Siyuan Liu

Xueyang Wu, Siyuan Liu, Kezhuo Yang et al.

Speech-based mental health screening offers scalable depression detection, yet clinical deployment faces a significant barrier: users' privacy concerns about demographic information exposure. Current techniques struggle to resolve this conflict. Adversarial training often fails against unseen threats, whereas Differential Privacy tends to compromise diagnostic performance by injecting noise across all features. This paper presents InfoShield, which minimizes mutual information between speech representations and sensitive attributes while preserving depression classification accuracy. We identify that standard MINE estimators struggle with sequential speech due to temporal-static misalignment, and introduce TimeAwareMINE with cross-modal attention to align acoustic frames with attribute embeddings. Experiments on the Androids Corpus show InfoShield reduces gender inference from 92.6\% to 55.5\% and age inference from 55.7\% to 30.3\% with limited utility loss (6\% F1 reduction), achieving F1=0.784 compared to prior SOTA's 0.723.

Kanghui Tian, Siyuan Liu, Ziang Yan et al.

On-policy distillation (OPD) improves reasoning by training a student on trajectories sampled from its own policy under supervision from a teacher. In multimodal reasoning, a common extension is to use a privileged teacher that observes training-time-only signals such as reference answers or rationales. However, such answer-side privilege creates a train-test mismatch: the teacher's supervision may depend on signals unavailable to the student, encouraging shortcut imitation rather than visually grounded reasoning. We propose ViCuR, a visually grounded privileged-teacher distillation framework that replaces answer-side privilege with visual cues (query-related evidence in the input). Because these cues are derived from the same visual input available at inference, their evidence is recoverable by the student. To support this, ViCuR introduces a lightweight cue recovery module that uses dedicated sink-token cross-attention during prefill to aggregate task-relevant visual evidence into an internal representation, without changing the inference interface or requiring auxiliary cue-generation losses. Across seven benchmarks with Qwen3-VL-2B and 8B students, ViCuR consistently improves over answer-based on-policy self-distillation by +1.19 and +1.24 on overall average performance. It also extends naturally to stronger-teacher OPD, surpassing OPD baselines by +0.64 and +1.08, with consistent out-of-domain gains at the 8B scale. These results show that, in multimodal on-policy distillation, the design of teacher privilege is as important as teacher strength.

Jiachen Zhang, Junyi Lao, Chenghao Liu et al.

Finite Element Analysis (FEA) serves as the cornerstone of modern engineering design. However, its workflow is inherently complex and relies heavily on domain expertise. Although recent efforts have integrated Large Language Models (LLMs) into FEA, existing approaches face limitations in handling multimodal inputs and executing complex tasks. To address these limitations, we propose VFEAgent, an end-to-end multi-agent system designed to automate FEA modeling and simulation directly from input images and problem descriptions. Our methodology integrates two core components: (1) a multimodal vision-language multi-agent pipeline that employs ReAct-driven reasoning to extract structured FEA specifications from heterogeneous inputs and (2) a verification-first code synthesis framework, incorporating robust self-debugging and fallback mechanisms to ensure executability and physical validity. We systematically evaluated the system across various engineering mechanics scenarios. The results demonstrate that VFEAgent achieves a high success rate in generating complete and physically valid simulations, outperforming LLM-based baseline methods in reliability and correctness. These findings validate the feasibility of automating the complete FEA workflow, highlighting the framework's potential to liberate engineers from tedious manual analysis.

Jiahao Ying, Boxian Ai, Wei Tang et al.

Skills, i.e., structured workflow instructions distilled for large language models (LLMs), are becoming an increasingly important mechanism for improving agent performance on real-world downstream tasks. However, as the open-source skill ecosystem rapidly expands, it remains unclear how different models and agent frameworks interact with skills, how to evaluate skill quality, and how users should select skills under practical cost-performance trade-offs. In this paper, we present \textsc{OpenSkillEval}, an automatic evaluation framework for both skill-augmented agent systems and the skills themselves. Instead of relying on static benchmarks, \textsc{OpenSkillEval} automatically constructs realistic task instances from evolving real-world artifacts across five categories of downstream applications: presentation generation, front-end web design, poster generation, data visualization, and report generation. It further collects and organizes community-contributed skills for controlled comparison under unified task settings. Using more than 600 dynamically generated task instances and 30 open-source skills, we conduct a systematic evaluation of state-of-the-art models and agent frameworks. Our results show that skill availability does not guarantee effective skill usage, that the benefit of skill augmentation depends strongly on both the underlying model and the agent framework, and that many publicly popular skills do not consistently outperform base agents without skills. These findings highlight the need for dynamic, task-grounded evaluation and provide practical insights into the design, selection, and deployment of skills for LLM agents. Additional cases and benchmark resources are available on the project website: https://yingjiahao14.github.io/OpenSkillEval-Web/.

Zehui Dong, Wenjing Liu, Siyuan Liu et al.

Federated Semi-supervised Learning (FSSL) combines techniques from both fields of federated and semi-supervised learning to improve the accuracy and performance of models in a distributed environment by using a small fraction of labeled data and a large amount of unlabeled data. Without the need to centralize all data in one place for training, it collect updates of model training after devices train models at local, and thus can protect the privacy of user data. However, during the federal training process, some of the devices fail to collect enough data for local training, while new devices will be included to the group training. This leads to an unbalanced global data distribution and thus affect the performance of the global model training. Most of the current research is focusing on class imbalance with a fixed number of classes, while little attention is paid to data imbalance with a variable number of classes. Therefore, in this paper, we propose Federated Semi-supervised Learning for Class Variable Imbalance (FCVI) to solve class variable imbalance. The class-variable learning algorithm is used to mitigate the data imbalance due to changes of the number of classes. Our scheme is proved to be significantly better than baseline methods, while maintaining client privacy.

Tommaso Zaccherini, Siyuan Liu, Dimos V. Dimarogonas

This paper addresses decentralized control of large-scale heterogeneous multi-agent systems subject to bounded external disturbances and limited communication, with the objective of satisfying cooperative Signal Temporal Logic (STL) specifications. The considered specifications involve spatiotemporal tasks that require collaboration among multiple agents, including agents beyond direct communication neighborhoods. To address the communication constraints, a $k$-hop Prescribed Performance State Observer ($k$-hop PPSO) is designed to enable each agent to estimate the states of agents up to $k$ communication hops away using only information from $1$-hop neighbors, while guaranteeing predefined performance bounds on the estimation errors. The estimation error bounds are explicitly incorporated into a reformulation of the spatial robustness of the STL specifications, yielding robustness measures that account for worst-case estimation uncertainty. Based on the modified robustness, a decentralized continuous-time feedback control law is designed to guarantee satisfaction of the STL specifications in the presence of bounded disturbances and estimation errors. The proposed framework provides formal correctness guarantees using only local information and limited communication. Numerical simulations illustrate the theoretical results.

