arXiv subjects

Siyuan Shen

Publications and source records attributed to Siyuan Shen.

At least 19 recordsLinked to original sources

arXiv2026

Meshy T2: Fast Native Mesh Generation with Flow Matching

Polygonal meshes are the standard surface representation of modern 3D pipelines, and generating high-quality meshes with artist-style topology is essential for film, gaming, and interactive 3D applications. Mainstream approaches serialize a mesh into a token sequence and decode it autoregressively, which is slow at inference and sensitive to error accumulation, making them impractical for interactive asset creation. We present Meshy T2, a fast native mesh generation framework built on flow matching. At its core is a vertex-set mesh VAE that encodes a mesh into one continuous latent token per vertex and decodes vertices, edge connectivity, and face winding order in a single pass, preserving high-precision geometry and artist-authored topology without vertex quantization or welding. Generation proceeds as a coarse-to-fine cascade of two flow-matching models: an image-conditioned voxel flow first sketches the overall shape as a coarse occupancy scaffold, and a mesh flow then populates the scaffold with per-vertex latent tokens, conditioned on the image, the scaffold, and a requested vertex budget. This design delivers three practical capabilities: interactive generation speed through parallel flow-based synthesis; effective face-count control through the requested vertex budget; and native support for multi-part assets, whose components emerge directly from the generated connectivity. In our experiments, Meshy T2 achieves state-of-the-art geometric fidelity and completes end-to-end image-to-mesh generation within a median of 6 seconds, over an order of magnitude faster than autoregressive baselines. Code and weights will be available at https://github.com/meshy-dev/meshy-t2.

cs.GR↗

arXiv2026

Every Microsecond Matters: Achieving Near Speed-of-Light Latency in GPU Collectives

GPU collective communication is typically optimized for bandwidth, yet many emerging workloads are increasingly limited by latency. Long-context decode-heavy large language model (LLM) inference is a prime example, where serving large models requires multiple GPUs, and many small collectives lie directly on the critical path of token generation. Therefore, even microsecond of overhead can impact performance and cost. In this work, we study how to approach the hardware Speed-of-Light (SoL) lower bound for GPU collectives within a scale-up network. We identify key principles for near-optimal designs, including barrier-free synchronization and efficient use of symmetric memory and multicast. Building on NCCL's device-side API, we develop low-latency interfaces for constructing custom collective kernels and use them to implement new symmetric collectives in NCCL. Microbenchmarks show substantial latency reductions for small and medium messages, reducing overhead to within 7% of the absolute SoL lower bound. When integrated into real applications, these kernels improve inter-token latency and throughput in LLM inference and accelerate cuSOLVERMp, demonstrating benefits for both AI inference and traditional HPC workloads.

cs.DC↗

arXiv2026

Demystifying NVSHMEM: A System-Level Analysis on Symmetric Memory and Device-Initiated Operations in GPU Communication

NVSHMEM is NVIDIA's OpenSHMEM-based PGAS communication library for GPU clusters, enabling GPU-initiated, one-sided communication through symmetric memory. Despite its growing adoption, a system-level understanding of its design and behavior remains scattered across documentation, source code, and application experience. This paper presents a concise study of NVSHMEM's programming model, implementation, and performance characteristics, focusing on symmetric memory, one-sided operations, and device-side collectives. We also examine DeepEP as a case study of NVSHMEM in performance-critical sparse deep learning workloads. Our analysis shows that NVSHMEM pioneered a device-side symmetric-memory programming model that enables fine-grained GPU-driven communication and is important for approaching the hardware performance limit. Overall, this work defines NVSHMEM's role as a systems building block, highlights its design tradeoffs, and identifies opportunities for improving GPU communication runtimes.

cs.DC↗

arXiv2026

Detecting AI-Generated Content in Academic Peer Reviews

The growing availability of large language models (LLMs) has raised questions about their role in academic peer review. This study examines the temporal emergence of AI-generated content in peer reviews by applying a detection model trained on historical reviews to later review cycles at International Conference on Learning Representations (ICLR) and Nature Communications (NC). We observe minimal detection of AI-generated content before 2022, followed by a substantial increase through 2025, with approximately 20% of ICLR reviews and 12% of Nature Communications reviews classified as AI-generated in 2025. The most pronounced growth of AI-generated reviews in NC occurs between the third and fourth quarter of 2024. Together, these findings provide suggestive evidence of a rapidly increasing presence of AI-assisted content in peer review and highlight the need for further study of its implications for scholarly evaluation.

