Jun Tao

Pengfei Liu, Yiming Ren, Jun Tao et al.

Large language models have made significant strides in natural language processing, enabling innovative applications in molecular science by processing textual representations of molecules. However, most existing language models cannot capture the rich information with complex molecular structures or images. In this paper, we introduce GIT-Mol, a multi-modal large language model that integrates the Graph, Image, and Text information. To facilitate the integration of multi-modal molecular data, we propose GIT-Former, a novel architecture that is capable of aligning all modalities into a unified latent space. We achieve a 5%-10% accuracy increase in properties prediction and a 20.2% boost in molecule generation validity compared to the baselines. With the any-to-language molecular translation strategy, our model has the potential to perform more downstream tasks, such as compound name recognition and chemical reaction prediction.

Yuantu Luo, Jun Tao, Linxiao Yu et al.

Graph-based deep learning methods have been widely employed in encrypted traffic analysis to exploit latent correlations across different granularities. However, while complex preprocessing pipelines and sophisticated model structures often achieve strong performance, they may obscure inherent protocol semantics during representation learning. Moreover, the hierarchical structure of protocol layers and their corresponding fields, defined by protocol specifications and routinely utilized in manual traffic analysis, remains underexplored in existing learning frameworks. In this paper, we propose Protocol Tree Graph Attention with Mixture of Experts (PTGAMoE), a semantic-preserving hierarchical graph-based expert framework for encrypted traffic analysis. The field-based graph construction and expert committee design enable PTGAMoE to quantify the model's preferences for specific fields and protocols. Extensive experimental results on representative benchmark datasets under strict no-data-leakage settings demonstrate that PTGAMoE significantly outperforms state-of-the-art (SOTA) models. Furthermore, the semantic-preserving design provides interpretable insights into protocol-level feature importance and expert-level contributions, reflecting the model's decision-making logic in encrypted traffic classification tasks.

Jiahe Shi, Yawen Wu, Dewen Zeng et al.

The ubiquity of edge devices has led to a growing amount of unlabeled data produced at the edge. Deep learning models deployed on edge devices are required to learn from these unlabeled data to continuously improve accuracy. Self-supervised representation learning has achieved promising performances using centralized unlabeled data. However, the increasing awareness of privacy protection limits centralizing the distributed unlabeled image data on edge devices. While federated learning has been widely adopted to enable distributed machine learning with privacy preservation, without a data selection method to efficiently select streaming data, the traditional federated learning framework fails to handle these huge amounts of decentralized unlabeled data with limited storage resources on edge. To address these challenges, we propose a Self-supervised On-device Federated learning framework with coreset selection, which we call SOFed, to automatically select a coreset that consists of the most representative samples into the replay buffer on each device. It preserves data privacy as each client does not share raw data while learning good visual representations. Experiments demonstrate the effectiveness and significance of the proposed method in visual representation learning.

MiniMax, Aili Chen, Aonian Li et al.

We introduce the MiniMax-M2 series, a family of Mixture-of-Experts language models built around the principle that mini activations can unleash maximum real-world intelligence. The flagship M2 contains 229.9B total parameters with only 9.8B activated per token. Designed end-to-end for agentic deployment, the M2 series rests on three components: (i) agent-driven data pipelines producing large-scale, verifiable trajectories across agentic coding and agentic cowork, each grounded in an executable workspace and an artifact-aligned reward; (ii) Forge, a scalable agent-native RL system that adapts to long-horizon agent trajectories, paired with windowed-FIFO scheduling, prefix-tree merging, inference optimization, and a clean training-inference-agent decoupling that supports both white-box and black-box agents; (iii) the latest M2.7 checkpoint takes an early step toward self-evolution -- autonomously debugging training runs and modifying its own scaffold. Across M2 through M2.7, this combination translates a mini-activation footprint into frontier-tier performance on agentic coding, deep search, office-task, and reasoning benchmarks.

Jun Tao, Qian Chen, James W. Snyder et al.

