arXiv subjects

Yiren Zhao

Publications and source records attributed to Yiren Zhao.

At least 55 records · Page 3Linked to original sources

arXiv2024

Absorb & Escape: Overcoming Single Model Limitations in Generating Genomic Sequences

Abstract Recent advances in immunology and synthetic biology have accelerated the development of deep generative methods for DNA sequence design. Two dominant approaches in this field are AutoRegressive (AR) models and Diffusion Models (DMs). However, genomic sequences are functionally heterogeneous, consisting of multiple connected regions (e.g., Promoter Regions, Exons, and Introns) where elements within each region come from the same probability distribution, but the overall sequence is non-homogeneous. This heterogeneous nature presents challenges for a single model to accurately generate genomic sequences. In this paper, we analyze the properties of AR models and DMs in heterogeneous genomic sequence generation, pointing out crucial limitations in both methods: (i) AR models capture the underlying distribution of data by factorizing and learning the transition probability but fail to capture the global property of DNA sequences. (ii) DMs learn to recover the global distribution but tend to produce errors at the base pair level. To overcome the limitations of both approaches, we propose a post-training sampling method, termed Absorb & Escape (A&E) to perform compositional generation from AR models and DMs. This approach starts with samples generated by DMs and refines the sample quality using an AR model through the alternation of the Absorb and Escape steps. To assess the quality of generated sequences, we conduct extensive experiments on 15 species for conditional and unconditional DNA generation. The experiment results from motif distribution, diversity checks, and genome integration tests unequivocally show that A&E outperforms state-of-the-art AR models and DMs in genomic sequence generation.

q-bio.GN↗

arXiv2024

Enhancing Node Representations for Real-World Complex Networks with Topological Augmentation

Graph augmentation methods play a crucial role in improving the performance and enhancing generalisation capabilities in Graph Neural Networks (GNNs). Existing graph augmentation methods mainly perturb the graph structures, and are usually limited to pairwise node relations. These methods cannot fully address the complexities of real-world large-scale networks, which often involve higher-order node relations beyond only being pairwise. Meanwhile, real-world graph datasets are predominantly modelled as simple graphs, due to the scarcity of data that can be used to form higher-order edges. Therefore, reconfiguring the higher-order edges as an integration into graph augmentation strategies lights up a promising research path to address the aforementioned issues. In this paper, we present Topological Augmentation (TopoAug), a novel graph augmentation method that builds a combinatorial complex from the original graph by constructing virtual hyperedges directly from the raw data. TopoAug then produces auxiliary node features by extracting information from the combinatorial complex, which are used for enhancing GNN performances on downstream tasks. We design three diverse virtual hyperedge construction strategies to accompany the construction of combinatorial complexes: (1) via graph statistics, (2) from multiple data perspectives, and (3) utilising multi-modality. Furthermore, to facilitate TopoAug evaluation, we provide 23 novel real-world graph datasets across various domains including social media, biology, and e-commerce. Our empirical study shows that TopoAug consistently and significantly outperforms GNN baselines and other graph augmentation methods, across a variety of application contexts, which clearly indicates that it can effectively incorporate higher-order node relations into the graph augmentation for real-world complex networks.

cs.LG↗

arXiv2024

Unlocking the Global Synergies in Low-Rank Adapters

Low-rank Adaption (LoRA) has been the de-facto parameter-efficient fine-tuning technique for large language models. We present HeteroLoRA, a light-weight search algorithm that leverages zero-cost proxies to allocate the limited LoRA trainable parameters across the model for better fine-tuned performance. In addition to the allocation for the standard LoRA-adapted models, we also demonstrate the efficacy of HeteroLoRA by performing the allocation in a more challenging search space that includes LoRA modules and LoRA-adapted shortcut connections. Experiments show that HeteroLoRA enables improvements in model performance given the same parameter budge. For example, on MRPC, we see an improvement of 1.6% in accuracy with similar training parameter budget. We will open-source our algorithm once the paper is accepted.

cs.LG↗

arXiv2024

Optimised Grouped-Query Attention Mechanism for Transformers

Grouped-query attention (GQA) has been widely adopted in LLMs to mitigate the complexity of multi-head attention (MHA). To transform an MHA to a GQA, neighbour queries in MHA are evenly split into groups where each group shares the value and key layers. In this work, we propose AsymGQA, an activation-informed approach to asymmetrically grouping an MHA to a GQA for better model performance. Our AsymGQA outperforms the GQA within the same model size budget. For example, AsymGQA LLaMA-2-7B has an accuracy increase of 7.5% on MMLU compared to neighbour grouping. Our approach addresses the GQA's trade-off problem between model performance and hardware efficiency.