cs.CL↗

arXiv2026

Demystifying NCCL: An In-depth Analysis of GPU Communication Protocols and Algorithms

The NVIDIA Collective Communication Library (NCCL) is a critical software layer enabling high-performance collectives on large-scale GPU clusters. Despite being open source with a documented API, its internal design remains largely opaque. The orchestration of communication channels, selection of protocols, and handling of memory movement across devices and nodes are not well understood, making it difficult to analyze performance or identify bottlenecks. This paper presents a comprehensive analysis of NCCL, focusing on its communication protocol variants (Simple, LL, and LL128), mechanisms governing intra-node and inter-node data movement, and ring- and tree-based collective communication algorithms. The insights obtained from this study serve as the foundation for ATLAHS, an application-trace-driven network simulation toolchain capable of accurately reproducing NCCL communication patterns in large-scale AI training workloads. By demystifying NCCL's internal architecture, this work provides guidance for system researchers and performance engineers working to optimize or simulate collective communication at scale.

cs.DC↗

arXiv2025

EDAN: Towards Understanding Memory Parallelism and Latency Sensitivity in HPC

Resource disaggregation is a promising technique for improving the efficiency of large-scale computing systems. However, this comes at the cost of increased memory access latency due to the need to rely on the network fabric to transfer data between remote nodes. As such, it is crucial to ascertain an application's memory latency sensitivity to minimize the overall performance impact. Existing tools for measuring memory latency sensitivity often rely on custom ad-hoc hardware or cycle-accurate simulators, which can be inflexible and time-consuming. To address this, we present EDAN (Execution DAG Analyzer), a novel performance analysis tool that leverages an application's runtime instruction trace to generate its corresponding execution DAG. This approach allows us to estimate the latency sensitivity of sequential programs and investigate the impact of different hardware configurations. EDAN not only provides us with the capability of calculating the theoretical bounds for performance metrics, but it also helps us gain insight into the memory-level parallelism inherent to HPC applications. We apply EDAN to applications and benchmarks such as PolyBench, HPCG, and LULESH to unveil the characteristics of their intrinsic memory-level parallelism and latency sensitivity.

cs.PF↗

arXiv2025

Hierarchical Structure-Property Alignment for Data-Efficient Molecular Generation and Editing

Property-constrained molecular generation and editing are crucial in AI-driven drug discovery but remain hindered by two factors: (i) capturing the complex relationships between molecular structures and multiple properties remains challenging, and (ii) the narrow coverage and incomplete annotations of molecular properties weaken the effectiveness of property-based models. To tackle these limitations, we propose HSPAG, a data-efficient framework featuring hierarchical structure-property alignment. By treating SMILES and molecular properties as complementary modalities, the model learns their relationships at atom, substructure, and whole-molecule levels. Moreover, we select representative samples through scaffold clustering and hard samples via an auxiliary variational auto-encoder (VAE), substantially reducing the required pre-training data. In addition, we incorporate a property relevance-aware masking mechanism and diversified perturbation strategies to enhance generation quality under sparse annotations. Experiments demonstrate that HSPAG captures fine-grained structure-property relationships and supports controllable generation under multiple property constraints. Two real-world case studies further validate the editing capabilities of HSPAG.

cs.LG↗

arXiv2025

$μ$NeuFMT: Optical-Property-Adaptive Fluorescence Molecular Tomography via Implicit Neural Representation

Fluorescence Molecular Tomography (FMT) is a promising technique for non-invasive 3D visualization of fluorescent probes, but its reconstruction remains challenging due to the inherent ill-posedness and reliance on inaccurate or often-unknown tissue optical properties. While deep learning methods have shown promise, their supervised nature limits generalization beyond training data. To address these problems, we propose $μ$NeuFMT, a self-supervised FMT reconstruction framework that integrates implicit neural-based scene representation with explicit physical modeling of photon propagation. Its key innovation lies in jointly optimize both the fluorescence distribution and the optical properties ($μ$) during reconstruction, eliminating the need for precise prior knowledge of tissue optics or pre-conditioned training data. We demonstrate that $μ$NeuFMT robustly recovers accurate fluorophore distributions and optical coefficients even with severely erroneous initial values (0.5$\times$ to 2$\times$ of ground truth). Extensive numerical, phantom, and in vivo validations show that $μ$NeuFMT outperforms conventional and supervised deep learning approaches across diverse heterogeneous scenarios. Our work establishes a new paradigm for robust and accurate FMT reconstruction, paving the way for more reliable molecular imaging in complex clinically related scenarios, such as fluorescence guided surgery.

