Ziyang Yu

Ziyang Yu, Xiang Li, Qiong Chang et al.

Point clouds are a primary sensory representation for robotic perception, underpinning LiDAR-based autonomous driving, simultaneous localization and mapping (SLAM), and navigation. Within these pipelines, Farthest Point Sampling (FPS) is the most well-known downsampling operator, as its uniform coverage preserves the geometric structure on which downstream perception relies. However, the large time complexity of classical FPS scales poorly with the million-point-per-second rates of modern 3D sensors, making it a dominant latency bottleneck that conflicts with the real-time and limited onboard compute budgets of robotic systems. Therefore, we propose RadiusFPS, an FPS acceleration framework based on spherical voxel pruning that preserves the standard FPS update rule under the same initialization and tie-breaking policy. By indexing the point cloud with spherical voxels, RadiusFPS derives a conservative geometric bound that prunes redundant distance computations in each iteration, complemented by a coordinate-wise point-skip test that removes residual updates. We further introduce RadiusFPS-G, a warp-level GPU implementation that fuses voxel selection, pruning, and distance update into memory-coalesced kernels, eliminating costly global-memory round-trips. On indoor (S3DIS, ScanNet) and outdoor LiDAR (SemanticKITTI) benchmarks, RadiusFPS-G attains up to 2.5x speedup over GPU-based FPS and matches or exceeds QuickFPS among the evaluated methods while using roughly half its GPU memory, with comparable segmentation accuracy. When coupled with the learning-based FastPoint sampler, the resulting pipeline achieves the fastest End-to-End inference among all evaluated configurations. These properties make high-quality FPS-style sampling practical for latency- and memory-constrained robotic vision.

Yuyu Liu, Jiannan Yang, Ziyang Yu et al.

Missing data in single-cell sequencing datasets poses significant challenges for extracting meaningful biological insights. However, existing imputation approaches, which often assume uniformity and data completeness, struggle to address cases with large patches of missing data. In this paper, we present CROT, an optimal transport-based imputation algorithm designed to handle patch-based missing data in tabular formats. Our approach effectively captures the underlying data structure in the presence of significant missingness. Notably, it achieves superior imputation accuracy while significantly reducing runtime, demonstrating its scalability and efficiency for large-scale datasets. This work introduces a robust solution for imputation in heterogeneous, high-dimensional datasets with structured data absence, addressing critical challenges in both biological and clinical data analysis. Our code is available at Anomalous Github.

Wenqian Zhao, Xufeng Yao, Ziyang Yu et al.

Optical proximity correction (OPC) is a widely-used resolution enhancement technique (RET) for printability optimization. Recently, rigorous numerical optimization and fast machine learning are the research focus of OPC in both academia and industry, each of which complements the other in terms of robustness or efficiency. We inspect the pattern distribution on a design layer and find that different sub-regions have different pattern complexity. Besides, we also find that many patterns repetitively appear in the design layout, and these patterns may possibly share optimized masks. We exploit these properties and propose a self-adaptive OPC framework to improve efficiency. Firstly we choose different OPC solvers adaptively for patterns of different complexity from an extensible solver pool to reach a speed/accuracy co-optimization. Apart from that, we prove the feasibility of reusing optimized masks for repeated patterns and hence, build a graph-based dynamic pattern library reusing stored masks to further speed up the OPC flow. Experimental results show that our framework achieves substantial improvement in both performance and efficiency.

Guojin Chen, Ziyang Yu, Hongduo Liu et al.

With the feature size continuously shrinking in advanced technology nodes, mask optimization is increasingly crucial in the conventional design flow, accompanied by an explosive growth in prohibitive computational overhead in optical proximity correction (OPC) methods. Recently, inverse lithography technique (ILT) has drawn significant attention and is becoming prevalent in emerging OPC solutions. However, ILT methods are either time-consuming or in weak performance of mask printability and manufacturability. In this paper, we present DevelSet, a GPU and deep neural network (DNN) accelerated level set OPC framework for metal layer. We first improve the conventional level set-based ILT algorithm by introducing the curvature term to reduce mask complexity and applying GPU acceleration to overcome computational bottlenecks. To further enhance printability and fast iterative convergence, we propose a novel deep neural network delicately designed with level set intrinsic principles to facilitate the joint optimization of DNN and GPU accelerated level set optimizer. Experimental results show that DevelSet framework surpasses the state-of-the-art methods in printability and boost the runtime performance achieving instant level (around 1 second).