Marketers employ various online advertising channels to reach customers, and they are particularly interested in attribution for measuring the degree to which individual touchpoints contribute to an eventual conversion. The availability of individual customer-level path-to-purchase data and the increasing number of online marketing channels and types of touchpoints bring new challenges to this fundamental problem. We aim to tackle the attribution problem with finer granularity by conducting attribution at the path level. To this end, we develop a novel graphical point process framework to study the direct conversion effects and the full relational structure among numerous types of touchpoints simultaneously. Utilizing the temporal point process of conversion and the graphical structure, we further propose graphical attribution methods to allocate proper path-level conversion credit, called the attribution score, to individual touchpoints or corresponding channels for each customer's path to purchase. Our proposed attribution methods consider the attribution score as the removal effect, and we use the rigorous probabilistic definition to derive two types of removal effects. We examine the performance of our proposed methods in extensive simulation studies and compare their performance with commonly used attribution models. We also demonstrate the performance of the proposed methods in a real-world attribution application.

Zehua Yu, Weihan Zhang, Sihan Pan et al.

Ordering has been extensively studied in many visualization applications, such as axis and matrix reordering, for the simple reason that the order will greatly impact the perceived pattern of data. Many quality metrics concerning data pattern, perception, and aesthetics are proposed, and respective optimization algorithms are developed. However, the optimization problems related to ordering are often difficult to solve (e.g., TSP is NP-complete), and developing specialized optimization algorithms is costly. In this paper, we propose Versatile Ordering Network (VON), which automatically learns the strategy to order given a quality metric. VON uses the quality metric to evaluate its solutions, and leverages reinforcement learning with a greedy rollout baseline to improve itself. This keeps the metric transparent and allows VON to optimize over different metrics. Additionally, VON uses the attention mechanism to collect information across scales and reposition the data points with respect to the current context. This allows VONs to deal with data points following different distributions. We examine the effectiveness of VON under different usage scenarios and metrics. The results demonstrate that VON can produce comparable results to specialized solvers. The code is available at https://github.com/sysuvis/VON.

Chen Zhang, Liwei Liu, Jun Tao et al.

Scientific time series are central to scientific AI but are typically sparse, highly heterogeneous, and limited in scale, making unified representation learning particularly challenging. Meanwhile, foundation models pretrained on relevant time series domains such as audio, general time series, and brain signals contain rich knowledge, but their applicability to scientific signals remains underexplored. In this paper, we investigate the transferability and complementarity of foundation models from relevant time series domains, and study how to effectively leverage them to build a unified encoder for scientific time series. We first systematically evaluate relevant foundation models, showing the effectiveness of knowledge transfer to scientific tasks and their complementary strengths. Based on this observation, we propose STEP, a Scientific Time Series Encoder Pretraining framework via cross domain distillation. STEP introduces adaptive patching to handle extreme-length sequences and a statistics compensation scheme to accommodate diverse numerical scales. It further leverages cross-domain distillation to integrate knowledge from multiple foundation models into a unified encoder. By combining complementary representations across different domains, STEP learns general-purpose and transferable features tailored for scientific signals. Experiments on seven scientific time series tasks demonstrate that STEP provides both an effective structure and an effective pretraining paradigm, taking a STEP toward scientific time series representation learning.

Pengfei Liu, Jun Tao, Zhixiang Ren

Deep learning has significantly advanced molecular modeling and design, enabling efficient understanding and discovery of novel molecules. In particular, large language models (LLMs) introduce a fresh research paradigm to tackle scientific problems from a natural language processing (NLP) perspective. LLMs significantly enhance our understanding and generation of molecules, often surpassing existing methods with their capabilities to decode and synthesize complex molecular patterns. However, two key issues remain: how to quantify the match between model and data modalities and how to identify the knowledge-learning preferences of models. To address these challenges, we propose a multi-modal benchmark, named ChEBI-20-MM, and perform 1263 experiments to assess the model's compatibility with data modalities and knowledge acquisition. Through the modal transition probability matrix, we provide insights into the most suitable modalities for tasks. Furthermore, we introduce a statistically interpretable approach to discover context-specific knowledge mapping by localized feature filtering. Our analysis offers an exploration of the learning mechanism and paves the way for advancing LLMs in molecular science.

Pengfei Liu, Shuang Ge, Jun Tao et al.

