Ye Wei

Shihang Zhang, Mingjin Kuai, Ye Wei et al.

Video Moment Retrieval (VMR) task requires accurately localizing temporal boundaries aligned with natural language queries, but many models suffer from a misalignment between continuous surrogate losses and non-differentiable metrics, leading to optimization stagnation during the late stages of training and trapping boundary predictions in suboptimal solutions. Although Reinforcement Learning (RL) post-training successfully optimizes localization results for large models, applying it directly to lightweight networks easily disrupts the fragile feature representations established during the supervised phase. To overcome this optimization bottleneck, we propose Gradient-Isolated Reinforcement Learning for DETR (GIRL-DETR), introducing RL post-training into a lightweight temporal localization framework for the first time. The input video and text features first establish early alignment through Cross-Modal Interaction (CMI) before entering the transformer encoder. Subsequently, a Text-Guided Gating (TGG) mechanism dynamically injects semantic priors into the queries before the transformer decoder generates candidate proposals, providing high signal-to-noise ratio inputs for temporal prediction. After the supervised training reaches convergence, the backbone network is frozen to protect the feature manifold, while the detection head directly optimizes the non-differentiable evaluation metric tIoU to enhance localization accuracy through a Three-stage Progressive Reinforcement Learning (TPRL) strategy. This approach achieves an orthogonal decoupling of state representation and metric optimization. Experiments on Charades-STA, QVHighlights, and TACoS demonstrate that GIRL-DETR effectively resolves surrogate loss degradation and achieves substantial accuracy improvements with minimal parameter updates, providing a robust new pathway for RL applications in lightweight VMR models.

Moritz Neun, Christian Eichenberger, Henry Martin et al.

The global trends of urbanization and increased personal mobility force us to rethink the way we live and use urban space. The Traffic4cast competition series tackles this problem in a data-driven way, advancing the latest methods in machine learning for modeling complex spatial systems over time. In this edition, our dynamic road graph data combine information from road maps, $10^{12}$ probe data points, and stationary vehicle detectors in three cities over the span of two years. While stationary vehicle detectors are the most accurate way to capture traffic volume, they are only available in few locations. Traffic4cast 2022 explores models that have the ability to generalize loosely related temporal vertex data on just a few nodes to predict dynamic future traffic states on the edges of the entire road graph. In the core challenge, participants are invited to predict the likelihoods of three congestion classes derived from the speed levels in the GPS data for the entire road graph in three cities 15 min into the future. We only provide vehicle count data from spatially sparse stationary vehicle detectors in these three cities as model input for this task. The data are aggregated in 15 min time bins for one hour prior to the prediction time. For the extended challenge, participants are tasked to predict the average travel times on super-segments 15 min into the future - super-segments are longer sequences of road segments in the graph. The competition results provide an important advance in the prediction of complex city-wide traffic states just from publicly available sparse vehicle data and without the need for large amounts of real-time floating vehicle data.

Yaosen Min, Ye Wei, Peizhuo Wang et al.

Accurate prediction of protein-ligand binding affinities is an essential challenge in structure-based drug design. Despite recent advances in data-driven methods for affinity prediction, their accuracy is still limited, partially because they only take advantage of static crystal structures while the actual binding affinities are generally determined by the thermodynamic ensembles between proteins and ligands. One effective way to approximate such a thermodynamic ensemble is to use molecular dynamics (MD) simulation. Here, an MD dataset containing 3,218 different protein-ligand complexes is curated, and Dynaformer, a graph-based deep learning model is further developed to predict the binding affinities by learning the geometric characteristics of the protein-ligand interactions from the MD trajectories. In silico experiments demonstrated that the model exhibits state-of-the-art scoring and ranking power on the CASF-2016 benchmark dataset, outperforming the methods hitherto reported. Moreover, in a virtual screening on heat shock protein 90 (HSP90) using Dynaformer, 20 candidates are identified and their binding affinities are further experimentally validated. Dynaformer displayed promising results in virtual drug screening, revealing 12 hit compounds (two are in the submicromolar range), including several novel scaffolds. Overall, these results demonstrated that the approach offer a promising avenue for accelerating the early drug discovery process.

Haibin Wen, Zhe Zhao, Fanfu Wang et al.