Guangji Bai, Ziyang Yu, Zheng Chai et al.

Despite the recent success of Graph Neural Networks (GNNs), it remains challenging to train GNNs on large-scale graphs due to neighbor explosions. As a remedy, distributed computing becomes a promising solution by leveraging abundant computing resources (e.g., GPU). However, the node dependency of graph data increases the difficulty of achieving high concurrency in distributed GNN training, which suffers from the massive communication overhead. To address it, Historical value approximation is deemed a promising class of distributed training techniques. It utilizes an offline memory to cache historical information (e.g., node embedding) as an affordable approximation of the exact value and achieves high concurrency. However, such benefits come at the cost of involving dated training information, leading to staleness, imprecision, and convergence issues. To overcome these challenges, this paper proposes SAT (Staleness-Alleviated Training), a novel and scalable distributed GNN training framework that reduces the embedding staleness adaptively. The key idea of SAT is to model the GNN's embedding evolution as a temporal graph and build a model upon it to predict future embedding, which effectively alleviates the staleness of the cached historical embedding. We propose an online algorithm to train the embedding predictor and the distributed GNN alternatively and further provide a convergence analysis. Empirically, we demonstrate that SAT can effectively reduce embedding staleness and thus achieve better performance and convergence speed on multiple large-scale graph datasets.

Ziyang Yu, Liang Zhao

Deploying Large Language Models (LLMs) for discriminative workloads is often limited by inference latency, compute, and API costs at scale. Active distillation reduces these costs by querying an LLM oracle to train compact discriminative students, but most pipelines distill only final labels, discarding intermediate reasoning signals and offering limited diagnostics of what reasoning is missing and where errors arise. We propose Graph of Concept Predictors (GCP), a reasoning-aware active distillation framework that externalizes the teacher's decision process as a directed acyclic graph and mirrors it with modular concept predictors in the student. GCP enhances sample efficiency through a graph-aware acquisition strategy that targets uncertainty and disagreement at critical reasoning nodes. Additionally, it improves training stability and efficiency by performing targeted sub-module retraining, which attributes downstream loss to specific concept predictors and updates only the most influential modules. Experiments on eight NLP classification benchmarks demonstrate that GCP enhances performance under limited annotation budgets while yielding more interpretable and controllable training dynamics. Code is available at: https://github.com/Ziyang-Yu/GCP.

Ziyang Yu, Wenbing Huang, Yang Liu

Molecular Dynamics (MD) is crucial in various fields such as materials science, chemistry, and pharmacology to name a few. Conventional MD software struggles with the balance between time cost and prediction accuracy, which restricts its wider application. Recently, data-driven approaches based on deep generative models have been devised for time-coarsened dynamics, which aim at learning dynamics of diverse molecular systems over a long timestep, enjoying both universality and efficiency. Nevertheless, most current methods are designed solely to learn from the data distribution regardless of the underlying Boltzmann distribution, and the physics priors such as energies and forces are constantly overlooked. In this work, we propose a conditional generative model called Force-guided Bridge Matching (FBM), which learns full-atom time-coarsened dynamics and targets the Boltzmann-constrained distribution. With the guidance of our delicately-designed intermediate force field, FBM leverages favourable physics priors into the generation process, giving rise to enhanced simulations. Experiments on two datasets consisting of peptides verify our superiority in terms of comprehensive metrics and demonstrate transferability to unseen systems.

Yongliang Miao, Ziyang Yu, Liang Zhao et al.