Advancements in artificial intelligence for molecular science are necessitating a paradigm shift from purely data-driven predictions to knowledge-guided computational reasoning. Existing molecular models are predominantly proprietary, lacking general molecular intelligence and generalizability. This underscores the necessity for computational methods that can effectively integrate scientific logic with deep learning architectures. Here we introduce a multi-task large reasoning model designed to emulate the cognitive processes of molecular scientists through structured reasoning and reflection. Our approach incorporates multi-specialist modules to provide versatile molecular expertise and a chain-of-thought (CoT) framework enhanced by reinforcement learning infused with molecular knowledge, enabling structured and reflective reasoning. Systematic evaluations across 10 molecular tasks and 47 metrics demonstrate that our model achieves an average 50.3% improvement over the base architecture, outperforming over 20 state-of-the-art baselines, including ultra-large-parameter foundation models, despite using significantly fewer training data and computational resources. This validates that embedding explicit reasoning mechanisms enables high-efficiency learning, allowing smaller-scale models to surpass massive counterparts in both efficacy and interpretability. The practical utility of this computational framework was validated through a case study on the design of central nervous system (CNS) drug candidates, illustrating its capacity to bridge data-driven and knowledge-integrated approaches for intelligent molecular design.

Pengfei Liu, Jun Tao, Zhixiang Ren

Drug-drug interaction event (DDIE) prediction is crucial for preventing adverse reactions and ensuring optimal therapeutic outcomes. However, existing methods often face challenges with imbalanced datasets, complex interaction mechanisms, and poor generalization to unknown drug combinations. To address these challenges, we propose a knowledge augmentation framework that adaptively infuses prior drug knowledge into a large language model (LLM). This framework utilizes reinforcement learning techniques to facilitate adaptive knowledge extraction and synthesis, thereby efficiently optimizing the strategy space to enhance the accuracy of LLMs for DDIE predictions. As a result of few-shot learning, we achieved a notable improvement compared to the baseline. This approach establishes an effective framework for scientific knowledge learning for DDIE predictions.

Yixiao Liu, Yizhou Yang, Jinwen Li et al.

Remote Sensing Change Detection (RSCD) typically identifies changes in land cover or surface conditions by analyzing multi-temporal images. Currently, most deep learning-based methods primarily focus on learning unimodal visual information, while neglecting the rich semantic information provided by multimodal data such as text. To address this limitation, we propose a novel Language-Guided Change Detection model (LG-CD). This model leverages natural language prompts to direct the network's attention to regions of interest, significantly improving the accuracy and robustness of change detection. Specifically, LG-CD utilizes a visual foundational model (SAM2) as a feature extractor to capture multi-scale pyramid features from high-resolution to low-resolution across bi-temporal remote sensing images. Subsequently, multi-layer adapters are employed to fine-tune the model for downstream tasks, ensuring its effectiveness in remote sensing change detection. Additionally, we design a Text Fusion Attention Module (TFAM) to align visual and textual information, enabling the model to focus on target change regions using text prompts. Finally, a Vision-Semantic Fusion Decoder (V-SFD) is implemented, which deeply integrates visual and semantic information through a cross-attention mechanism to produce highly accurate change detection masks. Our experiments on three datasets (LEVIR-CD, WHU-CD, and SYSU-CD) demonstrate that LG-CD consistently outperforms state-of-the-art change detection methods. Furthermore, our approach provides new insights into achieving generalized change detection by leveraging multimodal information.

Xuan Zhao, Jun Tao

Exploring volumetric data is crucial for interpreting scientific datasets. However, selecting optimal viewpoints for effective navigation can be challenging, particularly for users without extensive domain expertise or familiarity with 3D navigation. In this paper, we propose a novel framework that leverages natural language interaction to enhance volumetric data exploration. Our approach encodes volumetric blocks to capture and differentiate underlying structures. It further incorporates a CLIP Score mechanism, which provides semantic information to the blocks to guide navigation. The navigation is empowered by a reinforcement learning framework that leverage these semantic cues to efficiently search for and identify desired viewpoints that align with the user's intent. The selected viewpoints are evaluated using CLIP Score to ensure that they best reflect the user queries. By automating viewpoint selection, our method improves the efficiency of volumetric data navigation and enhances the interpretability of complex scientific phenomena.

Pengfei Liu, Jun Tao, Zhixiang Ren

The task of chemical reaction predictions (CRPs) plays a pivotal role in advancing drug discovery and material science. However, its effectiveness is constrained by the vast and uncertain chemical reaction space and challenges in capturing reaction selectivity, particularly due to existing methods' limitations in exploiting the data's inherent knowledge. To address these challenges, we introduce a data-curated self-feedback knowledge elicitation approach. This method starts from iterative optimization of molecular representations and facilitates the extraction of knowledge on chemical reaction types (RTs). Then, we employ adaptive prompt learning to infuse the prior knowledge into the large language model (LLM). As a result, we achieve significant enhancements: a 14.2% increase in retrosynthesis prediction accuracy, a 74.2% rise in reagent prediction accuracy, and an expansion in the model's capability for handling multi-task chemical reactions. This research offers a novel paradigm for knowledge elicitation in scientific research and showcases the untapped potential of LLMs in CRPs.