The discovery and design of functional molecules remain central challenges across chemistry,biology, and materials science. While recent advances in machine learning have accelerated molecular property prediction and candidate generation, existing models tend to excel either in physical fidelity without transparent reasoning, or in flexible reasoning without guarantees of chemical validity. This imbalance limits the reliability of artificial intelligence systems in real scientific design workflows.Here we present Logos, a compact molecular reasoning model that integrates multi-step logical reasoning with strict chemical consistency. Logos is trained using a staged strategy that first exposes the model to explicit reasoning examples linking molecular descriptions to structural decisions, and then progressively aligns these reasoning patterns with molecular representations. In a final training phase, chemical rules and invariants are incorporated directly into the optimization objective, guiding the model toward chemically valid outputs. Across multiple benchmark datasets, Logos achieves strong performance in both structural accuracy and chemical validity, matching or surpassing substantially larger general-purpose language models while operating with a fraction of their parameters. Beyond benchmark evaluation, the model exhibits stable behaviour in molecular optimization tasks involving multiple, potentially conflicting constraints. By explicitly exposing intermediate reasoning steps, Logos enables human inspection and assessment of the design logic underlying each generated structure. These results indicate that jointly optimizing for reasoning structure and physical consistency offers a practical pathway toward reliable and interpretable AI systems for molecular science, supporting closer integration of artificial intelligence into scientific discovery processes.

Zhe Zhao, Haibin Wen, Jiaming Ma et al.

An important recurring pattern in scientific breakthroughs is a two-stage process: an initial phase of undirected experimentation that yields an unexpected finding, followed by a retrospective phase that explains why the finding works and situates it within existing theory. We present ResearchEVO, an end-to-end framework that computationally instantiates this discover-then-explain paradigm. The Evolution Phase employs LLM-guided bi-dimensional co-evolution -- simultaneously optimizing both algorithmic logic and overall architecture -- to search the space of code implementations purely by fitness, without requiring any understanding of the solutions it produces. The Writing Phase then takes the best-performing algorithm and autonomously generates a complete, publication-ready research paper through sentence-level retrieval-augmented generation with explicit anti-hallucination verification and automated experiment design. To our knowledge, ResearchEVO is the first system to cover this full pipeline end to end: no prior work jointly performs principled algorithm evolution and literature-grounded scientific documentation. We validate the framework on two cross-disciplinary scientific problems -- Quantum Error Correction using real Google quantum hardware data, and Physics-Informed Neural Networks -- where the Evolution Phase discovered human-interpretable algorithmic mechanisms that had not been previously proposed in the respective domain literatures. In both cases, the Writing Phase autonomously produced compilable LaTeX manuscripts that correctly grounded these blind discoveries in existing theory via RAG, with zero fabricated citations.

Yang Zhou, Kunhao Yuan, Ye Wei et al.

Liver fibrosis represents the accumulation of excessive extracellular matrix caused by sustained hepatic injury. It disrupts normal lobular architecture and function, increasing the chances of cirrhosis and liver failure. Precise staging of fibrosis for early diagnosis and intervention is often invasive, which carries risks and complications. To address this challenge, recent advances in artificial intelligence-based liver segmentation and fibrosis staging offer a non-invasive alternative. As a result, the CARE 2025 Challenge aimed for automated methods to quantify and analyse liver fibrosis in real-world scenarios, using multi-centre, multi-modal, and multi-phase MRI data. This challenge included tasks of precise liver segmentation (LiSeg) and fibrosis staging (LiFS). In this study, we developed an automated pipeline for both tasks across all the provided MRI modalities. This pipeline integrates pseudo-labelling based on multi-modal co-registration, liver segmentation using deep neural networks, and liver fibrosis staging based on shape, textural, appearance, and directional (STAD) features derived from segmentation masks and MRI images. By solely using the released data with limited annotations, our proposed pipeline demonstrated excellent generalisability for all MRI modalities, achieving top-tier performance across all competition subtasks. This approach provides a rapid and reproducible framework for quantitative MRI-based liver fibrosis assessment, supporting early diagnosis and clinical decision-making. Code is available at https://github.com/YangForever/care2025_liver_biodreamer.

Ye Wei, Rama Srinivas Varanasi, Torsten Schwarz et al.

Mass spectrometry is a widespread approach to work out what are the constituents of a material. Atoms and molecules are removed from the material and collected, and subsequently, a critical step is to infer their correct identities based from patterns formed in their mass-to-charge ratios and relative isotopic abundances. However, this identification step still mainly relies on individual user's expertise, making its standardization challenging, and hindering efficient data processing. Here, we introduce an approach that leverages modern machine learning technique to identify peak patterns in time-of-flight mass spectra within microseconds, outperforming human users without loss of accuracy. Our approach is cross-validated on mass spectra generated from different time-of-flight mass spectrometry(ToF-MS) techniques, offering the ToF-MS community an open-source, intelligent mass spectra analysis.

