Sep 2026· Zenodo (CERN European Organization for Nuclear Research)
Computational Drug Discovery Methods
Abstract
Purpose: Medicinal plants are the richest source of structurally diverse biologically active compounds. Herbal leads discovery can also be accelerated using artificial intelligence and multi omics technologies. This review evaluates and summarizes the applications of artificial intelligence (AI), multi-omics, synthetic biology, and biomanufacturing in advancing research for herbal therapeutics. Virtual computational screening, deep learning, and molecular docking extremely accelerate lead identifications, structure-activity predictions, and target identification. Method: We comprehensively examine literature on virtual computational screening, deep learning, molecular docking, multi-omics platforms, genome mining, CRISPR-based synthetic biology, and emerging tools like organ-on-a-chip systems and nanobiotechnology using PubMed, ScienceDirect and Google Scholar. Result: Virtual screening, deep learning, and molecular docking extremely accelerate lead identifications, structure-activity predictions, and target identification. Simultaneously, multi-omics platforms evaluate system-level metabolic networks, regulatory pathways, and host–microbiome interactions. Genome mining and CRISPR-based synthetic biology unlock cryptic metabolic pathways and enable scalable, sustainable production of high-value natural products. Furthermore, tools like organ-on-a-chip systems and nanobiotechnology bridge the gap toward precision herbal medicine and standardization. Conclusion: By integrating these multidisciplinary strategies, herbal drug discovery is evolving from empirical observation toward predictive, sustainable, and mechanism-driven pharmaceutical science. Finally, key challenges like data standardization, explainable AI, experimental validation, and regulatory approval must be addressed for clinical translation.
Various recent Artificial Intelligence (AI) system failures, some of which have made the global headlines, have highlighted issues in these systems. These failures have resulted in calls for more ethical AI systems that better take into account their effects on various stakeholders. However, implementing AI ethics into practice is still an on-going challenge. High-level guidelines for doing so exist, devised by governments and private organizations alike, but lack practicality for developers. To address this issue, in this paper, we present a method for implementing AI ethics. The method, ECCOLA, has been iteratively developed using a cyclical action design research approach. The method aims at making the high-level AI ethics principles more practical, making it possible for developers to more easily implement them in practice.
Ville Vakkuri, Kai-Kristian Kemell, P. Abrahamsson· EUROMICRO Conference on Soft...· 64 citations· ⚡6
In this paper, we present a novel approach to improving software quality and efficiency through a Large Language Model (LLM)-based model designed to review code and identify potential issues. Our proposed LLM-based AI agent model is trained on large code repositories. This training includes code reviews, bug reports, and documentation of best practices. It aims to detect code smells, identify potential bugs, provide suggestions for improvement, and optimize the code. Unlike traditional static code analysis tools, our LLM-based AI agent has the ability to predict future potential risks in the code. This supports a dual goal of improving code quality and enhancing developer education by encouraging a deeper understanding of best practices and efficient coding techniques. Furthermore, we explore the model's effectiveness in suggesting improvements that significantly reduce post-release bugs and enhance code review processes, as evidenced by an analysis of developer sentiment toward LLM feedback. For future work, we aim to assess the accuracy and efficiency of LLM-generated documentation updates in comparison to manual methods. This will involve an empirical study focusing on manually conducted code reviews to identify code smells and bugs, alongside an evaluation of best practice documentation, augmented by insights from developer discussions and code reviews. Our goal is to not only refine the accuracy of our LLM-based tool but also to underscore its potential in streamlining the software development lifecycle through proactive code improvement and education.