Skill libraries have become a practical way for LLM agents to reuse procedural experience across tasks. However, existing systems typically treat skills as flat, single-resolution prompt blocks. This creates a tension between relevance and cost: injecting coarse skills can introduce irrelevant or misleading context, while rewriting entire skills is expensive and often unnecessary. We propose SkillLens, a hierarchical skill-evolution framework that organizes skills into a four-layer graph of policies, strategies, procedures, and primitives, and retrieves them at mixed granularity. Given a task, SkillLens first retrieves semantically relevant skill seeds, expands them through degree-corrected random walk over the skill graph, and then uses a verifier to decide whether each visited unit should be accepted, decomposed, rewritten, or skipped. This enables the agent to reuse compatible subskills directly while adapting only locally mismatched components. To improve the system over time, SkillLens further refines multi-granularity skills and verifier in order to improve its routing decisions. We provide theoretical analysis showing that mixed-granularity adaptation incurs sublinear cost under sparse mismatch assumptions and that the evolutionary update rule monotonically improves the validation objective until a local optimum. Across MuLocbench and ALFWorld, SkillLens consistently improves over strong skill-based baselines, achieving up to a 6.31 percentage-point Acc@1 gain for bug localization and raising agent success rate from 45.00% to 51.31%.

Guangji Bai, Zheng Chai, Chen Ling et al.

The burgeoning field of Large Language Models (LLMs), exemplified by sophisticated models like OpenAI's ChatGPT, represents a significant advancement in artificial intelligence. These models, however, bring forth substantial challenges in the high consumption of computational, memory, energy, and financial resources, especially in environments with limited resource capabilities. This survey aims to systematically address these challenges by reviewing a broad spectrum of techniques designed to enhance the resource efficiency of LLMs. We categorize methods based on their optimization focus: computational, memory, energy, financial, and network resources and their applicability across various stages of an LLM's lifecycle, including architecture design, pretraining, finetuning, and system design. Additionally, the survey introduces a nuanced categorization of resource efficiency techniques by their specific resource types, which uncovers the intricate relationships and mappings between various resources and corresponding optimization techniques. A standardized set of evaluation metrics and datasets is also presented to facilitate consistent and fair comparisons across different models and techniques. By offering a comprehensive overview of the current sota and identifying open research avenues, this survey serves as a foundational reference for researchers and practitioners, aiding them in developing more sustainable and efficient LLMs in a rapidly evolving landscape.

Ziyang Yu, Qiyue Li, Liang Zhao

Tool-augmented language models can extend small language models with external executable skills, but scaling the tool library creates a coupled challenge: the library must evolve with the planner as new reusable subroutines emerge, while retrieval from the growing library must remain within a fixed context budget. Existing tool-use and skill-library methods typically treat tools as flat or text-indexed memories, causing prompt cost to grow with library size and obscuring the typed, compositional structure of executable code. We propose CoCoDA, a framework that co-evolves the planner and tool library through a single code-native structure: a compositional code DAG. Nodes are primitive or composite tools, edges encode invocation dependencies, and each node stores a typed signature, description, pre/post-condition specification, and worked examples. At inference time, Typed DAG Retrieval prunes candidates by symbolic signature unification, ranks survivors by descriptions, filters them by behavioral specifications, and disambiguates with examples, keeping expensive context materialization on progressively smaller candidate sets. At training time, successful trajectories are folded into validated composite tools, while the planner is updated with a DAG-induced reward that credits composites by their primitive expansion size. We provide theoretical results showing retrieval cost reduction, sublinear retrieval time, compositional advantage under the shaped reward, monotone co-evolution under conservative updates, and DAG well-formedness. Across mathematical reasoning, tabular analysis, and code task benchmarks, CoCoDA enables an 8B student to match or exceed a 32B teacher on GSM8K and MATH and consistently improves over strong tool-use and library-learning baselines.

Jiaqi Han, Jiacheng Cen, Liming Wu et al.