Lei Jiang, Ye Wei, Hao Ni

Diffusion models have become a popular choice for human motion synthesis due to their powerful generative capabilities. However, their high computational complexity and large sampling steps pose challenges for real-time applications. Fortunately, the Consistency Model (CM) provides a solution to greatly reduce the number of sampling steps from hundreds to a few, typically fewer than four, significantly accelerating the synthesis of diffusion models. However, applying CM to text-conditioned human motion synthesis in latent space yields unsatisfactory generation results. In this paper, we introduce \textbf{MotionPCM}, a phased consistency model-based approach designed to improve the quality and efficiency for real-time motion synthesis in latent space. Experimental results on the HumanML3D dataset show that our model achieves real-time inference at over 30 frames per second in a single sampling step while outperforming the previous state-of-the-art with a 38.9\% improvement in FID. The code will be available for reproduction.

Zhe Zhao, Haibin Wen, Pengkun Wang et al.

Large language models (LLMs) have greatly accelerated the automation of algorithm generation and optimization. However, current methods such as EoH and FunSearch mainly rely on predefined templates and expert-specified functions that focus solely on the local evolution of key functionalities. Consequently, they fail to fully leverage the synergistic benefits of the overall architecture and the potential of global optimization. In this paper, we introduce an end-to-end algorithm generation and optimization framework based on LLMs. Our approach utilizes the deep semantic understanding of LLMs to convert natural language requirements or human-authored papers into code solutions, and employs a two-dimensional co-evolution strategy to optimize both functional and structural aspects. This closed-loop process spans problem analysis, code generation, and global optimization, automatically identifying key algorithm modules for multi-level joint optimization and continually enhancing performance and design innovation. Extensive experiments demonstrate that our method outperforms traditional local optimization approaches in both performance and innovation, while also exhibiting strong adaptability to unknown environments and breakthrough potential in structural design. By building on human research, our framework generates and optimizes novel algorithms that surpass those designed by human experts, broadening the applicability of LLMs for algorithm design and providing a novel solution pathway for automated algorithm development.

Yue Li, Ye Wei, Alaukik Saxena et al.

Atom probe tomography (APT) is a burgeoning characterization technique that provides compositional mapping of materials in three-dimensions at near-atomic scale. Since its significant expansion in the past 30 years, we estimate that one million APT datasets have been collected, each containing millions to billions of individual ions. Their analysis and the extraction of microstructural information has largely relied upon individual users whose varied level of expertise causes clear and documented bias. Current practices hinder efficient data processing, and make challenging standardization and the deployment of data analysis workflows that would be compliant with FAIR data principles. Over the past decade, building upon the long-standing expertise of the APT community in the development of advanced data processing or data mining techniques, there has been a surge of novel machine learning (ML) approaches aiming for user-independence, and that are efficient, reproducible, and robust from a statistics perspective. Here, we provide a snapshot review of this rapidly evolving field. We begin with a brief introduction to APT and the nature of the APT data. This is followed by an overview of relevant ML algorithms and a comprehensive review of their applications to APT. We also discuss how ML can enable discoveries beyond human capability, offering new insights into the mechanisms within materials. Finally, we provide guidance for future directions in this domain.

Ye Wei, Bo Peng, Ruiwen Xie et al.

A tremendous range of design tasks in materials, physics, and biology can be formulated as finding the optimum of an objective function depending on many parameters without knowing its closed-form expression or the derivative. Traditional derivative-free optimization techniques often rely on strong assumptions about objective functions, thereby failing at optimizing non-convex systems beyond 100 dimensions. Here, we present a tree search method for derivative-free optimization that enables accelerated optimal design of high-dimensional complex systems. Specifically, we introduce stochastic tree expansion, dynamic upper confidence bound, and short-range backpropagation mechanism to evade local optimum, iteratively approximating the global optimum using machine learning models. This development effectively confronts the dimensionally challenging problems, achieving convergence to global optima across various benchmark functions up to 2,000 dimensions, surpassing the existing methods by 10- to 20-fold. Our method demonstrates wide applicability to a wide range of real-world complex systems spanning materials, physics, and biology, considerably outperforming state-of-the-art algorithms. This enables efficient autonomous knowledge discovery and facilitates self-driving virtual laboratories. Although we focus on problems within the realm of natural science, the advancements in optimization techniques achieved herein are applicable to a broader spectrum of challenges across all quantitative disciplines.