Z. Rasheed, Malik Abdul Sami, Muhammad Waseem et al.· arXiv.org· 62 citations· ⚡3
Progress in the field of artificial intelligence has been accelerating rapidly in the past two decades. Various autonomous systems from purely digital ones to autonomous vehicles are being developed and deployed out on the field. As these systems exert a growing impact on society, ethics in relation to artificial intelligence and autonomous systems have recently seen growing attention among the academia. However, the current literature on the topic has focused almost exclusively on theory and more specifically on conceptualization in the area. To widen the body of knowledge in the area, we conduct an empirical study on the current state of practice in artificial intelligence ethics. We do so by means of a multiple case study of five case companies, the results of which indicate a gap between research and practice in the area. Based on our findings we propose ways to tackle the gap.
Ville Vakkuri, Kai-Kristian Kemell, Joni Kultanen et al.· arXiv.org· 56 citations· ⚡6
In agile software development, maintaining high-quality user stories is crucial, but also challenging. This study explores the use of large language models to automatically improve the user story quality in Austrian Post Group IT agile teams. We developed a reference model for an Autonomous LLM-based Agent System and implemented it at the company. The quality of user stories in the study and the effectiveness of these agents for user story quality improvement was assessed by 11 participants across six agile teams. Our findings demonstrate the potential of LLMs in improving user story quality, contributing to the research on AI role in agile development, and providing a practical example of the transformative impact of AI in an industry setting.
Zheying Zhang, M. Rayhan, Tomas Herda et al.· International Conference on...· 48 citations· ⚡4
Systematic literature review (SLR) is foundational to evidence-based research, enabling scholars to identify, classify, and synthesize existing studies to address specific research questions. Conducting an SLR is, however, largely a manual process. In recent years, researchers have made significant progress in automating portions of the SLR pipeline to reduce the effort and time required for high-quality reviews; nevertheless, there remains a lack of AI-agent-based systems that automate the entire SLR workflow. To this end, we introduce a novel multi-AI-agent system designed to fully automate SLRs. Leveraging large language models (LLMs), our system streamlines the review process to enhance efficiency and accuracy. Through a user-friendly interface, researchers specify a topic; the system then generates a search string to retrieve relevant academic papers. Next, an inclusion/exclusion filtering step is applied to titles relevant to the research area. The system subsequently summarizes paper abstracts and retains only those directly related to the field of study. In the final phase, it conducts a thorough analysis of the selected papers with respect to predefined research questions. This paper presents the system, describes its operational framework, and demonstrates how it substantially reduces the time and effort traditionally required for SLRs while maintaining comprehensiveness and precision. The code for this project is available at: https://github.com/GPT-Laboratory/SLR-automation .
Malik Abdul Sami, Z. Rasheed, Kai-Kristian Kemell et al.· arXiv.org· 43 citations· ⚡2
Context: Manual qualitative data analysis is time-intensive and can compromise validity and replicability, affecting analysis design, implementation, and reporting. Large Language Models (LLMs) enable human-bot collaboration in Software Engineering (SE), but their potential for qualitative data analysis in SE remains largely unexplored. Objective: The objective of this study is to design and develop an LLM-based multi-agent system that synergizes human decision support with AI to automate various qualitative data analysis approaches. Methods: We used LLM-based multi-agents systems to assist the qualitative data analysis process, deploying 27 agents, each responsible for a specific task, such as text summarization, initial code generation, and extracting themes and patterns. Results: The main findings are: (1) the LLM-based multi-agent system accelerates the qualitative data analysis process, (2) the system effectively automates tasks such as text summarization, initial code generation, and theme extraction, and (3) the publicly accessible code facilitates validation and further evaluation. Conclusion: The proposed LLM-based multi-agent system automates qualitative data analysis process, creating opportunities for researchers and practitioners. Future improvements focus on enhancing multilingual performance and integrating continuous expert feedback. The source code of proposed system and system details can be found here: https://github.com/GPT-Laboratory/Qualitative-Analysis-with-an-LLM-Based-Agentts
Z. Rasheed, Muhammad Waseem, Aakash Ahmad et al.· arXiv.org· 40 citations
The professor of physics and inaugural director of the NSF AI Institute for Artificial Intelligence and Fundamental Interactions will lead LNS and continue his research in particle physics.
