data science

Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications

A comprehensive overview of how enhanced sampling methods are reshaping the field, with a particular focus on the data-driven construction of collective variables, is provided.

RSGPT: a generative transformer model for retrosynthesis planning pre-trained on ten billion datapoints

RSGPT, a generative model pre-trained on ten billion data points, achieving state-of-the-art performance for synthesis planning, and introduces reinforcement learning to capture the relationships among products, reactants, and templates more accurately.

AntiBMPNN: Structure‐Guided Graph Neural Networks for Precision Antibody Engineering

AntiBMPNN consistently outperforms AbMPNN, AntiFold, and ProteinMPNN in designing complementarity determining regions (CDR) 1‐3, yielding stronger binding affinities and confirming its potential to improve therapeutic antibody design.

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

ERAM aligns pre-trained molecular representations from Protein Language Model with the knowledge of enzyme catalysis by modeling enzymatic reactions as multi-relational data, and demonstrates its potential as a versatile and effective tool for enzyme catalysis research.

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

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 trip...

BioTD: An Online Database of Biotoxins

The Biotoxins Database (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.

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

BBBP-Atlas is proposed, a structure-aware BBB permeability prediction model designed for unified modeling of small molecules and peptides with the first cross-modal dataset OmniBBBP, which offers a versatile and cross-modal approach for single-compound prediction, batch screening, and dataset exploration for CNS drug d...

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

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

The proposed LLM-based multi-agent system automates qualitative data analysis process, creating opportunities for researchers and practitioners, and future improvements focus on enhancing multilingual performance and integrating continuous expert feedback.

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

This work designs and operationalizes a governance-aware, multi-tenant AI sandbox that supports structured experimentation and produces reusable evaluation evidence across stakeholders and yields lessons learned and practical considerations that inform deployment and future evolution of governance-aware sandbox platfor...

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

AI Sandbox: Technical Report

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.