Xiaoyang Chen, Jinjian Wu, Wenjiao Lyu et al.

Automatic segmentation of brain MR images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) is critical for tissue volumetric analysis and cortical surface reconstruction. Due to dramatic structural and appearance changes associated with developmental and aging processes, existing brain tissue segmentation methods are only viable for specific age groups. Consequently, methods developed for one age group may fail for another. In this paper, we make the first attempt to segment brain tissues across the entire human lifespan (0-100 years of age) using a unified deep learning model. To overcome the challenges related to structural variability underpinned by biological processes, intensity inhomogeneity, motion artifacts, scanner-induced differences, and acquisition protocols, we propose to use contrastive learning to improve the quality of feature representations in a latent space for effective lifespan tissue segmentation. We compared our approach with commonly used segmentation methods on a large-scale dataset of 2,464 MR images. Experimental results show that our model accurately segments brain tissues across the lifespan and outperforms existing methods.

He Zhang, Siyuan Liu, Jiacheng You et al.

Orbital-free density functional theory (OFDFT) is a quantum chemistry formulation that has a lower cost scaling than the prevailing Kohn-Sham DFT, which is increasingly desired for contemporary molecular research. However, its accuracy is limited by the kinetic energy density functional, which is notoriously hard to approximate for non-periodic molecular systems. Here we propose M-OFDFT, an OFDFT approach capable of solving molecular systems using a deep learning functional model. We build the essential non-locality into the model, which is made affordable by the concise density representation as expansion coefficients under an atomic basis. With techniques to address unconventional learning challenges therein, M-OFDFT achieves a comparable accuracy with Kohn-Sham DFT on a wide range of molecules untouched by OFDFT before. More attractively, M-OFDFT extrapolates well to molecules much larger than those seen in training, which unleashes the appealing scaling of OFDFT for studying large molecules including proteins, representing an advancement of the accuracy-efficiency trade-off frontier in quantum chemistry.

MiniCPM Team, Wenhao An, Yingfa Chen et al. · tsinghua

The evolution of large language models (LLMs) towards applications with ultra-long contexts faces challenges posed by the high computational and memory costs of the Transformer architecture. While existing sparse and linear attention mechanisms attempt to mitigate these issues, they typically involve a trade-off between memory efficiency and model performance. This paper introduces MiniCPM-SALA, a 9B-parameter hybrid architecture that integrates the high-fidelity long-context modeling of sparse attention (InfLLM-V2) with the global efficiency of linear attention (Lightning Attention). By employing a layer selection algorithm to integrate these mechanisms in a 1:3 ratio and utilizing a hybrid positional encoding (HyPE), the model maintains efficiency and performance for long-context tasks. Furthermore, we introduce a cost-effective continual training framework that transforms pre-trained Transformer-based models into hybrid models, which reduces training costs by approximately 75% compared to training from scratch. Extensive experiments show that MiniCPM-SALA maintains general capabilities comparable to full-attention models while offering improved efficiency. On a single NVIDIA A6000D GPU, the model achieves up to 3.5x the inference speed of the full-attention model at the sequence length of 256K tokens and supports context lengths of up to 1M tokens, a scale where traditional full-attention 8B models fail because of memory constraints.

Cheryl Wang, Chun Kwang Tan, Balint K. Hodossy et al.

Athletic performance represents the pinnacle of human motor intelligence, demanding rapid choices, precise control, agility, and coordinated physical execution. Replicating this seamless combination of capabilities remains elusive in current artificial intelligence and robotic systems. Concurrently, understanding the biological mastery of these movements is hindered because complex muscle coordination is rarely measured in vivo due to the limitations of physical equipment. To bridge this fundamental gap in understanding, MyoChallenge at NeurIPS 2025 established a pioneering benchmark for motor control intelligence in sports, leveraging high-fidelity musculoskeletal models within physics simulation combined with machine learning-driven algorithms. The competition introduces two distinct tracks emphasizing either upper or lower limbs control: a table tennis rally task utilizing a biomechanic upper limb composed of an arm with a hand and a trunk; and a soccer penalty kick using a biomechanic model of legs and a trunk. Marking the fourth iteration of the MyoChallenge series, this event attracted almost 70 teams and over 560 submissions globally, uniting a diverse community ranging from physicians and neuroscientists to machine learning experts. The competition facilitated the development of several state-of-the-art control algorithms for a musculoskeletal system capable of sports agility, leveraging techniques such as physics-based motion planners, on-policy behaviour cloning, hierarchical planning, and muscle synergies. By integrating standardized tasks and physiologically realistic models into the open-source framework of MyoSuite, MyoChallenge'25 serves as a reproducible and reusable testbed to accelerate interdisciplinary research across machine learning, biomechanics, sports science, and neuroscience. Project page: https://www.myosuite.org//myochallenge/myochallenge-2025.

Ruohan Wang, Siyuan Liu, Zhiyong Sun et al.

Discrete-time stochastic systems with continuous spaces are hard to verify and control, even with MDP abstractions due to the curse of dimensionality. We propose an abstraction-based framework with robust dynamic programming mappings that deliver control strategies with provable lower bounds on temporal-logic satisfaction, quantified via approximate stochastic simulation relations. Exploiting decoupled dynamics, we reveal a Canonical Polyadic Decomposition tensor structure in value functions that makes dynamic programming scalable. The proposed method provides correct-by-design probabilistic guarantees for temporal logic specifications. We validate our results on continuous-state linear stochastic systems.

Qiang Gao, Xinzhu Zhou, Kunpeng Zhang et al.

Stock selection attempts to rank a list of stocks for optimizing investment decision making, aiming at minimizing investment risks while maximizing profit returns. Recently, researchers have developed various (recurrent) neural network-based methods to tackle this problem. Without exceptions, they primarily leverage historical market volatility to enhance the selection performance. However, these approaches greatly rely on discrete sampled market observations, which either fail to consider the uncertainty of stock fluctuations or predict continuous stock dynamics in the future. Besides, some studies have considered the explicit stock interdependence derived from multiple domains (e.g., industry and shareholder). Nevertheless, the implicit cross-dependencies among different domains are under-explored. To address such limitations, we present a novel stock selection solution -- StockODE, a latent variable model with Gaussian prior. Specifically, we devise a Movement Trend Correlation module to expose the time-varying relationships regarding stock movements. We design Neural Recursive Ordinary Differential Equation Networks (NRODEs) to capture the temporal evolution of stock volatility in a continuous dynamic manner. Moreover, we build a hierarchical hypergraph to incorporate the domain-aware dependencies among the stocks. Experiments conducted on two real-world stock market datasets demonstrate that StockODE significantly outperforms several baselines, such as up to 18.57% average improvement regarding Sharpe Ratio.