eess.IV↗

arXiv2025

PerfDojo: Automated ML Library Generation for Heterogeneous Architectures

The increasing complexity of machine learning models and the proliferation of diverse hardware architectures (CPUs, GPUs, accelerators) make achieving optimal performance a significant challenge. Heterogeneity in instruction sets, specialized kernel requirements for different data types and model features (e.g., sparsity, quantization), and architecture-specific optimizations complicate performance tuning. Manual optimization is resource-intensive, while existing automatic approaches often rely on complex hardware-specific heuristics and uninterpretable intermediate representations, hindering performance portability. We introduce PerfLLM, a novel automatic optimization methodology leveraging Large Language Models (LLMs) and Reinforcement Learning (RL). Central to this is PerfDojo, an environment framing optimization as an RL game using a human-readable, mathematically-inspired code representation that guarantees semantic validity through transformations. This allows effective optimization without prior hardware knowledge, facilitating both human analysis and RL agent training. We demonstrate PerfLLM's ability to achieve significant performance gains across diverse CPU (x86, Arm, RISC-V) and GPU architectures.

cs.PF↗

arXiv2025

RailX: A Flexible, Scalable, and Low-Cost Network Architecture for Hyper-Scale LLM Training Systems

Increasingly large AI workloads are calling for hyper-scale infrastructure; however, traditional interconnection network architecture is neither scalable nor cost-effective enough. Tree-based topologies such as the \textit{Rail-optimized} network are extremely expensive, while direct topologies such as \textit{Torus} have insufficient bisection bandwidth and flexibility. In this paper, we propose \textit{RailX}, a reconfigurable network architecture based on intra-node direct connectivity and inter-node circuit switching. Nodes and optical switches are physically 2D-organized, achieving better scalability than existing centralized circuit switching networks. We propose a novel interconnection method based on \textit{Hamiltonian Decomposition} theory to organize separate rail-based rings into \textit{all-to-all} topology, simultaneously optimizing ring-collective and all-to-all communication. More than $100$K chips with hyper bandwidth can be interconnected with a flat switching layer, and the diameter is only $2\sim4$ inter-node hops. The network cost per injection/All-Reduce bandwidth of \textit{RailX} is less than $10\%$ of the Fat-Tree, and the cost per bisection/All-to-All bandwidth is less than $50\%$ of the Fat-Tree. Specifically, only $\sim$\$$1.3$B is required to interconnect 200K chips with 1.8TB bandwidth. \textit{RailX} can also be used in the ML-as-a-service (MLaaS) scenario, where single or multiple training workloads with various shapes, scales, and parallelism strategies can be flexibly mapped, and failures can be worked around.

cs.AR↗

arXiv2025

YOLOv11-RGBT: Towards a Comprehensive Single-Stage Multispectral Object Detection Framework

Multispectral object detection, which integrates information from multiple bands, can enhance detection accuracy and environmental adaptability, holding great application potential across various fields. Although existing methods have made progress in cross-modal interaction, low-light conditions, and model lightweight, there are still challenges like the lack of a unified single-stage framework, difficulty in balancing performance and fusion strategy, and unreasonable modality weight allocation. To address these, based on the YOLOv11 framework, we present YOLOv11-RGBT, a new comprehensive multimodal object detection framework. We designed six multispectral fusion modes and successfully applied them to models from YOLOv3 to YOLOv12 and RT-DETR. After reevaluating the importance of the two modalities, we proposed a P3 mid-fusion strategy and multispectral controllable fine-tuning (MCF) strategy for multispectral models. These improvements optimize feature fusion, reduce redundancy and mismatches, and boost overall model performance. Experiments show our framework excels on three major open-source multispectral object detection datasets, like LLVIP and FLIR. Particularly, the multispectral controllable fine-tuning strategy significantly enhanced model adaptability and robustness. On the FLIR dataset, it consistently improved YOLOv11 models' mAP by 3.41%-5.65%, reaching a maximum of 47.61%, verifying the framework and strategies' effectiveness. The code is available at: https://github.com/wandahangFY/YOLOv11-RGBT.

