medicinal chemistry, ...
  • Comprehensive analysis of lipid metabolism pathways and marker genes in brain cell types using single- cell RNA sequencing 
    Prakash, Ayush; Ashwani; Ray, Arjun (Advisor) (IIIT-Delhi, 2024-11-27)
    Lipid metabolism is a critical component of brain physiology, encompassing the synthesis, degradation, and regulation of lipids necessary for cellular homeostasis and signaling. Dysregulation in lipid metabolism pathways ...
  • Fact verification in CQA platforms 
    Udit; Akhtar, Md. Shad (Advisor) (IIIT-Delhi, 2024-11-27)
    Healthcare Community Question Answering (CQA) platforms provide valuable information on medical topics but are often rife with misinformation, posing significant risks to users’ health. Inspired by the need for factual ...
  • Belief space planning in multirobot 
    Yadav, Aditya; Tanmoy, Kundu (Advisor) (IIIT-Delhi, 2024-11-27)
    In multi-robot systems, maintaining belief consistency is essential for optimal performance during joint tasks. However, due to limited communication, robots may develop inconsistent beliefs over time, leading to suboptimal ...

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