arXiv subjects

Yichao Zhang

Publications and source records attributed to Yichao Zhang.

At least 55 records · Page 3Linked to original sources

arXiv2025

Advanced Deep Learning Methods for Protein Structure Prediction and Design

After AlphaFold won the Nobel Prize, protein prediction with deep learning once again became a hot topic. We comprehensively explore advanced deep learning methods applied to protein structure prediction and design. It begins by examining recent innovations in prediction architectures, with detailed discussions on improvements such as diffusion based frameworks and novel pairwise attention modules. The text analyses key components including structure generation, evaluation metrics, multiple sequence alignment processing, and network architecture, thereby illustrating the current state of the art in computational protein modelling. Subsequent chapters focus on practical applications, presenting case studies that range from individual protein predictions to complex biomolecular interactions. Strategies for enhancing prediction accuracy and integrating deep learning techniques with experimental validation are thoroughly explored. The later sections review the industry landscape of protein design, highlighting the transformative role of artificial intelligence in biotechnology and discussing emerging market trends and future challenges. Supplementary appendices provide essential resources such as databases and open source tools, making this volume a valuable reference for researchers and students.

q-bio.BM↗

arXiv2025

MemPool Flavors: Between Versatility and Specialization in a RISC-V Manycore Cluster

As computational paradigms evolve, applications such as attention-based models, wireless telecommunications, and computer vision impose increasingly challenging requirements on computer architectures: significant memory footprints and computing resources are demanded while maintaining flexibility and programmability at a low power budget. Thanks to their advantageous trade-offs, shared-L1-memory clusters have become a common building block of massively parallel computing architectures tackling these issues. MemPool is an open-source, RISC-V-based manycore cluster scaling up to 1024 processing elements (PEs). MemPool offers a scalable, extensible, and programmable solution to the challenges of shared-L1 clusters, establishing itself as an open-source research platform for architectural variants covering a wide trade-off space between versatility and performance. As a demonstration, this paper compares the three main MemPool flavors, Baseline MemPool, Systolic MemPool, and Vectorial MemPool, detailing their architecture, targets, and achieved trade-offs.

cs.AR↗

arXiv2025

Generative Adversarial Networks Bridging Art and Machine Intelligence

Generative Adversarial Networks (GAN) have greatly influenced the development of computer vision and artificial intelligence in the past decade and also connected art and machine intelligence together. This book begins with a detailed introduction to the fundamental principles and historical development of GANs, contrasting them with traditional generative models and elucidating the core adversarial mechanisms through illustrative Python examples. The text systematically addresses the mathematical and theoretical underpinnings including probability theory, statistics, and game theory providing a solid framework for understanding the objectives, loss functions, and optimisation challenges inherent to GAN training. Subsequent chapters review classic variants such as Conditional GANs, DCGANs, InfoGAN, and LAPGAN before progressing to advanced training methodologies like Wasserstein GANs, GANs with gradient penalty, least squares GANs, and spectral normalisation techniques. The book further examines architectural enhancements and task-specific adaptations in generators and discriminators, showcasing practical implementations in high resolution image generation, artistic style transfer, video synthesis, text to image generation and other multimedia applications. The concluding sections offer insights into emerging research trends, including self-attention mechanisms, transformer-based generative models, and a comparative analysis with diffusion models, thus charting promising directions for future developments in both academic and applied settings.

cs.LG↗

arXiv2025

TCDM Burst Access: Breaking the Bandwidth Barrier in Shared-L1 RVV Clusters Beyond 1000 FPUs