cs.CV↗

arXiv2025

MARMOT: Masked Autoencoder for Modeling Transient Imaging

Pretrained models have demonstrated impressive success in many modalities such as language and vision. Recent works facilitate the pretraining paradigm in imaging research. Transients are a novel modality, which are captured for an object as photon counts versus arrival times using a precisely time-resolved sensor. In particular for non-line-of-sight (NLOS) scenarios, transients of hidden objects are measured beyond the sensor's direct line of sight. Using NLOS transients, the majority of previous works optimize volume density or surfaces to reconstruct the hidden objects and do not transfer priors learned from datasets. In this work, we present a masked autoencoder for modeling transient imaging, or MARMOT, to facilitate NLOS applications. Our MARMOT is a self-supervised model pretrianed on massive and diverse NLOS transient datasets. Using a Transformer-based encoder-decoder, MARMOT learns features from partially masked transients via a scanning pattern mask (SPM), where the unmasked subset is functionally equivalent to arbitrary sampling, and predicts full measurements. Pretrained on TransVerse-a synthesized transient dataset of 500K 3D models-MARMOT adapts to downstream imaging tasks using direct feature transfer or decoder finetuning. Comprehensive experiments are carried out in comparisons with state-of-the-art methods. Quantitative and qualitative results demonstrate the efficiency of our MARMOT.

cs.CV↗

arXiv2025

ATLAHS: An Application-centric Network Simulator Toolchain for AI, HPC, and Distributed Storage

Network simulators play a crucial role in evaluating the performance of large-scale systems. However, existing simulators rely heavily on synthetic microbenchmarks or narrowly focus on specific domains, limiting their ability to provide comprehensive performance insights. In this work, we introduce ATLAHS, a flexible, extensible, and open-source toolchain designed to trace real-world applications and accurately simulate their workloads. ATLAHS leverages the GOAL format to model communication and computation patterns in AI, HPC, and distributed storage applications. It supports multiple network simulation backends and handles multi-job and multi-tenant scenarios. Through extensive validation, we demonstrate that ATLAHS achieves high accuracy in simulating realistic workloads (consistently less than 5% error), while significantly outperforming AstraSim, the current state-of-the-art AI systems simulator, in terms of simulation runtime and trace size efficiency. We further illustrate ATLAHS's utility via detailed case studies, highlighting the impact of congestion control algorithms on the performance of distributed storage systems, as well as the influence of job-placement strategies on application runtimes.

cs.DC↗

arXiv2025

SDR-RDMA: Software-Defined Reliability Architecture for Planetary Scale RDMA Communication

RDMA is vital for efficient distributed training across datacenters, but millisecond-scale latencies complicate the design of its reliability layer. We show that depending on long-haul link characteristics, such as drop rate, distance and bandwidth, the widely used Selective Repeat algorithm can be inefficient, warranting alternatives like Erasure Coding. To enable such alternatives on existing hardware, we propose SDR-RDMA, a software-defined reliability stack for RDMA. Its core is a lightweight SDR SDK that extends standard point-to-point RDMA semantics -- fundamental to AI networking stacks -- with a receive buffer bitmap. SDR bitmap enables partial message completion to let applications implement custom reliability schemes tailored to specific deployments, while preserving zero-copy RDMA benefits. By offloading the SDR backend to NVIDIA's Data Path Accelerator (DPA), we achieve line-rate performance, enabling efficient inter-datacenter communication and advancing reliability innovation for inter-datacenter training.

cs.NI↗

arXiv2025

TransiT: Transient Transformer for Non-line-of-sight Videography

High quality and high speed videography using Non-Line-of-Sight (NLOS) imaging benefit autonomous navigation, collision prevention, and post-disaster search and rescue tasks. Current solutions have to balance between the frame rate and image quality. High frame rates, for example, can be achieved by reducing either per-point scanning time or scanning density, but at the cost of lowering the information density at individual frames. Fast scanning process further reduces the signal-to-noise ratio and different scanning systems exhibit different distortion characteristics. In this work, we design and employ a new Transient Transformer architecture called TransiT to achieve real-time NLOS recovery under fast scans. TransiT directly compresses the temporal dimension of input transients to extract features, reducing computation costs and meeting high frame rate requirements. It further adopts a feature fusion mechanism as well as employs a spatial-temporal Transformer to help capture features of NLOS transient videos. Moreover, TransiT applies transfer learning to bridge the gap between synthetic and real-measured data. In real experiments, TransiT manages to reconstruct from sparse transients of $16 \times 16$ measured at an exposure time of 0.4 ms per point to NLOS videos at a $64 \times 64$ resolution at 10 frames per second. We will make our code and dataset available to the community.