Nan Chen, Zhihong Li, Jun Tao

Flow fields are often partitioned into data blocks for massively parallel computation and analysis based on blockwise relationships. However, most of the previous techniques only consider the first-order dependencies among blocks, which is insufficient in describing complex flow patterns. In this work, we present FlowHON, an approach to construct higher-order networks (HONs) from flow fields. FlowHON captures the inherent higher-order dependencies in flow fields as nodes and estimates the transitions among them as edges. We formulate the HON construction as an optimization problem with three linear transformations. The first two layers correspond to the node generation and the third one corresponds to edge estimation. Our formulation allows the node generation and edge estimation to be solved in a unified framework. With FlowHON, the rich set of traditional graph algorithms can be applied without any modification to analyze flow fields, while leveraging the higher-order information to understand the inherent structure and manage flow data for efficiency. We demonstrate the effectiveness of FlowHON using a series of downstream tasks, including estimating the density of particles during tracing, partitioning flow fields for data management, and understanding flow fields using the node-link diagram representation of networks.

Jun Tao, Bing Li, Lingzhou Xue

We introduce a nonparametric graphical model for discrete node variables based on additive conditional independence. Additive conditional independence is a three way statistical relation that shares similar properties with conditional independence by satisfying the semi-graphoid axioms. Based on this relation we build an additive graphical model for discrete variables that does not suffer from the restriction of a parametric model such as the Ising model. We develop an estimator of the new graphical model via the penalized estimation of the discrete version of the additive precision operator and establish the consistency of the estimator under the ultrahigh-dimensional setting. Along with these methodological developments, we also exploit the properties of discrete random variables to uncover a deeper relation between additive conditional independence and conditional independence than previously known. The new graphical model reduces to a conditional independence graphical model under certain sparsity conditions. We conduct simulation experiments and analysis of an HIV antiretroviral therapy data set to compare the new method with existing ones.

Yifan Xu, Pan Xu, Jianping Pan et al.

With the popularity of the Internet, traditional offline resource allocation has evolved into a new form, called online resource allocation. It features the online arrivals of agents in the system and the real-time decision-making requirement upon the arrival of each online agent. Both offline and online resource allocation have wide applications in various real-world matching markets ranging from ridesharing to crowdsourcing. There are some emerging applications such as rebalancing in bike sharing and trip-vehicle dispatching in ridesharing, which involve a two-stage resource allocation process. The process consists of an offline phase and another sequential online phase, and both phases compete for the same set of resources. In this paper, we propose a unified model which incorporates both offline and online resource allocation into a single framework. Our model assumes non-uniform and known arrival distributions for online agents in the second online phase, which can be learned from historical data. We propose a parameterized linear programming (LP)-based algorithm, which is shown to be at most a constant factor of $1/4$ from the optimal. Experimental results on the real dataset show that our LP-based approaches outperform the LP-agnostic heuristics in terms of robustness and effectiveness.

Zhengqi Gao, Jun Tao, Yangfeng Su et al.

Pareto Front (PF) modeling is essential in decision making problems across all domains such as economics, medicine or engineering. In Operation Research literature, this task has been addressed based on multi-objective optimization algorithms. However, without learning models for PF, these methods cannot examine whether a new provided point locates on PF or not. In this paper, we reconsider the task from Data Mining perspective. A novel projection based active Gaussian process regression (P- aGPR) method is proposed for efficient PF modeling. First, P- aGPR chooses a series of projection spaces with dimensionalities ranking from low to high. Next, in each projection space, a Gaussian process regression (GPR) model is trained to represent the constraint that PF should satisfy in that space. Moreover, in order to improve modeling efficacy and stability, an active learning framework has been developed by exploiting the uncertainty information obtained in the GPR models. Different from all existing methods, our proposed P-aGPR method can not only provide a generative PF model, but also fast examine whether a provided point locates on PF or not. The numerical results demonstrate that compared to state-of-the-art passive learning methods the proposed P-aGPR method can achieve higher modeling accuracy and stability.