As computing demand and memory footprint of deep learning applications accelerate, clusters of cores sharing local (L1) multi-banked memory are widely used as key building blocks in large-scale architectures. When the cluster's core count increases, a flat all-to-all interconnect between cores and L1 memory banks becomes a physical implementation bottleneck, and hierarchical network topologies are required. However, hierarchical, multi-level intra-cluster networks are subject to internal contention which may lead to significant performance degradation, especially for SIMD or vector cores, as their memory access is bursty. We present the TCDM Burst Access architecture, a software-transparent burst transaction support to improve bandwidth utilization in clusters with many vector cores tightly coupled to a multi-banked L1 data memory. In our solution, a Burst Manager dispatches burst requests to L1 memory banks, multiple 32b words from burst responses are retired in parallel on channels with parametric data-width. We validate our design on a RISC-V Vector (RVV) many-core cluster, evaluating the benefits on different core counts. With minimal logic area overhead (less than 8%), we improve the bandwidth of a 16-, a 256-, and a 1024--Floating Point Unit (FPU) baseline clusters, without Tightly Coupled Data Memory (TCDM) Burst Access, by 118%, 226%, and 77% respectively. Reaching up to 80% of the cores-memory peak bandwidth, our design demonstrates ultra-high bandwidth utilization and enables efficient performance scaling. Implemented in 12-nm FinFET technology node, compared to the serialized access baseline, our solution achieves up to 1.9x energy efficiency and 2.76x performance in real-world kernel benchmarkings.

cs.AR↗

arXiv2025

Occamy: A 432-Core Dual-Chiplet Dual-HBM2E 768-DP-GFLOP/s RISC-V System for 8-to-64-bit Dense and Sparse Computing in 12nm FinFET

ML and HPC applications increasingly combine dense and sparse memory access computations to maximize storage efficiency. However, existing CPUs and GPUs struggle to flexibly handle these heterogeneous workloads with consistently high compute efficiency. We present Occamy, a 432-Core, 768-DP-GFLOP/s, dual-HBM2E, dual-chiplet RISC-V system with a latency-tolerant hierarchical interconnect and in-core streaming units (SUs) designed to accelerate dense and sparse FP8-to-FP64 ML and HPC workloads. We implement Occamy's compute chiplets in 12 nm FinFET, and its passive interposer, Hedwig, in a 65 nm node. On dense linear algebra (LA), Occamy achieves a competitive FPU utilization of 89%. On stencil codes, Occamy reaches an FPU utilization of 83% and a technology-node-normalized compute density of 11.1 DP-GFLOP/s/mm2,leading state-of-the-art (SoA) processors by 1.7x and 1.2x, respectively. On sparse-dense linear algebra (LA), it achieves 42% FPU utilization and a normalized compute density of 5.95 DP-GFLOP/s/mm2, surpassing the SoA by 5.2x and 11x, respectively. On, sparse-sparse LA, Occamy reaches a throughput of up to 187 GCOMP/s at 17.4 GCOMP/s/W and a compute density of 3.63 GCOMP/s/mm2. Finally, we reach up to 75% and 54% FPU utilization on and dense (LLM) and graph-sparse (GCN) ML inference workloads. Occamy's RTL is freely available under a permissive open-source license.

cs.AR↗

arXiv2025

From Aleatoric to Epistemic: Exploring Uncertainty Quantification Techniques in Artificial Intelligence

Uncertainty quantification (UQ) is a critical aspect of artificial intelligence (AI) systems, particularly in high-risk domains such as healthcare, autonomous systems, and financial technology, where decision-making processes must account for uncertainty. This review explores the evolution of uncertainty quantification techniques in AI, distinguishing between aleatoric and epistemic uncertainties, and discusses the mathematical foundations and methods used to quantify these uncertainties. We provide an overview of advanced techniques, including probabilistic methods, ensemble learning, sampling-based approaches, and generative models, while also highlighting hybrid approaches that integrate domain-specific knowledge. Furthermore, we examine the diverse applications of UQ across various fields, emphasizing its impact on decision-making, predictive accuracy, and system robustness. The review also addresses key challenges such as scalability, efficiency, and integration with explainable AI, and outlines future directions for research in this rapidly developing area. Through this comprehensive survey, we aim to provide a deeper understanding of UQ's role in enhancing the reliability, safety, and trustworthiness of AI systems.