Xinze Li, Ziyue Zhu, Siyuan Liu et al.

We introduce EMemBench, a programmatic benchmark for evaluating long-term memory of agents through interactive games. Rather than using a fixed set of questions, EMemBench generates questions from each agent's own trajectory, covering both text and visual game environments. Each template computes verifiable ground truth from underlying game signals, with controlled answerability and balanced coverage over memory skills: single/multi-hop recall, induction, temporal, spatial, logical, and adversarial. We evaluate memory agents with strong LMs/VLMs as backbones, using in-context prompting as baselines. Across 15 text games and multiple visual seeds, results are far from saturated: induction and spatial reasoning are persistent bottlenecks, especially in visual setting. Persistent memory yields clear gains for open backbones on text games, but improvements are less consistent for VLM agents, suggesting that visually grounded episodic memory remains an open challenge. A human study further confirms the difficulty of EMemBench.

Xinyuan Qiu, Ruohan Wang, Siyuan Liu et al.

Correct-by-design synthesis provides a principled framework for establishing formal safety guarantees for stochastic multi-agent systems (MAS). However, conventional approaches based on finite abstractions often incur prohibitive computational costs as the number of agents and the complexity of temporal logic specifications increase. In this work, we study homogeneous stochastic MAS under counting linear temporal logic (cLTL) specifications, and show that the corresponding satisfaction probability admits a structured tensor decomposition via leveraging deterministic finite automata (DFA). Building on this structure, we develop a dual-tree-based value iteration framework that reduces redundant computation in the process of dynamic programming. Numerical results demonstrate the proposed approach's effectiveness and scalability for complex specifications and large-scale MAS.

Veera Raghava Reddy Kovvuri, Siyuan Liu, Monika Seisenberger et al.

Feature attribution XAI algorithms enable their users to gain insight into the underlying patterns of large datasets through their feature importance calculation. Existing feature attribution algorithms treat all features in a dataset homogeneously, which may lead to misinterpretation of consequences of changing feature values. In this work, we consider partitioning features into controllable and uncontrollable parts and propose the Controllable fActor Feature Attribution (CAFA) approach to compute the relative importance of controllable features. We carried out experiments applying CAFA to two existing datasets and our own COVID-19 non-pharmaceutical control measures dataset. Experimental results show that with CAFA, we are able to exclude influences from uncontrollable features in our explanation while keeping the full dataset for prediction.

Wenjin Xie, Siyuan Liu, Xiaomeng Wang et al.

Name ambiguity is common in academic digital libraries, such as multiple authors having the same name. This creates challenges for academic data management and analysis, thus name disambiguation becomes necessary. The procedure of name disambiguation is to divide publications with the same name into different groups, each group belonging to a unique author. A large amount of attribute information in publications makes traditional methods fall into the quagmire of feature selection. These methods always select attributes artificially and equally, which usually causes a negative impact on accuracy. The proposed method is mainly based on representation learning for heterogeneous networks and clustering and exploits the self-attention technology to solve the problem. The presentation of publications is a synthesis of structural and semantic representations. The structural representation is obtained by meta-path-based sampling and a skip-gram-based embedding method, and meta-path level attention is introduced to automatically learn the weight of each feature. The semantic representation is generated using NLP tools. Our proposal performs better in terms of name disambiguation accuracy compared with baselines and the ablation experiments demonstrate the improvement by feature selection and the meta-path level attention in our method. The experimental results show the superiority of our new method for capturing the most attributes from publications and reducing the impact of redundant information.

Siyuan Liu, Jiahui Xu, Feng Jiang et al.

Achieving human-like responsiveness is a critical yet challenging goal for cascaded spoken dialogue systems. Conventional ASR-LLM-TTS pipelines follow a strictly sequential paradigm, requiring complete transcription and full reasoning before speech synthesis can begin, which results in high response latency. We propose the Discourse-Aware Dual-Track Streaming Response (DDTSR) framework, a low-latency architecture that enables listen-while-thinking and speak-while-thinking. DDTSR is built upon three key mechanisms: (1) connective-guided small-large model synergy, where an auxiliary small model generates minimal-committal discourse connectives while a large model performs knowledge-intensive reasoning in parallel; (2) streaming-based cross-modal collaboration, which dynamically overlaps ASR, LLM inference, and TTS to advance the earliest speakable moment; and (3) curriculum-learning-based discourse continuity enhancement, which maintains coherence and logical consistency between early responses and subsequent reasoning outputs. Experiments on two spoken dialogue benchmarks demonstrate that DDTSR reduces response latency by 19%-51% while preserving discourse quality. Further analysis shows that DDTSR functions as a plug-and-play module compatible with diverse LLM backbones, and remains robust across varying utterance lengths, indicating strong practicality and scalability for real-time spoken interaction.

Xiaoyan Liu, Zehui Dong, Zhiwei Xu et al.

Advanced researches on connected vehicles have recently targeted to the integration of vehicle-to-everything (V2X) networks with Machine Learning (ML) tools and distributed decision making. Federated learning (FL) is emerging as a new paradigm to train machine learning (ML) models in distributed systems, including vehicles in V2X networks. Rather than sharing and uploading the training data to the server, the updating of model parameters (e.g., neural networks' weights and biases) is applied by large populations of interconnected vehicles, acting as local learners. Despite these benefits, the limitation of existing approaches is the centralized optimization which relies on a server for aggregation and fusion of local parameters, leading to the drawback of a single point of failure and scaling issues for increasing V2X network size. Meanwhile, in intelligent transport scenarios, data collected from onboard sensors are redundant, which degrades the performance of aggregation. To tackle these problems, we explore a novel idea of decentralized data processing and introduce a federated learning framework for in-network vehicles, C-DFL(Consensus based Decentralized Federated Learning), to tackle federated learning on connected vehicles and improve learning quality. Extensive simulations have been implemented to evaluate the performance of C-DFL, that demonstrates C-DFL outperforms the performance of conventional methods in all cases.

Shengxin Hong, Chang Cai, Sixuan Du et al.

Interactive feedback, where feedback flows in both directions between teacher and student, is more effective than traditional one-way feedback. However, it is often too time-consuming for widespread use in educational practice. While Large Language Models (LLMs) have potential for automating feedback, they struggle with reasoning and interaction in an interactive setting. This paper introduces CAELF, a Contestable AI Empowered LLM Framework for automating interactive feedback. CAELF allows students to query, challenge, and clarify their feedback by integrating a multi-agent system with computational argumentation. Essays are first assessed by multiple Teaching-Assistant Agents (TA Agents), and then a Teacher Agent aggregates the evaluations through formal reasoning to generate feedback and grades. Students can further engage with the feedback to refine their understanding. A case study on 500 critical thinking essays with user studies demonstrates that CAELF significantly improves interactive feedback, enhancing the reasoning and interaction capabilities of LLMs. This approach offers a promising solution to overcoming the time and resource barriers that have limited the adoption of interactive feedback in educational settings.