Geometric graphs are a special kind of graph with geometric features, which are vital to model many scientific problems. Unlike generic graphs, geometric graphs often exhibit physical symmetries of translations, rotations, and reflections, making them ineffectively processed by current Graph Neural Networks (GNNs). To address this issue, researchers proposed a variety of geometric GNNs equipped with invariant/equivariant properties to better characterize the geometry and topology of geometric graphs. Given the current progress in this field, it is imperative to conduct a comprehensive survey of data structures, models, and applications related to geometric GNNs. In this paper, based on the necessary but concise mathematical preliminaries, we formalize geometric graph as the data structure, on top of which we provide a unified view of existing models from the geometric message passing perspective. Additionally, we summarize the applications as well as the related datasets to facilitate later research for methodology development and experimental evaluation. We also discuss the challenges and future potential directions of geometric GNNs at the end of this survey.

Ziyang Yu, Yi He, Wenbing Huang et al.

Estimating free energy differences quantifies thermodynamic preferences in molecular interactions, which is central to chemistry and drug discovery. Despite fruitful progress, existing methods still face key limitations: classical computational approaches remain prohibitively expensive due to their reliance on extensive molecular dynamics simulations, while deep learning-based methods are constrained by either less-expressive generative models or input dimensions tied to a specific system, resulting in negligible generalization. To address these challenges, we propose CARD, a generative framework that employs a novel radix-based decomposition to bijectively convert 3D coordinates into mixed discrete-continuous sequences, enabling coarse-to-fine autoregressive modeling with enhanced expressiveness. Notably, the model corresponds to a distribution with zero free energy, serving as a proposal for absolute free energy computation of arbitrary systems without relying on alchemical pathways. Experiments across diverse tasks demonstrate that CARD matches the accuracy of classical computational methods on unseen systems with diverse topologies, while achieving an approximately 40-fold speedup in inference.

Ziyang Yu, Wenbing Huang, Yang Liu

The study of rigid protein-protein docking plays an essential role in a variety of tasks such as drug design and protein engineering. Recently, several learning-based methods have been proposed for the task, exhibiting much faster docking speed than those computational methods. In this paper, we propose a novel learning-based method called ElliDock, which predicts an elliptic paraboloid to represent the protein-protein docking interface. To be specific, our model estimates elliptic paraboloid interfaces for the two input proteins respectively, and obtains the roto-translation transformation for docking by making two interfaces coincide. By its design, ElliDock is independently equivariant with respect to arbitrary rotations/translations of the proteins, which is an indispensable property to ensure the generalization of the docking process. Experimental evaluations show that ElliDock achieves the fastest inference time among all compared methods and is strongly competitive with current state-of-the-art learning-based models such as DiffDock-PP and Multimer particularly for antibody-antigen docking.

Justice Ou, Tinglin Huang, Yilun Zhao et al.

To improve the reliability of Large Language Models (LLMs) in clinical applications, retrieval-augmented generation (RAG) is extensively applied to provide factual medical knowledge. However, beyond general medical knowledge from open-ended datasets, clinical case-based knowledge is also critical for effective medical reasoning, as it provides context grounded in real-world patient experiences.Motivated by this, we propose Experience Retrieval-Augmentation ExpRAG framework based on Electronic Health Record(EHR), aiming to offer the relevant context from other patients' discharge reports. ExpRAG performs retrieval through a coarse-to-fine process, utilizing an EHR-based report ranker to efficiently identify similar patients, followed by an experience retriever to extract task-relevant content for enhanced medical reasoning.To evaluate ExpRAG, we introduce DischargeQA, a clinical QA dataset with 1,280 discharge-related questions across diagnosis, medication, and instruction tasks. Each problem is generated using EHR data to ensure realistic and challenging scenarios. Experimental results demonstrate that ExpRAG consistently outperforms a text-based ranker, achieving an average relative improvement of 5.2%, highlighting the importance of case-based knowledge for medical reasoning.

Rui Jiao, Xiangzhe Kong, Li Zhang et al.