cs.AI↗

arXiv2024

Deep Learning Model Security: Threats and Defenses

Deep learning has transformed AI applications but faces critical security challenges, including adversarial attacks, data poisoning, model theft, and privacy leakage. This survey examines these vulnerabilities, detailing their mechanisms and impact on model integrity and confidentiality. Practical implementations, including adversarial examples, label flipping, and backdoor attacks, are explored alongside defenses such as adversarial training, differential privacy, and federated learning, highlighting their strengths and limitations. Advanced methods like contrastive and self-supervised learning are presented for enhancing robustness. The survey concludes with future directions, emphasizing automated defenses, zero-trust architectures, and the security challenges of large AI models. A balanced approach to performance and security is essential for developing reliable deep learning systems.

cs.CR↗

arXiv2024

From Noise to Nuance: Advances in Deep Generative Image Models

Deep learning-based image generation has undergone a paradigm shift since 2021, marked by fundamental architectural breakthroughs and computational innovations. Through reviewing architectural innovations and empirical results, this paper analyzes the transition from traditional generative methods to advanced architectures, with focus on compute-efficient diffusion models and vision transformer architectures. We examine how recent developments in Stable Diffusion, DALL-E, and consistency models have redefined the capabilities and performance boundaries of image synthesis, while addressing persistent challenges in efficiency and quality. Our analysis focuses on the evolution of latent space representations, cross-attention mechanisms, and parameter-efficient training methodologies that enable accelerated inference under resource constraints. While more efficient training methods enable faster inference, advanced control mechanisms like ControlNet and regional attention systems have simultaneously improved generation precision and content customization. We investigate how enhanced multi-modal understanding and zero-shot generation capabilities are reshaping practical applications across industries. Our analysis demonstrates that despite remarkable advances in generation quality and computational efficiency, critical challenges remain in developing resource-conscious architectures and interpretable generation systems for industrial applications. The paper concludes by mapping promising research directions, including neural architecture optimization and explainable generation frameworks.

cs.CV↗

arXiv2024

A Comprehensive Guide to Explainable AI: From Classical Models to LLMs

Explainable Artificial Intelligence (XAI) addresses the growing need for transparency and interpretability in AI systems, enabling trust and accountability in decision-making processes. This book offers a comprehensive guide to XAI, bridging foundational concepts with advanced methodologies. It explores interpretability in traditional models such as Decision Trees, Linear Regression, and Support Vector Machines, alongside the challenges of explaining deep learning architectures like CNNs, RNNs, and Large Language Models (LLMs), including BERT, GPT, and T5. The book presents practical techniques such as SHAP, LIME, Grad-CAM, counterfactual explanations, and causal inference, supported by Python code examples for real-world applications. Case studies illustrate XAI's role in healthcare, finance, and policymaking, demonstrating its impact on fairness and decision support. The book also covers evaluation metrics for explanation quality, an overview of cutting-edge XAI tools and frameworks, and emerging research directions, such as interpretability in federated learning and ethical AI considerations. Designed for a broad audience, this resource equips readers with the theoretical insights and practical skills needed to master XAI. Hands-on examples and additional resources are available at the companion GitHub repository: https://github.com/Echoslayer/XAI_From_Classical_Models_to_LLMs.

cs.LG↗

arXiv2024

Deep Learning, Machine Learning, Advancing Big Data Analytics and Management

Advancements in artificial intelligence, machine learning, and deep learning have catalyzed the transformation of big data analytics and management into pivotal domains for research and application. This work explores the theoretical foundations, methodological advancements, and practical implementations of these technologies, emphasizing their role in uncovering actionable insights from massive, high-dimensional datasets. The study presents a systematic overview of data preprocessing techniques, including data cleaning, normalization, integration, and dimensionality reduction, to prepare raw data for analysis. Core analytics methodologies such as classification, clustering, regression, and anomaly detection are examined, with a focus on algorithmic innovation and scalability. Furthermore, the text delves into state-of-the-art frameworks for data mining and predictive modeling, highlighting the role of neural networks, support vector machines, and ensemble methods in tackling complex analytical challenges. Special emphasis is placed on the convergence of big data with distributed computing paradigms, including cloud and edge computing, to address challenges in storage, computation, and real-time analytics. The integration of ethical considerations, including data privacy and compliance with global standards, ensures a holistic perspective on data management. Practical applications across healthcare, finance, marketing, and policy-making illustrate the real-world impact of these technologies. Through comprehensive case studies and Python-based implementations, this work equips researchers, practitioners, and data enthusiasts with the tools to navigate the complexities of modern data analytics. It bridges the gap between theory and practice, fostering the development of innovative solutions for managing and leveraging data in the era of artificial intelligence.