cs.CV↗

arXiv2025

Robust Dynamic Facial Expression Recognition

The study of Dynamic Facial Expression Recognition (DFER) is a nascent field of research that involves the automated recognition of facial expressions in video data. Although existing research has primarily focused on learning representations under noisy and hard samples, the issue of the coexistence of both types of samples remains unresolved. In order to overcome this challenge, this paper proposes a robust method of distinguishing between hard and noisy samples. This is achieved by evaluating the prediction agreement of the model on different sampled clips of the video. Subsequently, methodologies that reinforce the learning of hard samples and mitigate the impact of noisy samples can be employed. Moreover, to identify the principal expression in a video and enhance the model's capacity for representation learning, comprising a key expression re-sampling framework and a dual-stream hierarchical network is proposed, namely Robust Dynamic Facial Expression Recognition (RDFER). The key expression re-sampling framework is designed to identify the key expression, thereby mitigating the potential confusion caused by non-target expressions. RDFER employs two sequence models with the objective of disentangling short-term facial movements and long-term emotional changes. The proposed method has been shown to outperform current State-Of-The-Art approaches in DFER through extensive experimentation on benchmark datasets such as DFEW and FERV39K. A comprehensive analysis provides valuable insights and observations regarding the proposed agreement. This work has significant implications for the field of dynamic facial expression recognition and promotes the further development of the field of noise-consistent robust learning in dynamic facial expression recognition. The code is available from [https://github.com/Cross-Innovation-Lab/RDFER].

cs.CV↗

arXiv2024

Elastic Locomotion with Mixed Second-order Differentiation

We present a framework of elastic locomotion, which allows users to enliven an elastic body to produce interesting locomotion by prescribing its high-level kinematics. We formulate this problem as an inverse simulation problem and seek the optimal muscle activations to drive the body to complete the desired actions. We employ the interior-point method to model wide-area contacts between the body and the environment with logarithmic barrier penalties. The core of our framework is a mixed second-order differentiation algorithm. By combining both analytic differentiation and numerical differentiation modalities, a general-purpose second-order differentiation scheme is made possible. Specifically, we augment complex-step finite difference (CSFD) with reverse automatic differentiation (AD). We treat AD as a generic function, mapping a computing procedure to its derivative w.r.t. output loss, and promote CSFD along the AD computation. To this end, we carefully implement all the arithmetics used in elastic locomotion, from elementary functions to linear algebra and matrix operation for CSFD promotion. With this novel differentiation tool, elastic locomotion can directly exploit Newton's method and use its strong second-order convergence to find the needed activations at muscle fibers. This is not possible with existing first-order inverse or differentiable simulation techniques. We showcase a wide range of interesting locomotions of soft bodies and creatures to validate our method.

cs.GR↗

arXiv2024

LLAMP: Assessing Network Latency Tolerance of HPC Applications with Linear Programming

The shift towards high-bandwidth networks driven by AI workloads in data centers and HPC clusters has unintentionally aggravated network latency, adversely affecting the performance of communication-intensive HPC applications. As large-scale MPI applications often exhibit significant differences in their network latency tolerance, it is crucial to accurately determine the extent of network latency an application can withstand without significant performance degradation. Current approaches to assessing this metric often rely on specialized hardware or network simulators, which can be inflexible and time-consuming. In response, we introduce LLAMP, a novel toolchain that offers an efficient, analytical approach to evaluating HPC applications' network latency tolerance using the LogGPS model and linear programming. LLAMP equips software developers and network architects with essential insights for optimizing HPC infrastructures and strategically deploying applications to minimize latency impacts. Through our validation on a variety of MPI applications like MILC, LULESH, and LAMMPS, we demonstrate our tool's high accuracy, with relative prediction errors generally below 2%. Additionally, we include a case study of the ICON weather and climate model to illustrate LLAMP's broad applicability in evaluating collective algorithms and network topologies.

cs.DC↗