arXiv subjects

Minjie Shen

Publications and source records attributed to Minjie Shen.

9 recordsLinked to original sources

arXiv2026

From Mind to Machine: The Rise of Manus AI as a Fully Autonomous Digital Agent

Manus AI is a general-purpose AI agent introduced in early 2025, marking a significant advancement in autonomous artificial intelligence. Developed by the Chinese startup Monica.im, Manus is designed to bridge the gap between "mind" and "hand" - combining the reasoning and planning capabilities of large language models with the ability to execute complex, end-to-end tasks that produce tangible outcomes. This paper presents a comprehensive overview of Manus AI, exploring its core technical architecture, diverse applications across sectors such as healthcare, finance, manufacturing, robotics, and gaming, as well as its key strengths, current limitations, and future potential. Positioned as a preview of what lies ahead, Manus AI represents a shift toward intelligent agents that can translate high-level intentions into real-world actions, heralding a new era of human-AI collaboration.

cs.AI↗

arXiv2026

Quantum-inspired Reinforcement Learning for Synthesizable Drug Design

Synthesizable molecular design (also known as synthesizable molecular optimization) is a fundamental problem in drug discovery, and involves designing novel molecular structures to improve their properties according to drug-relevant oracle functions (i.e., objective) while ensuring synthetic feasibility. However, existing methods are mostly based on random search. To address this issue, in this paper, we introduce a novel approach using the reinforcement learning method with quantum-inspired simulated annealing policy neural network to navigate the vast discrete space of chemical structures intelligently. Specifically, we employ a deterministic REINFORCE algorithm using policy neural networks to output transitional probability to guide state transitions and local search using genetic algorithm to refine solutions to a local optimum within each iteration. Our methods are evaluated with the Practical Molecular Optimization (PMO) benchmark framework with a 10K query budget. We further showcase the competitive performance of our method by comparing it against the state-of-the-art genetic algorithms-based method.

cs.LG↗

arXiv2026

PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking

Existing protein-ligand docking studies typically focus on the self-docking scenario, which is less practical in real applications. Moreover, some studies involve heavy frameworks requiring extensive training, posing challenges for convenient and efficient assessment of docking methods. To fill these gaps, we design PoseX, an open-source benchmark to evaluate both self-docking and cross-docking, enabling a practical and comprehensive assessment of algorithmic advances. Specifically, we curated a novel dataset comprising 718 entries for self-docking and 1,312 entries for cross-docking; second, we incorporated 23 docking methods in three methodological categories, including physics-based methods (e.g., Schrödinger Glide), AI docking methods (e.g., DiffDock) and AI co-folding methods (e.g., AlphaFold3); third, we developed a relaxation method for post-processing to minimize conformational energy and refine binding poses; fourth, we built a leaderboard to rank submitted models in real-time. We derived some key insights and conclusions from extensive experiments: (1) AI approaches have consistently outperformed physics-based methods in overall docking success rate. (2) Most intra- and intermolecular clashes of AI approaches can be greatly alleviated with relaxation, which means combining AI modeling with physics-based post-processing could achieve excellent performance. (3) AI co-folding methods exhibit ligand chirality issues, except for Boltz-1x, which introduced physics-inspired potentials to fix hallucinations, suggesting modeling on stereochemistry improves the structural plausibility markedly. (4) Specifying binding pockets significantly promotes docking performance, indicating that pocket information can be leveraged adequately, particularly for AI co-folding methods, in future modeling efforts. The code, dataset, and leaderboard are released at https://github.com/CataAI/PoseX.

cs.LG↗

arXiv2026

SMILES-Mamba: Chemical Mamba Foundation Models for Drug ADMET Prediction

In drug discovery, predicting the absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of small-molecule drugs is critical for ensuring safety and efficacy. However, the process of accurately predicting these properties is often resource-intensive and requires extensive experimental data. To address this challenge, we propose SMILES-Mamba, a two-stage model that leverages both unlabeled and labeled data through a combination of self-supervised pretraining and fine-tuning strategies. The model first pre-trains on a large corpus of unlabeled SMILES strings to capture the underlying chemical structure and relationships, before being fine-tuned on smaller, labeled datasets specific to ADMET tasks. Our results demonstrate that SMILES-Mamba exhibits competitive performance across 22 ADMET datasets, achieving the highest score in 14 tasks, highlighting the potential of self-supervised learning in improving molecular property prediction. This approach not only enhances prediction accuracy but also reduces the dependence on large, labeled datasets, offering a promising direction for future research in drug discovery.

