data science

Accurate and task-agnostic modeling of enzymatic reactions through multimodal relational learning

Enzymatic reactions play an emerging role in a broad spectrum of scientific and industrial applications. The inherent complexity of enzymes, such as their substrate specificity, conformational flexibility, and the vast diversity of reactions involved, poses substantial challenges for the advanced computational prediction of enzymatic reactions with desirable accuracy. Moreover, existing approaches are mostly tailored for a specific sub-task, such as substrate prediction or binding site annotation, which limits their applicability. In this study, we introduce ERAM, a task-agnostic multimodal learning framework capable of addressing a broad range of downstream applications with both accuracy and efficiency. ERAM aligns pre-trained molecular representations from Protein Language Model with the knowledge of enzyme catalysis by modeling enzymatic reactions as multi-relational data. In enzyme retrieval tasks, ERAM achieves an improvement of 28.31% in mean average precision compared with the state-of-the-art (SOTA) method, CREEP. In substrate prediction tasks, ERAM outperforms the SOTA method ESP, achieving average improvements of 35.53% and 22.97% in Matthews correlation coefficient across two datasets. Additionally, ERAM exhibits commendable interpretability by assigning higher attention weights to binding sites, resulting in lower false-positive rates (42.36%) and higher overlap scores (70.59%) in the unsupervised binding site prediction task compared to RXNAA Mapper. By learning embeddings of substrates, enzymes, and products within a unified knowledge graph latent space, ERAM demonstrates its potential as a versatile and effective tool for enzyme catalysis research.

LaMGen: LLM-based 3D molecular generation for multi-target drug design

Multi-target drugs hold great promise for treating complex diseases, yet existing methodologies predominantly rely on ligand-based approaches, which lack sufficient biological context and are often confined to specific target pairs, resulting in limited generalizability. Here, we introduce LaMGen, a general-purpose multi-target drug design framework powered by large language models (LLMs). Built on MTD2025, a dataset comprising over 600,000 quantum-accurate molecular conformations and 700,000 multi-target associations, LaMGen directly yields energy-favorable conformations with quantum-level accuracy. The framework integrates ESM-C protein embeddings, rotation-aware ligand tokens, and a TriCoupleAttention module to capture multi-level target–ligand interactions. Across independent benchmarks, LaMGen outperforms diffusion-based model across multiple properties, generating molecules in an average of 0.44 s, while preserving high conformational plausibility. Retrospective analyses demonstrate that LaMGen not only can reproduce molecules identical to known actives, but also consistently produces structurally novel candidates with conserved core scaffolds and superior binding affinities. Designing effective multi-target therapeutics remains a major challenge, as existing ligand- or protein-centric methods struggle to generate biologically contextualized, spatially valid 3D molecules, particularly for triple-target systems. This study introduces LaMGen, an LLM-powered framework that leverages large-scale protein-ligand data and rotation-aware molecular encoding to rapidly produce chemically plausible multi-target candidates, achieving strong zero-shot generalization, superior molecular quality, and robust performance across dual- and triple-target design tasks.

BioTD: An Online Database of Biotoxins

Biotoxins, mainly produced by venomous animals, plants, and microorganisms, exhibit high physiological activity and unique effects such as lowering blood pressure and analgesia. A number of venom-derived drugs are already available on the market, with many more candidates currently undergoing clinical and laboratory studies. However, drug design resources related to biotoxins are insufficient, particularly because of a lack of accurate and extensive activity data. To fulfill this demand, we developed the Biotoxins Database (BioTD). BioTD is the largest open-source database for toxins, offering open access to 14,607 data records (8,185 activity records), covering 8,975 toxins sourced from 5,220 references and patents across over 900 species. The activity data in BioTD are categorized into five groups: Activity, Safety, Kinetics, Hemolysis, and other physiological indicators. Moreover, BioTD provides data on 1,532 mutants, refines the whole sequence and signal peptide sequences of toxins, and annotates disulfide-bond information. All of the data in the database can be downloaded for free. Given the importance of biotoxins and their associated data, this new database is expected to attract broad interest from diverse research fields in drug discovery. BioTD is freely accessible at http://biotoxin.net/.