cs.LG↗

arXiv2024

Fire-Flyer AI-HPC: A Cost-Effective Software-Hardware Co-Design for Deep Learning

The rapid progress in Deep Learning (DL) and Large Language Models (LLMs) has exponentially increased demands of computational power and bandwidth. This, combined with the high costs of faster computing chips and interconnects, has significantly inflated High Performance Computing (HPC) construction costs. To address these challenges, we introduce the Fire-Flyer AI-HPC architecture, a synergistic hardware-software co-design framework and its best practices. For DL training, we deployed the Fire-Flyer 2 with 10,000 PCIe A100 GPUs, achieved performance approximating the DGX-A100 while reducing costs by half and energy consumption by 40%. We specifically engineered HFReduce to accelerate allreduce communication and implemented numerous measures to keep our Computation-Storage Integrated Network congestion-free. Through our software stack, including HaiScale, 3FS, and HAI-Platform, we achieved substantial scalability by overlapping computation and communication. Our system-oriented experience from DL training provides valuable insights to drive future advancements in AI-HPC.

cs.DC↗

arXiv2024

A 1024 RV-Cores Shared-L1 Cluster with High Bandwidth Memory Link for Low-Latency 6G-SDR

We introduce an open-source architecture for next-generation Radio-Access Network baseband processing: 1024 latency-tolerant 32-bit RISC-V cores share 4 MiB of L1 memory via an ultra-low latency interconnect (7-11 cycles), a modular Direct Memory Access engine provides an efficient link to a high bandwidth memory, such as HBM2E (98% peak bandwidth at 910GBps). The system achieves leading-edge energy efficiency at sub-ms latency in key 6G baseband processing kernels: Fast Fourier Transform (93 GOPS/W), Beamforming (125 GOPS/W), Channel Estimation (96 GOPS/W), and Linear System Inversion (61 GOPS/W), with only 9% data movement overhead.

cs.DC↗

arXiv2024

CausalFormer: An Interpretable Transformer for Temporal Causal Discovery

Temporal causal discovery is a crucial task aimed at uncovering the causal relations within time series data. The latest temporal causal discovery methods usually train deep learning models on prediction tasks to uncover the causality between time series. They capture causal relations by analyzing the parameters of some components of the trained models, e.g., attention weights and convolution weights. However, this is an incomplete mapping process from the model parameters to the causality and fails to investigate the other components, e.g., fully connected layers and activation functions, that are also significant for causal discovery. To facilitate the utilization of the whole deep learning models in temporal causal discovery, we proposed an interpretable transformer-based causal discovery model termed CausalFormer, which consists of the causality-aware transformer and the decomposition-based causality detector. The causality-aware transformer learns the causal representation of time series data using a prediction task with the designed multi-kernel causal convolution which aggregates each input time series along the temporal dimension under the temporal priority constraint. Then, the decomposition-based causality detector interprets the global structure of the trained causality-aware transformer with the proposed regression relevance propagation to identify potential causal relations and finally construct the causal graph. Experiments on synthetic, simulated, and real datasets demonstrate the state-of-the-art performance of CausalFormer on discovering temporal causality. Our code is available at https://github.com/lingbai-kong/CausalFormer.

cs.LG↗

arXiv2024

Occamy: A 432-Core 28.1 DP-GFLOP/s/W 83% FPU Utilization Dual-Chiplet, Dual-HBM2E RISC-V-based Accelerator for Stencil and Sparse Linear Algebra Computations with 8-to-64-bit Floating-Point Support in 12nm FinFET