cs.LG↗

arXiv2025

A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

cs.CL↗

arXiv2025

Virtual Cells: From Conceptual Frameworks to Biomedical Applications

The challenge of translating vast, multimodal biological data into predictive and mechanistic understanding of cellular function is a central theme in modern biology. Virtual cells, or digital cellular twins, have emerged as a critical paradigm to meet this challenge by creating integrative computational models of cellular processes. This review synthesizes the evolution and current state of the virtual cell, from foundational mechanistic frameworks like the Virtual Cell that employ deterministic and stochastic simulations to the recent transformative impact of artificial intelligence and foundation models. We examine the core technological pillars required to build these models, including the integration of various data types, such as single-cell and spatial omics, the spectrum of modeling approaches, and the bioengineering principles that connect simulation to application. We further discuss key applications, frameworks for model benchmarking and validation, and the significant hurdles that remain, including computational scalability, parameter inference, and ethical considerations, which provides a roadmap for development of predictive virtual cells that promise to revolutionize biomedical research and clinical practice.

q-bio.QM↗

arXiv2025

A Comprehensive Review of AI Agents: Transforming Possibilities in Technology and Beyond

Artificial Intelligence (AI) agents have rapidly evolved from specialized, rule-based programs to versatile, learning-driven autonomous systems capable of perception, reasoning, and action in complex environments. The explosion of data, advances in deep learning, reinforcement learning, and multi-agent coordination have accelerated this transformation. Yet, designing and deploying unified AI agents that seamlessly integrate cognition, planning, and interaction remains a grand challenge. In this review, we systematically examine the architectural principles, foundational components, and emergent paradigms that define the landscape of contemporary AI agents. We synthesize insights from cognitive science-inspired models, hierarchical reinforcement learning frameworks, and large language model-based reasoning. Moreover, we discuss the pressing ethical, safety, and interpretability concerns associated with deploying these agents in real-world scenarios. By highlighting major breakthroughs, persistent challenges, and promising research directions, this review aims to guide the next generation of AI agent systems toward more robust, adaptable, and trustworthy autonomous intelligence.

cs.MA↗

arXiv2025

Machine Learning for Synthetic Data Generation: A Review

Machine learning heavily relies on data, but real-world applications often encounter various data-related issues. These include data of poor quality, insufficient data points leading to under-fitting of machine learning models, and difficulties in data access due to concerns surrounding privacy, safety, and regulations. In light of these challenges, the concept of synthetic data generation emerges as a promising alternative that allows for data sharing and utilization in ways that real-world data cannot facilitate. This paper presents a comprehensive systematic review of existing studies that employ machine learning models for the purpose of generating synthetic data. The review encompasses various perspectives, starting with the applications of synthetic data generation, spanning computer vision, speech, natural language processing, healthcare, and business domains. Additionally, it explores different machine learning methods, with particular emphasis on neural network architectures and deep generative models. The paper also addresses the crucial aspects of privacy and fairness concerns related to synthetic data generation. Furthermore, this study identifies the challenges and opportunities prevalent in this emerging field, shedding light on the potential avenues for future research. By delving into the intricacies of synthetic data generation, this paper aims to contribute to the advancement of knowledge and inspire further exploration in synthetic data generation.

cs.LG↗

arXiv2024

GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization

The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive software solution designed to handle the entire pipeline of omics data processing. GenoCraft offers a unified platform featuring advanced bioinformatics tools, covering all aspects of omics data analysis. It encompasses a range of functionalities, such as normalization, quality control, differential analysis, network analysis, pathway analysis, and diverse visualization techniques. This software makes state-of-the-art omics data analysis more accessible to a wider range of users. With GenoCraft, researchers and data scientists have access to an array of cutting-edge bioinformatics tools under a user-friendly interface, making it a valuable resource for managing and analyzing large-scale omics data. The API with an interactive web interface is publicly available at https://genocraft.stanford. edu/. We also release all the codes in https://github.com/futianfan/GenoCraft.

q-bio.GN↗