BBBP-Atlas: Unified Interpretable Modeling of Blood–Brain Barrier Permeability across Small Molecules and Peptides

Accurate prediction of blood-brain barrier permeability (BBBP) is essential for central nervous system drug discovery, yet existing models are often limited by their reliance on predefined physicochemical descriptors, small-molecule-centered training sets, or conformation-dependent representations, which restricts their transferability across chemically diverse modalities especially peptides. In addition, publicly available BBBP datasets remain fragmented, inconsistently standardized, and weakly controlled for molecular redundancy, increasing the risk of data leakage and overestimated model performance. In this study, we propose BBBP-Atlas, a structure-aware BBB permeability prediction model designed for unified modeling of small molecules and peptides with the first cross-modal dataset OmniBBBP. Designed to bypass descriptor and conformation dependencies, our model represents standardized molecular structures as atom-level graphs to capture local atom-bond environments and long-range topological dependencies associated with BBB transport. This design enables direct learning of structure-permeability relationships from molecular topology. For model training and evaluation, we curated a cross-modal, redundancy-filtered database OmniBBBP that seamlessly unifies small molecules and complex peptides, containing 10,218 unique compounds with 9,316 small molecules and 902 peptides. BBBP-Atlas achieved an accuracy of 0.8914 and an MCC of 0.7678 on the independent test set. On a balanced external benchmark of 200 compounds, our model reached an AUC of 0.9108, an accuracy of 0.8500, and an MCC of 0.7000, outperforming LightBBB by an absolute MCC gain of 6%. Case studies further showed that BBBP-Atlas captured clinically meaningful BBB permeability patterns, correctly identifying lorlatinib as BBB-permeable and vancomycin as BBB-impermeable with high confidence. The OmniBBBP-backed BBBP-Atlas offers a versatile and cross-modal approach for single-compound prediction, batch screening, and dataset exploration for CNS drug discovery. BBBP-Atlas is available at https://cadd.drugflow.com/bbbp/.

CodePori: Large-Scale System for Autonomous Software Development Using Multi-Agent Technology

Context: LLM-based multi-agent systems enable automation and decision support in software development, yet existing studies rely on benchmark datasets offering only binary pass-or-fail results, limiting insight into real-world applicability. Objective: This study empirically investigates the potential and limitations of LLM-based agents in autonomous software development tasks. Method: A two-phase approach was employed: developing a multi-agent system, CodePori, for automated code generation, and conducting participant-based evaluation to assess practical performance. Results: Participant feedback reveals key strengths, challenges, and areas for improvement in LLM-based multi-agent systems, highlighting aspects missed by standard code-generation benchmarks. Conclusions: While LLM-based multi-agent systems show potential for large-scale software development, successful integration requires addressing challenges such as memory limitations, hallucinations, and code smells, alongside a practitioner-centric perspective.

Can Large Language Models Serve as Data Analysts? A Multi-Agent Assisted Approach for Qualitative Data Analysis

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

Engineering a Governance-Aware AI Sandbox: Design, Implementation, and Lessons Learned

Collaborative AI experimentation in industry-academia requires environments that support rapid trials while maintaining controlled access, organisational isolation, and traceable workflows. Although interest in AI sandboxes is increasing, practical guidance on designing and building governance-aware experimentation platforms remains limited. This work designs and operationalizes a governance-aware, multi-tenant AI sandbox that supports structured experimentation and produces reusable evaluation evidence across stakeholders. The sandbox was developed in an industry-academia ecosystem using iteratively validated requirements gathered from industrial partners. The solution adopts a layered reference architecture that separates a multi-tenant presentation layer from a backend control plane and isolates execution and data management concerns into dedicated layers. The sandbox supports governed onboarding, project-based collaboration, controlled access to AI services, and traceable experimentation through approval workflows and audit logging. By structuring experiment context and governance decisions as persistent records, the sandbox enables evaluation evidence to be reused and compared across projects and stakeholders. The development experience yields lessons learned and practical considerations that inform deployment and future evolution of governance-aware sandbox platforms.

TERE4AI: A Knowledge Graph-Based Tool for Generating EU AI Act Compliant Requirements

AI Sandbox: Technical Report

Collaborative AI experimentation across industry and academia requires platforms that enable rapid prototyping while preserving controlled access, tenant separation, and transparent workflows. Despite growing interest in AI sandboxes, there is still limited practical guidance on how to design and implement platforms that integrate experimentation capabilities with governance requirements. This work presents the design and implementation of a governance-aware, multi-tenant AI sandbox for structured experimentation and the generation of reusable evaluation evidence across projects and stakeholder groups. The sandbox was developed within an industry-academia collaboration based on requirements that were iteratively refined with industrial partners. Its reference architecture separates the multi-tenant user interface from the backend control plane and places execution and data-management functions in dedicated layers. The platform supports governed user onboarding, project-centered collaboration, managed access to AI services, approval workflows, audit logging, and traceable experimentation. Experiment configurations, contextual information, and governance decisions are stored as persistent records, allowing evidence and outcomes to be compared and reused across projects. The development process provides practical lessons for deploying and extending governance-aware AI sandbox platforms in collaborative research and industrial environments.