Siyuan Liu, Jiawei Du, Sicheng Xiang et al.

Long-horizon embodied planning underpins embodied AI. To accomplish long-horizon tasks, one of the most feasible ways is to decompose abstract instructions into a sequence of actionable steps. Foundation models still face logical errors and hallucinations in long-horizon planning, unless provided with highly relevant examples to the tasks. However, providing highly relevant examples for any random task is unpractical. Therefore, we present ReLEP, a novel framework for Real-time Long-horizon Embodied Planning. ReLEP can complete a wide range of long-horizon tasks without in-context examples by learning implicit logical inference through fine-tuning. The fine-tuned large vision-language model formulates plans as sequences of skill functions. These functions are selected from a carefully designed skill library. ReLEP is also equipped with a Memory module for plan and status recall, and a Robot Configuration module for versatility across robot types. In addition, we propose a data generation pipeline to tackle dataset scarcity. When constructing the dataset, we considered the implicit logical relationships, enabling the model to learn implicit logical relationships and dispel hallucinations. Through comprehensive evaluations across various long-horizon tasks, ReLEP demonstrates high success rates and compliance to execution even on unseen tasks and outperforms state-of-the-art baseline methods.

Dongzhe Fan, Zheyi Xue, Siyuan Liu et al.

Retrieval-augmented generation (RAG) and its graph-based extensions (GraphRAG) are effective paradigms for improving large language model (LLM) reasoning by grounding generation in external knowledge. However, most existing RAG and GraphRAG systems operate under static or one-shot retrieval, where a fixed set of documents is provided to the LLM in a single pass. In contrast, recent agentic search systems enable dynamic, multi-round retrieval and sequential decision-making during inference, and have shown strong gains when combined with vanilla RAG by introducing implicit structure through interaction. This progress raises a fundamental question: can agentic search compensate for the absence of explicit graph structure, reducing the need for costly GraphRAG pipelines? To answer this question, we introduce RAGSearch, a unified benchmark that evaluates dense RAG and representative GraphRAG methods as retrieval infrastructures under agentic search. RAGSearch covers both training-free and training-based agentic inference across multiple question answering benchmarks. To ensure fair and reproducible comparison, we standardize the LLM backbone, retrieval budgets, and inference protocols, and report results on full test sets. Beyond answer accuracy, we report offline preprocessing cost, online inference efficiency, and stability. Our results show that agentic search substantially improves dense RAG and narrows the performance gap to GraphRAG, particularly in RL-based settings. Nevertheless, GraphRAG remains advantageous for complex multi-hop reasoning, exhibiting more stable agentic search behavior when its offline cost is amortized. Together, these findings clarify the complementary roles of explicit graph structure and agentic search, and provide practical guidance on retrieval design for modern agentic RAG systems.

Georgios Mitsos, Dimos V. Dimarogonas, Siyuan Liu

This paper presents a secure-by-construction planning and control framework for multi-agent systems subject to linear temporal logic (LTL) specifications. The framework protects sensitive information from a passive intruder with partial observations of the agents' motion. Security in multi-agent coordination is captured by two notions that prevent the intruder from inferring whether a secret task has been executed and from identifying the agent responsible for its execution. The proposed framework incorporates the security constraints directly into the LTL synthesis procedure by constructing a secure finite transition system that removes all paths violating these constraints. Standard LTL synthesis is then applied to this secure abstraction to generate discrete plans, which are then refined into dynamically feasible continuous trajectories. This synthesis procedure provides formal guarantees that the resulting behavior of the multi-agent system satisfies both the global LTL specification and the security constraints. The effectiveness of the proposed framework is demonstrated through a two-drone case study.

Siyuan Liu, Tinghong Chen, Xinghan Li et al.

Data selection during supervised fine-tuning (SFT) can critically change the behavior of large language models (LLMs). Although existing work has studied the effect of selecting data based on heuristics such as perplexity, difficulty, or length, the reported findings are often inconsistent or context-dependent. In this work, we systematically study the role of data difficulty in fine-tuning from both empirical and theoretical perspectives, and find that there is no universally optimal difficulty level; rather, its effectiveness depends on the dataset size. We show that for a fixed data budget, there exists an optimal data difficulty for SFT, and that this optimal difficulty shifts toward harder data as the data budget increases. To explain this phenomenon, we conduct controlled synthetic experiments that reveal a simple underlying mechanism: the interplay between the (in-distribution) generalization gap and the extrapolation gap. We further support this mechanism through a theoretical analysis using PAC-Bayesian generalization bounds. Overall, our results clarify how data size and difficulty jointly affect the trade-off between generalization and extrapolation in SFT, providing guidance for difficulty-based data selection under certain model and data conditions.

Siyuan Liu, Chaoqun Zheng, Xin Zhou et al.

Scene-level point cloud understanding remains challenging due to diverse geometries, imbalanced category distributions, and highly varied spatial layouts. Existing methods improve object-level performance but rely on static network parameters during inference, limiting their adaptability to dynamic scene data. We propose PointTPA, a Test-time Parameter Adaptation framework that generates input-aware network parameters for scene-level point clouds. PointTPA adopts a Serialization-based Neighborhood Grouping (SNG) to form locally coherent patches and a Dynamic Parameter Projector (DPP) to produce patch-wise adaptive weights, enabling the backbone to adjust its behavior according to scene-specific variations while maintaining a low parameter overhead. Integrated into the PTv3 structure, PointTPA demonstrates strong parameter efficiency by introducing two lightweight modules of less than 2% of the backbone's parameters. Despite this minimal parameter overhead, PointTPA achieves 78.4% mIoU on ScanNet validation, surpassing existing parameter-efficient fine-tuning (PEFT) methods across multiple benchmarks, highlighting the efficacy of our test-time dynamic network parameter adaptation mechanism in enhancing 3D scene understanding. The code is available at https://github.com/H-EmbodVis/PointTPA.

Siyuan Liu, Zhice Yang, Huangxun Chen

Multimodal IoT systems coordinate diverse IoT devices to deliver human-centered services. The ability to incorporate new IoT devices under the management of a centralized platform is an essential requirement. However, it requires significant human expertise and effort to program the complex IoT integration code that enables the platform to understand and control the device functions. Therefore, we propose AutoBridge to automate IoT integration code generation. Specifically, AutoBridge adopts a divide-and-conquer strategy: it first generates device control logic by progressively retrieving device-specific knowledge, then synthesizes platformcompliant integration code using platform-specific knowledge. To ensure correctness, AutoBridge features a multi-stage debugging pipeline, including an automated debugger for virtual IoT device testing and an interactive hardware-in-the-loop debugger that requires only binary user feedback (yes and no) for real-device verification. We evaluate AutoBridge on a benchmark of 34 IoT devices across two open-source IoT platforms. The results demonstrate that AutoBridge can achieves an average success rate of 93.87% and an average function coverage of 94.87%, without any human involvement. With minimal binary yes and no feedback from users, the code is then revised to reach 100% function coverage. A user study with 15 participants further shows that AutoBridge outperforms expert programmers by 50% to 80% in code accuracy, even when the programmers are allowed to use commercial code LLMs.