We present Occamy, a 432-core RISC-V dual-chiplet 2.5D system for efficient sparse linear algebra and stencil computations on FP64 and narrow (32-, 16-, 8-bit) SIMD FP data. Occamy features 48 clusters of RISC-V cores with custom extensions, two 64-bit host cores, and a latency-tolerant multi-chiplet interconnect and memory system with 32 GiB of HBM2E. It achieves leading-edge utilization on stencils (83 %), sparse-dense (42 %), and sparse-sparse (49 %) matrix multiply.

cs.AR↗

arXiv2024

Rankin-Cohen Brackets of Hilbert Hecke Eigenforms

Over any fixed totally real number field with narrow class number one, we prove that the Rankin-Cohen bracket of two Hecke eigenforms for the Hilbert modular group can only be a Hecke eigenform for dimension reasons, except for a couple of cases where the Rankin-Selberg method does not apply. We shall also prove a conjecture of Freitag on the volume of Hilbert modular groups, and assuming a conjecture of Freitag on the dimension of the cuspform space, we obtain a finiteness result on eigenform product identities.

math.NT↗

arXiv2024

On Rankin-Cohen Brackets of Hecke Eigenforms and Modular Forms of Half-Integral Weight

We generalize the linear relation formula between the square of normalized Hecke eigenforms of weight $k$ and normalized Hecke eigenforms of weight $2k$, to Rankin-Cohen brackets of general degree. As an ingredient of the proof, we also generalize a formula of Zagier on the Petersson inner product of Rankin-Cohen brackets involving Eisenstein series.

math.NT↗

arXiv2024

TeraPool-SDR: An 1.89TOPS 1024 RV-Cores 4MiB Shared-L1 Cluster for Next-Generation Open-Source Software-Defined Radios

Radio Access Networks (RAN) workloads are rapidly scaling up in data processing intensity and throughput as the 5G (and beyond) standards grow in number of antennas and sub-carriers. Offering flexible Processing Elements (PEs), efficient memory access, and a productive parallel programming model, many-core clusters are a well-matched architecture for next-generation software-defined RANs, but staggering performance requirements demand a high number of PEs coupled with extreme Power, Performance and Area (PPA) efficiency. We present the architecture, design, and full physical implementation of Terapool-SDR, a cluster for Software Defined Radio (SDR) with 1024 latency-tolerant, compact RV32 PEs, sharing a global view of a 4MiB, 4096-banked, L1 memory. We report various feasible configurations of TeraPool-SDR featuring an ultra-high bandwidth PE-to-L1-memory interconnect, clocked at 730MHz, 880MHz, and 924MHz (TT/0.80 V/25 °C) in 12nm FinFET technology. The TeraPool-SDR cluster achieves high energy efficiency on all SDR key kernels for 5G RANs: Fast Fourier Transform (93GOPS/W), Matrix-Multiplication (125GOPS/W), Channel Estimation (96GOPS/W), and Linear System Inversion (61GOPS/W). For all the kernels, it consumes less than 10W, in compliance with industry standards.

cs.DC↗

arXiv2024

Stability-Oriented Prediction Horizons Design of Generalized Predictive Control for DC/DC Boost Converter

This paper introduces a novel approach in designing prediction horizons on a generalized predictive control for a DC/DC boost converter. This method involves constructing a closed-loop system model and assessing the impact of different prediction horizons on system stability. In contrast to conventional design approaches that often rely on empirical prediction horizon selection or incorporate non-linear observers, the proposed method establishes a rigorous boundary for the prediction horizon to ensure system stability. This approach facilitates the selection of an appropriate prediction horizon while avoiding excessively short horizons that can lead to instability and preventing the adoption of unnecessarily long horizons that would burden the controller with high computational demands. Finally, the accuracy of the design method has been confirmed through experimental testing. Moreover, it has been demonstrated that the prediction horizon determined by this method reduces the computational burden by 10\%-20\% compared to the empirically selected prediction horizon.

eess.SY↗