LLM-Based Multi-Agent Systems for Code Generation: A Multi-Vocal Literature Review

Large Language Models (LLMs) have enabled multi-agent systems to perform autonomous code generation for complex tasks. Despite the recent growth in research and industrial applications in this area, there is little work on synthesizing evidence from both academic and industrial sources to capture the current state of research on LLM-based multi-agent systems for code generation. To this end, we conducted a Multi-Vocal Literature Review (MLR), combining insights from both academia and industry, including peer-reviewed studies and grey literature. The aim of this study is to systematically synthesize and analyze existing knowledge on LLM-based multi-agent systems for code generation. Specifically, the review examines the motivations for their use, employed benchmarks and models, key challenges, proposed solutions, and potential directions for future research. We selected and reviewed 114 studies, and the key findings are: 1) the identified reasons for adopting multi-agent systems for code generation were classified into nine categories; 2) the models and evaluation benchmarks utilized across the studies were systematically analyzed to provide a structured overview of commonly adopted LLM configurations and assessment practices; 3) the reported challenges and corresponding solutions were synthesized into six main categories and 26 subcategories; and 4) future research directions were identified and organized into six main categories and 18 subcategories. The results of this MLR will assist researchers and practitioners in pursuing further studies and supporting the real-world adoption of multi-agent systems in industrial settings.

Agentic Frameworks for Reasoning Tasks: An Empirical Study

Recent advances in agentic frameworks have enabled AI agents to perform complex reasoning and decision-making. However, evidence comparing their reasoning performance, efficiency, and practical suitability remains limited. To address this gap, we empirically evaluate 22 widely used agentic frameworks across three reasoning benchmarks: BBH, GSM8K, and ARC. The frameworks were selected from 1,200 GitHub repositories collected between January 2023 and July 2025 and organized into a taxonomy based on architectural design. We evaluated them under a unified setting, measuring reasoning accuracy, execution time, computational cost, and cross-benchmark consistency. Our results show that 19 of the 22 frameworks completed all three benchmarks. Among these, 12 showed stable performance, with mean accuracy of 74.6-75.9%, execution time of 4-6 seconds per task, and cost of 0.14-0.18 cents per task. Poorer results were mainly caused by orchestration problems rather than reasoning limits. For example, Camel failed to complete BBH after 11 days because of uncontrolled context growth, while Upsonic consumed USD 1,434 in one day because repeated extraction failures triggered costly retries. AutoGen and Mastra also exhausted API quotas through iterative interactions that increased prompt length without improving results. We also found a sharp drop in mathematical reasoning. Mean accuracy on GSM8K was 44.35%, compared with 89.80% on BBH and 89.56% on ARC. Overall, this study provides the first large-scale empirical comparison of agentic frameworks for reasoning-intensive software engineering tasks and shows that framework selection should prioritize orchestration quality, especially memory control, failure handling, and cost management.

Autonomous Agents in Software Development: A Vision Paper

Large Language Models (LLM) and Generative Pre-trained Transformers (GPT), are reshaping the field of Software Engineering (SE). They enable innovative methods for executing many software engineering tasks, including automated code generation, debugging, maintenance, etc. However, only a limited number of existing works have thoroughly explored the potential of GPT agents in SE. This vision paper inquires about the role of GPT-based agents in SE. Our vision is to leverage the capabilities of multiple GPT agents to contribute to SE tasks and to propose an initial road map for future work. We argue that multiple GPT agents can perform creative and demanding tasks far beyond coding and debugging. GPT agents can also do project planning, requirements engineering, and software design. These can be done through high-level descriptions given by the human developer. We have shown in our initial experimental analysis for simple software (e.g., Snake Game, Tic-Tac-Toe, Notepad) that multiple GPT agents can produce high-quality code and document it carefully. We argue that it shows a promise of unforeseen efficiency and will dramatically reduce lead-times. To this end, we intend to expand our efforts to understand how we can scale these autonomous capabilities further.