Jingbo Zhou, Qi Guo, H. V. Jagadish et al.

We propose a novel generic inverted index framework on the GPU (called GENIE), aiming to reduce the programming complexity of the GPU for parallel similarity search of different data types. Not every data type and similarity measure are supported by GENIE, but many popular ones are. We present the system design of GENIE, and demonstrate similarity search with GENIE on several data types along with a theoretical analysis of search results. A new concept of locality sensitive hashing (LSH) named $τ$-ANN search, and a novel data structure c-PQ on the GPU are also proposed for achieving this purpose. Extensive experiments on different real-life datasets demonstrate the efficiency and effectiveness of our framework. The implemented system has been released as open source.

Siyuan Liu, Hongbang Yuan, Xinze Li et al.

Large language model (LLM) agents have demonstrated remarkable capabilities in complex decision-making and tool-use tasks, yet their ability to generalize across varying environments remains a under-examined concern. Current evaluation paradigms predominantly rely on trajectory-based metrics that measure task success, while failing to assess whether agents possess a grounded, transferable model of the environment. To address this gap, we propose Task-to-Quiz (T2Q), a deterministic and automated evaluation paradigm designed to decouple task execution from world-state understanding. We instantiate this paradigm in T2QBench, a suite comprising 30 environments and 1,967 grounded QA pairs across multiple difficulty levels. Our extensive experiments reveal that task success is often a poor proxy for environment understanding, and that current memory machanism can not effectively help agents acquire a grounded model of the environment. These findings identify proactive exploration and fine-grained state representation as primary bottlenecks, offering a robust foundation for developing more generalizable autonomous agents.

Siyuan Liu, Wenjin Xie, Wenyu Chen et al.

Purpose: This study compares the hierarchical structure of scientific teams across countries and investigates factors associated with the observed cross-national differences. Design/methodology/approach: Drawing on 150,817 publications with author contribution statements, we focus on the 15 countries with the largest volume of scientific publications, examine cross-country variations in the proportion of tall teams, and analyze how this proportion correlates with other factors. Findings: Scientific output from East Asia is dominated by tall teams, which persist after controlling for team size, indicating that this pattern cannot be fully accounted for by the prevalence of larger teams in these countries. Cultural factors, measured by Power Distance, as well as the observed funding patterns of major basic science agencies, are associated with the dominance of tall teams in East Asia. Research limitations: This study is limited by its reliance on publications with author contribution statements, which may introduce selection bias; its focus on cultural and funding factors, while leaving other institutional contexts unexamined; and its use of a leadership concentration measure that does not capture other dimensions of hierarchy. Practical implications: Understanding cross-national differences in research team structures and their associated cultural and institutional factors can inform science policy and team management. Originality/value: This study provides a systematic cross-national comparison of team hierarchy and offers a mechanistic understanding of the dominance of tall teams in East Asia, highlighting associations with cultural and funding factors.

Xin Li, Yeying Jin, Xin Jin et al.

This paper reviews the NTIRE 2025 Challenge on Day and Night Raindrop Removal for Dual-Focused Images. This challenge received a wide range of impressive solutions, which are developed and evaluated using our collected real-world Raindrop Clarity dataset. Unlike existing deraining datasets, our Raindrop Clarity dataset is more diverse and challenging in degradation types and contents, which includes day raindrop-focused, day background-focused, night raindrop-focused, and night background-focused degradations. This dataset is divided into three subsets for competition: 14,139 images for training, 240 images for validation, and 731 images for testing. The primary objective of this challenge is to establish a new and powerful benchmark for the task of removing raindrops under varying lighting and focus conditions. There are a total of 361 participants in the competition, and 32 teams submitting valid solutions and fact sheets for the final testing phase. These submissions achieved state-of-the-art (SOTA) performance on the Raindrop Clarity dataset. The project can be found at https://lixinustc.github.io/CVPR-NTIRE2025-RainDrop-Competition.github.io/.

Le Shen, Qian Qiao, Tan Yu et al.

Deploying massive diffusion models for real-time, infinite-duration, audio-driven avatar generation presents a significant engineering challenge, primarily due to the conflict between computational load and strict latency constraints. Existing approaches often compromise visual fidelity by enforcing strictly unidirectional attention mechanisms or reducing model capacity. To address this problem, we introduce \textbf{SoulX-FlashTalk}, a 14B-parameter framework optimized for high-fidelity real-time streaming. Diverging from conventional unidirectional paradigms, we use a \textbf{Self-correcting Bidirectional Distillation} strategy that retains bidirectional attention within video chunks. This design preserves critical spatiotemporal correlations, significantly enhancing motion coherence and visual detail. To ensure stability during infinite generation, we incorporate a \textbf{Multi-step Retrospective Self-Correction Mechanism}, enabling the model to autonomously recover from accumulated errors and preventing collapse. Furthermore, we engineered a full-stack inference acceleration suite incorporating hybrid sequence parallelism, Parallel VAE, and kernel-level optimizations. Extensive evaluations confirm that SoulX-FlashTalk is the first 14B-scale system to achieve a \textbf{sub-second start-up latency (0.87s)} while reaching a real-time throughput of \textbf{32 FPS}, setting a new standard for high-fidelity interactive digital human synthesis.

Qingsi Lai, Fanjie Xu, Lin Yao et al.

Powder X-ray diffraction (PXRD) is a prevalent technique in materials characterization. While the analysis of PXRD often requires extensive human manual intervention, and most automated method only achieved at coarse-grained level. The more difficult and important task of fine-grained crystal structure prediction from PXRD remains unaddressed. This study introduces XtalNet, the first equivariant deep generative model for end-to-end crystal structure prediction from PXRD. Unlike previous crystal structure prediction methods that rely solely on composition, XtalNet leverages PXRD as an additional condition, eliminating ambiguity and enabling the generation of complex organic structures with up to 400 atoms in the unit cell. XtalNet comprises two modules: a Contrastive PXRD-Crystal Pretraining (CPCP) module that aligns PXRD space with crystal structure space, and a Conditional Crystal Structure Generation (CCSG) module that generates candidate crystal structures conditioned on PXRD patterns. Evaluation on two MOF datasets (hMOF-100 and hMOF-400) demonstrates XtalNet's effectiveness. XtalNet achieves a top-10 Match Rate of 90.2% and 79% for hMOF-100 and hMOF-400 in conditional crystal structure prediction task, respectively. XtalNet enables the direct prediction of crystal structures from experimental measurements, eliminating the need for manual intervention and external databases. This opens up new possibilities for automated crystal structure determination and the accelerated discovery of novel materials.