Pretraining on a large number of unlabeled 3D molecules has showcased superiority in various scientific applications. However, prior efforts typically focus on pretraining models in a specific domain, either proteins or small molecules, missing the opportunity to leverage cross-domain knowledge. To mitigate this gap, we introduce Equivariant Pretrained Transformer (EPT), an all-atom foundation model that can be pretrained from multiple domain 3D molecules. Built upon an E(3)-equivariant transformer, EPT is able to not only process atom-level information but also incorporate block-level features (e.g. residuals in proteins). Additionally, we employ a block-level denoising task, rather than the conventional atom-level denoising, as the pretraining objective. To pretrain EPT, we construct a large-scale dataset of 5.89M entries, comprising small molecules, proteins, protein-protein complexes, and protein-molecule complexes. Experimental evaluations on downstream tasks including ligand binding affinity prediction, protein property prediction, and molecular property prediction, show that EPT significantly outperforms previous state-of-the-art methods in the first task and achieves competitively superior performance for the remaining two tasks. Furthermore, we demonstrate the potential of EPT in identifying small molecule drug candidates targeting 3CL protease, a critical target in the replication of SARS-CoV-2. Among 1,978 FDA-approved drugs, EPT ranks 7 out of 8 known anti-COVID-19 drugs in the top 200, indicating the high recall of EPT. By using Molecular Dynamics (MD) simulations, EPT further discoveries 7 novel compounds whose binding affinities are higher than that of the top-ranked known anti-COVID-19 drug, showcasing its powerful capabilities in drug discovery.

Ziyang Yu, Wenbing Huang, Yang Liu

Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off between accuracy and efficiency, while recent deep learning-based improvements have mostly focused on single-domain molecules, lacking transferability to unfamiliar molecular systems. Therefore, we propose \textbf{Uni}fied \textbf{Sim}ulator (UniSim), which leverages cross-domain knowledge to enhance the understanding of atomic interactions. First, we employ a multi-head pretraining approach to learn a unified atomic representation model from a large and diverse set of molecular data. Then, based on the stochastic interpolant framework, we learn the state transition patterns over long timesteps from MD trajectories, and introduce a force guidance module for rapidly adapting to different chemical environments. Our experiments demonstrate that UniSim achieves highly competitive performance across small molecules, peptides, and proteins.

Jamil Fayyad, Nourhan Bayasi, Ziyang Yu et al.

Deep learning models for skin disease classification require large, diverse, and well-annotated datasets. However, such resources are often limited due to privacy concerns, high annotation costs, and insufficient demographic representation. While text-to-image diffusion probabilistic models (T2I-DPMs) offer promise for medical data synthesis, their use in dermatology remains underexplored, largely due to the scarcity of rich textual descriptions in existing skin image datasets. In this work, we introduce LesionGen, a clinically informed T2I-DPM framework for dermatology image synthesis. Unlike prior methods that rely on simplistic disease labels, LesionGen is trained on structured, concept-rich dermatological captions derived from expert annotations and pseudo-generated, concept-guided reports. By fine-tuning a pretrained diffusion model on these high-quality image-caption pairs, we enable the generation of realistic and diverse skin lesion images conditioned on meaningful dermatological descriptions. Our results demonstrate that models trained solely on our synthetic dataset achieve classification accuracy comparable to those trained on real images, with notable gains in worst-case subgroup performance. Code and data are available here.

Ziyang Yu, Yuyu Liu

Despite the recent success of Large Language Models (LLMs), it remains challenging to feed LLMs with long prompts due to the fixed size of LLM inputs. As a remedy, prompt compression becomes a promising solution by removing redundant tokens in the prompt. However, using LLM in the existing works requires additional computation resources and leads to memory overheads. To address it, we propose ICPC (In-context Prompt Compression), a novel and scalable prompt compression method that adaptively reduces the prompt length. The key idea of ICPC is to calculate the probability of each word appearing in the prompt using encoders and calculate information carried by each word through the information function, which effectively reduces the information loss during prompt compression and increases the speed of compression. Empirically, we demonstrate that ICPC can effectively compress long texts of different categories and thus achieve better performance and speed on different types of NLP tasks.