Yuxin Liu, Mingye Zhu, Siyuan Liu et al.

The utility of Role-Playing Language Agents in sociological research is growing alongside the adoption of Large Language Models. For realism in social simulation, these agents must adhere to their personas defined by character profiles, yet existing strategies-static prompt engineering or costly fine-tuning-fail to adapt personas to dynamic scenarios. Psychological theories, such as the Cognitive-Affective Personality Systems, provide a crucial explanation for this failure: a persona's influence on behavior is not static but varies with the scenarios. This context-dependence highlights the critical need for adaptive persona management. To address this gap, we propose a novel, theory-driven method that dynamically estimates context-dependent persona importance and integrates it into weighted reward-guided decoding, enabling inference-time persona following. Specifically, we introduce the Persona Dynamic Decoding (PDD) framework, which consists of two key components: (1) Persona Importance Estimation (PIE) module, which dynamically quantifies the contextual importance of persona attributes without requiring ground-truth supervision; and (2) Persona-Guided Inference-Time Alignment (PIA) paradigm, which leverages these importance scores to construct weighted multi-objective rewards and modulate generation probabilities during inference. Extensive experiments show the effectiveness of our method in utterance consistency and behavioral fidelity.

Dingcheng Zhen, Shunshun Yin, Shiyang Qin et al.

In this work, we introduce the first autoregressive framework for real-time, audio-driven portrait animation, a.k.a, talking head. Beyond the challenge of lengthy animation times, a critical challenge in realistic talking head generation lies in preserving the natural movement of diverse body parts. To this end, we propose Teller, the first streaming audio-driven protrait animation framework with autoregressive motion generation. Specifically, Teller first decomposes facial and body detail animation into two components: Facial Motion Latent Generation (FMLG) based on an autoregressive transfromer, and movement authenticity refinement using a Efficient Temporal Module (ETM).Concretely, FMLG employs a Residual VQ model to map the facial motion latent from the implicit keypoint-based model into discrete motion tokens, which are then temporally sliced with audio embeddings. This enables the AR tranformer to learn real-time, stream-based mappings from audio to motion. Furthermore, Teller incorporate ETM to capture finer motion details. This module ensures the physical consistency of body parts and accessories, such as neck muscles and earrings, improving the realism of these movements. Teller is designed to be efficient, surpassing the inference speed of diffusion-based models (Hallo 20.93s vs. Teller 0.92s for one second video generation), and achieves a real-time streaming performance of up to 25 FPS. Extensive experiments demonstrate that our method outperforms recent audio-driven portrait animation models, especially in small movements, as validated by human evaluations with a significant margin in quality and realism.

Shuqi Lu, Xiaohong Ji, Bohang Zhang et al.

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components: (1) grid-based space discretization; (2) grid sampling/merging; and (3) efficient 3D positional encoding. Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

Rongxin Cheng, Kai Zhou, Xingda Wei et al.

Rollout dominates the training time in large language model (LLM) post-training, where the trained model is used to generate tokens given a batch of prompts. SpecActor achieves fast rollout with speculative decoding that deploys a fast path (e.g., a smaller model) to accelerate the unparallelizable generation, while the correctness is guaranteed by fast parallel verification of the outputs with the original model. SpecActor addresses two foundational challenges in speculative rollout by (1) a \emph{dynamic decoupled speculation} execution method that maximizes the GPU computational efficiency to realize speedup for large-batch execution -- a configuration common in training but unfriendly to speculative execution and (2) a \emph{dynamic Best-of-N speculation} method that selects and combines different drafting methods according to the rollout progress. It substantially improves the speculation accuracy even when the best drafting method is unknown a priori, meanwhile without requiring adding extra computation resources. {\sys} is {1.3--1.7}\,$\times$ faster than common post-training baselines, and is {1.3--1.5}\,$\times$ faster compared to naively adopting speculative decoding for rollout.

Siyuan Liu, Junting Lin

Aiming at the problems of missed detection, false detection and low detection efficiency in transmission line foreign object detection under railway environment, we proposed an improved algorithm MRS-YOLO based on YOLO11. Firstly, a multi-scale Adaptive Kernel Depth Feature Fusion (MAKDF) module is proposed and fused with the C3k2 module to form C3k2_MAKDF, which enhances the model's feature extraction capability for foreign objects of different sizes and shapes. Secondly, a novel Re-calibration Feature Fusion Pyramid Network (RCFPN) is designed as a neck structure to enhance the model's ability to integrate and utilize multi-level features effectively. Then, Spatial and Channel Reconstruction Detect Head (SC_Detect) based on spatial and channel preprocessing is designed to enhance the model's overall detection performance. Finally, the channel pruning technique is used to reduce the redundancy of the improved model, drastically reduce Parameters and Giga Floating Point Operations Per Second (GFLOPs), and improve the detection efficiency. The experimental results show that the mAP50 and mAP50:95 of the MRS-YOLO algorithm proposed in this paper are improved to 94.8% and 86.4%, respectively, which are 0.7 and 2.3 percentage points higher compared to the baseline, while Parameters and GFLOPs are reduced by 44.2% and 17.5%, respectively. It is demonstrated that the improved algorithm can be better applied to the task of foreign object detection in railroad transmission lines.

Zhe Liu, Yuyan Ni, Zhichen Pu et al.

Recently, sophisticated deep learning-based approaches have been developed for generating efficient initial guesses to accelerate the convergence of density functional theory (DFT) calculations. While the actual initial guesses are often density matrices (DM), quantities that can convert into density matrices also qualify as alternative forms of initial guesses. Hence, existing works mostly rely on the prediction of the Hamiltonian matrix for obtaining high-quality initial guesses. However, the Hamiltonian matrix is both numerically difficult to predict and intrinsically non-transferable, hindering the application of such models in real scenarios. In light of this, we propose a method that constructs DFT initial guesses by predicting the electron density in a compact auxiliary basis representation using E(3)-equivariant neural networks. Trained on small molecules with up to 20 atoms, our model is able to achieve an average 33.3% self-consistent field (SCF) step reduction on systems up to 60 atoms, substantially outperforming Hamiltonian-centric and DM-centric models. Critically, this acceleration remains nearly constant with increasing system sizes and exhibits strong transferring behaviors across orbital basis sets and exchange-correlation (XC) functionals. To the best of our knowledge, this work represents the first and robust candidate for a universally transferable DFT acceleration method. We are also releasing the SCFbench dataset and its accompanying code to facilitate future research in this promising direction.

Woon Yee Ng, Li Rong Wang, Siyuan Liu et al.

Explaining machine learning (ML) predictions has become crucial as ML models are increasingly deployed in high-stakes domains such as healthcare. While SHapley Additive exPlanations (SHAP) is widely used for model interpretability, it fails to differentiate between causality and correlation, often misattributing feature importance when features are highly correlated. We propose Causal SHAP, a novel framework that integrates causal relationships into feature attribution while preserving many desirable properties of SHAP. By combining the Peter-Clark (PC) algorithm for causal discovery and the Intervention Calculus when the DAG is Absent (IDA) algorithm for causal strength quantification, our approach addresses the weakness of SHAP. Specifically, Causal SHAP reduces attribution scores for features that are merely correlated with the target, as validated through experiments on both synthetic and real-world datasets. This study contributes to the field of Explainable AI (XAI) by providing a practical framework for causal-aware model explanations. Our approach is particularly valuable in domains such as healthcare, where understanding true causal relationships is critical for informed decision-making.

Fangyu Du, Taiqing Li, Ziwei Zhang et al.

Audio-driven portrait animation aims to synthesize realistic and natural talking head videos from an input audio signal and a single reference image. While existing methods achieve high-quality results by leveraging high-dimensional intermediate representations and explicitly modeling motion dynamics, their computational complexity renders them unsuitable for real-time deployment. Real-time inference imposes stringent latency and memory constraints, often necessitating the use of highly compressed latent representations. However, operating in such compact spaces hinders the preservation of fine-grained spatiotemporal details, thereby complicating audio-visual synchronization RAP (Real-time Audio-driven Portrait animation), a unified framework for generating high-quality talking portraits under real-time constraints. Specifically, RAP introduces a hybrid attention mechanism for fine-grained audio control, and a static-dynamic training-inference paradigm that avoids explicit motion supervision. Through these techniques, RAP achieves precise audio-driven control, mitigates long-term temporal drift, and maintains high visual fidelity. Extensive experiments demonstrate that RAP achieves state-of-the-art performance while operating under real-time constraints.

Siyuan Liu, Wenjing Liu, Zhiwei Xu et al.

Empowered by large language models (LLMs), intelligent agents have become a popular paradigm for interacting with open environments to facilitate AI deployment. However, hallucinations generated by LLMs-where outputs are inconsistent with facts-pose a significant challenge, undermining the credibility of intelligent agents. Only if hallucinations can be mitigated, the intelligent agents can be used in real-world without any catastrophic risk. Therefore, effective detection and mitigation of hallucinations are crucial to ensure the dependability of agents. Unfortunately, the related approaches either depend on white-box access to LLMs or fail to accurately identify hallucinations. To address the challenge posed by hallucinations of intelligent agents, we present HalMit, a novel black-box watchdog framework that models the generalization bound of LLM-empowered agents and thus detect hallucinations without requiring internal knowledge of the LLM's architecture. Specifically, a probabilistic fractal sampling technique is proposed to generate a sufficient number of queries to trigger the incredible responses in parallel, efficiently identifying the generalization bound of the target agent. Experimental evaluations demonstrate that HalMit significantly outperforms existing approaches in hallucination monitoring. Its black-box nature and superior performance make HalMit a promising solution for enhancing the dependability of LLM-powered systems.

Dingcheng Zhen, Qian Qiao, Xu Zheng et al.

We introduce TransDiff, the first image generation model that marries Autoregressive (AR) Transformer with diffusion models. In this joint modeling framework, TransDiff encodes labels and images into high-level semantic features and employs a diffusion model to estimate the distribution of image samples. On the ImageNet 256x256 benchmark, TransDiff significantly outperforms other image generation models based on standalone AR Transformer or diffusion models. Specifically, TransDiff achieves a Frechet Inception Distance (FID) of 1.61 and an Inception Score (IS) of 293.4, and further provides x2 faster inference latency compared to state-of-the-art methods based on AR Transformer and x112 faster inference compared to diffusion-only models. Furthermore, building on the TransDiff model, we introduce a novel image generation paradigm called Multi-Reference Autoregression (MRAR), which performs autoregressive generation by predicting the next image. MRAR enables the model to reference multiple previously generated images, thereby facilitating the learning of more diverse representations and improving the quality of generated images in subsequent iterations. By applying MRAR, the performance of TransDiff is improved, with the FID reduced from 1.61 to 1.42. We expect TransDiff to open up a new frontier in the field of image generation.

Mingkuan Feng, Jinyang Wu, Siyuan Liu et al.

The deployment of large language models (LLMs) is largely hindered by their large number of parameters. Structural pruning has emerged as a promising solution. Prior structured pruning methods directly remove unimportant parameters based on certain metrics, which often causes knowledge loss and necessitates extensive retraining. To overcome this, we introduce a novel pruning method TRSP: Two-Stage Regularization-Based Structured Pruning for LLMs. Specifically, we multiply the output of each transformer layer by an initial learnable weight and iteratively learn these weights by adding their $\ell_1$-norm as a regularization term to the loss function, serving as the first-stage regularization. Subsequently, we apply additional regularization to the difference between the output and input of layers with smaller weights, encouraging the shift of knowledge to the preserved layers. This serves as the second-stage regularization. TRSP retains more knowledge and better preserves model performance than direct parameter elimination. Through extensive experimentation we show that TRSP outperforms strong layer-wise structured pruning methods without requiring retraining. As a layer-wise pruning method, it delivers notable end-to-end acceleration, making it a promising solution for efficient LLM deployment.

Luyuan Xie, Manqing Lin, Siyuan Liu et al.

In medical image segmentation, personalized cross-silo federated learning (FL) is becoming popular for utilizing varied data across healthcare settings to overcome data scarcity and privacy concerns. However, existing methods often suffer from client drift, leading to inconsistent performance and delayed training. We propose a new framework, Personalized Federated Learning via Feature Enhancement (pFLFE), designed to mitigate these challenges. pFLFE consists of two main stages: feature enhancement and supervised learning. The first stage improves differentiation between foreground and background features, and the second uses these enhanced features for learning from segmentation masks. We also design an alternative training approach that requires fewer communication rounds without compromising segmentation quality, even with limited communication resources. Through experiments on three medical segmentation tasks, we demonstrate that pFLFE outperforms the state-of-the-art methods.

He Zhang, Chang Liu, Zun Wang et al.

Predicting the mean-field Hamiltonian matrix in density functional theory is a fundamental formulation to leverage machine learning for solving molecular science problems. Yet, its applicability is limited by insufficient labeled data for training. In this work, we highlight that Hamiltonian prediction possesses a self-consistency principle, based on which we propose self-consistency training, an exact training method that does not require labeled data. It distinguishes the task from predicting other molecular properties by the following benefits: (1) it enables the model to be trained on a large amount of unlabeled data, hence addresses the data scarcity challenge and enhances generalization; (2) it is more efficient than running DFT to generate labels for supervised training, since it amortizes DFT calculation over a set of queries. We empirically demonstrate the better generalization in data-scarce and out-of-distribution scenarios, and the better efficiency over DFT labeling. These benefits push forward the applicability of Hamiltonian prediction to an ever-larger scale.

Xiaoyang Chen, Junjie Zhao, Siyuan Liu et al.

Cortical surface reconstruction (CSR) from MRI is key to investigating brain structure and function. While recent deep learning approaches have significantly improved the speed of CSR, a substantial amount of runtime is still needed to map the cortex to a topologically-correct spherical manifold to facilitate downstream geometric analyses. Moreover, this mapping is possible only if the topology of the surface mesh is homotopic to a sphere. Here, we present a method for simultaneous CSR and spherical mapping efficiently within seconds. Our approach seamlessly connects two sub-networks for white and pial surface generation. Residual diffeomorphic deformations are learned iteratively to gradually warp a spherical template mesh to the white and pial surfaces while preserving mesh topology and uniformity. The one-to-one vertex correspondence between the template sphere and the cortical surfaces allows easy and direct mapping of geometric features like convexity and curvature to the sphere for visualization and downstream processing. We demonstrate the efficacy of our approach on infant brain MRI, which poses significant challenges to CSR due to tissue contrast changes associated with rapid brain development during the first postnatal year. Performance evaluation based on a dataset of infants from 0 to 12 months demonstrates that our method substantially enhances mesh regularity and reduces geometric errors, outperforming state-of-the-art deep learning approaches, all while maintaining high computational efficiency.

Siyuan Liu, Ashutosh Trivedi, Xiang Yin et al.

Correct-by-construction synthesis is a cornerstone of the confluence of formal methods and control theory towards designing safety-critical systems. Instead of following the time-tested, albeit laborious (re)design-verify-validate loop, correct-by-construction methodology advocates the use of continual refinements of formal requirements -- connected by chains of formal proofs -- to build a system that assures the correctness by design. A remarkable progress has been made in scaling the scope of applicability of correct-by-construction synthesis -- with a focus on cyber-physical systems that tie discrete-event control with continuous environment -- to enlarge control systems by combining symbolic approaches with principled state-space reduction techniques. Unfortunately, in the security-critical control systems, the security properties are verified ex post facto the design process in a way that undermines the correct-by-construction paradigm. We posit that, to truly realize the dream of correct-by-construction synthesis for security-critical systems, security considerations must take center-stage with the safety considerations. Moreover, catalyzed by the recent progress on the opacity sub-classes of security properties and the notion of hyperproperties capable of combining security with safety properties, we believe that the time is ripe for the research community to holistically target the challenge of secure-by-construction synthesis. This paper details our vision by highlighting the recent progress and open challenges that may serve as bricks for providing a solid foundation for secure-by-construction synthesis of cyber-physical systems.

Liang He, Shizhuo Zhang, Lijun Wu et al.

Understanding protein sequences is vital and urgent for biology, healthcare, and medicine. Labeling approaches are expensive yet time-consuming, while the amount of unlabeled data is increasing quite faster than that of the labeled data due to low-cost, high-throughput sequencing methods. In order to extract knowledge from these unlabeled data, representation learning is of significant value for protein-related tasks and has great potential for helping us learn more about protein functions and structures. The key problem in the protein sequence representation learning is to capture the co-evolutionary information reflected by the inter-residue co-variation in the sequences. Instead of leveraging multiple sequence alignment as is usually done, we propose a novel method to capture this information directly by pre-training via a dedicated language model, i.e., Pairwise Masked Language Model (PMLM). In a conventional masked language model, the masked tokens are modeled by conditioning on the unmasked tokens only, but processed independently to each other. However, our proposed PMLM takes the dependency among masked tokens into consideration, i.e., the probability of a token pair is not equal to the product of the probability of the two tokens. By applying this model, the pre-trained encoder is able to generate a better representation for protein sequences. Our result shows that the proposed method can effectively capture the inter-residue correlations and improves the performance of contact prediction by up to 9% compared to the MLM baseline under the same setting. The proposed model also significantly outperforms the MSA baseline by more than 7% on the TAPE contact prediction benchmark when pre-trained on a subset of the sequence database which the MSA is generated from, revealing the potential of the sequence pre-training method to surpass MSA based methods in general.

Siyuan Liu, Yusong Wang, Tong Wang et al.

The identification of active binding drugs for target proteins (termed as drug-target interaction prediction) is the key challenge in virtual screening, which plays an essential role in drug discovery. Although recent deep learning-based approaches achieved better performance than molecular docking, existing models often neglect certain aspects of the intermolecular information, hindering the performance of prediction. We recognize this problem and propose a novel approach named Intermolecular Graph Transformer (IGT) that employs a dedicated attention mechanism to model intermolecular information with a three-way Transformer-based architecture. IGT outperforms state-of-the-art approaches by 9.1% and 20.5% over the second best for binding activity and binding pose prediction respectively, and shows superior generalization ability to unseen receptor proteins. Furthermore, IGT exhibits promising drug screening ability against SARS-CoV-2 by identifying 83.1% active drugs that have been validated by wet-lab experiments with near-native predicted binding poses.

Siyuan Liu, Kim-Han Thung, Liangqiong Qu et al.

Retrospective artifact correction (RAC) improves image quality post acquisition and enhances image usability. Recent machine learning driven techniques for RAC are predominantly based on supervised learning and therefore practical utility can be limited as data with paired artifact-free and artifact-corrupted images are typically insufficient or even non-existent. Here we show that unwanted image artifacts can be disentangled and removed from an image via an RAC neural network learned with unpaired data. This implies that our method does not require matching artifact-corrupted data to be either collected via acquisition or generated via simulation. Experimental results demonstrate that our method is remarkably effective in removing artifacts and retaining anatomical details in images with different contrasts.

Siyuan Liu, Pew-Thian Yap

Harmonization improves data consistency and is central to effective integration of diverse imaging data acquired across multiple sites. Recent deep learning techniques for harmonization are predominantly supervised in nature and hence require imaging data of the same human subjects to be acquired at multiple sites. Data collection as such requires the human subjects to travel across sites and is hence challenging, costly, and impractical, more so when sufficient sample size is needed for reliable network training. Here we show how harmonization can be achieved with a deep neural network that does not rely on traveling human phantom data. Our method disentangles site-specific appearance information and site-invariant anatomical information from images acquired at multiple sites and then employs the disentangled information to generate the image of each subject for any target site. We demonstrate with more than 6,000 multi-site T1- and T2-weighted images that our method is remarkably effective in generating images with realistic site-specific appearances without altering anatomical details. Our method allows retrospective harmonization of data in a wide range of existing modern large-scale imaging studies, conducted via different scanners and protocols, without additional data collection.