cs.LG↗

arXiv2024

HASS: Hardware-Aware Sparsity Search for Dataflow DNN Accelerator

Deep Neural Networks (DNNs) excel in learning hierarchical representations from raw data, such as images, audio, and text. To compute these DNN models with high performance and energy efficiency, these models are usually deployed onto customized hardware accelerators. Among various accelerator designs, dataflow architecture has shown promising performance due to its layer-pipelined structure and its scalability in data parallelism. Exploiting weights and activations sparsity can further enhance memory storage and computation efficiency. However, existing approaches focus on exploiting sparsity in non-dataflow accelerators, which cannot be applied onto dataflow accelerators because of the large hardware design space introduced. As such, this could miss opportunities to find an optimal combination of sparsity features and hardware designs. In this paper, we propose a novel approach to exploit unstructured weights and activations sparsity for dataflow accelerators, using software and hardware co-optimization. We propose a Hardware-Aware Sparsity Search (HASS) to systematically determine an efficient sparsity solution for dataflow accelerators. Over a set of models, we achieve an efficiency improvement ranging from 1.3$\times$ to 4.2$\times$ compared to existing sparse designs, which are either non-dataflow or non-hardware-aware. Particularly, the throughput of MobileNetV3 can be optimized to 4895 images per second. HASS is open-source: \url{https://github.com/Yu-Zhewen/HASS}

cs.AR↗

arXiv2024

$Δ$-DiT: A Training-Free Acceleration Method Tailored for Diffusion Transformers

Diffusion models are widely recognized for generating high-quality and diverse images, but their poor real-time performance has led to numerous acceleration works, primarily focusing on UNet-based structures. With the more successful results achieved by diffusion transformers (DiT), there is still a lack of exploration regarding the impact of DiT structure on generation, as well as the absence of an acceleration framework tailored to the DiT architecture. To tackle these challenges, we conduct an investigation into the correlation between DiT blocks and image generation. Our findings reveal that the front blocks of DiT are associated with the outline of the generated images, while the rear blocks are linked to the details. Based on this insight, we propose an overall training-free inference acceleration framework $Δ$-DiT: using a designed cache mechanism to accelerate the rear DiT blocks in the early sampling stages and the front DiT blocks in the later stages. Specifically, a DiT-specific cache mechanism called $Δ$-Cache is proposed, which considers the inputs of the previous sampling image and reduces the bias in the inference. Extensive experiments on PIXART-$α$ and DiT-XL demonstrate that the $Δ$-DiT can achieve a $1.6\times$ speedup on the 20-step generation and even improves performance in most cases. In the scenario of 4-step consistent model generation and the more challenging $1.12\times$ acceleration, our method significantly outperforms existing methods. Our code will be publicly available.

cs.CV↗

arXiv2024

LQER: Low-Rank Quantization Error Reconstruction for LLMs

Post-training quantization of Large Language Models (LLMs) is challenging. In this work, we introduce Low-rank Quantization Error Reduction (LQER), which combines quantization and low-rank approximation to recover the model capability. LQER leverages an activation-induced scale matrix to drive the singular value distribution of quantization error towards a desirable distribution, which enables nearly-lossless W4A8 quantization on various LLMs and downstream tasks without the need for knowledge distillation, grid search, or gradient-base iterative optimization. Unlike existing methods, the computation pattern of LQER eliminates the need for specialized Scatter and Gather processes to collect high-precision weights from irregular memory locations. Our W4A8 LLMs achieve near-lossless performance on six popular downstream tasks, while using 1.36$\times$ fewer hardware resources than the leading state-of-the-art method. We open-source our framework at https://github.com/ChengZhang-98/lqer

cs.LG↗

arXiv2024

A Dataflow Compiler for Efficient LLM Inference using Custom Microscaling Formats

Model quantization represents both parameters (weights) and intermediate values (activations) in a more compact format, thereby directly reducing both computational and memory cost in hardware. The quantization of recent large language models (LLMs) faces challenges to achieve competitive memory density compared to other models such as convolutional neural networks, since values in LLMs require larger dynamic ranges. Current hardware can expedite computation for LLMs using compact numerical formats such as low-bitwidth integers or floating-point numbers. Each has advantages: integer operations simplify circuit design, whereas floating-point calculations can enhance accuracy when a wider dynamic range is required. In this work, we seek an efficient data format that combines the best of both worlds: Microscaling (MX) formats. MX formats are efficient data formats that achieve both large dynamic ranges and high memory density. In this paper, we propose a compiler named MASE for exploring mixed-precision MX formats on dataflow hardware accelerators for LLM inference. Our main contributions are twofold. First, we propose a novel orchestration abstraction to explore both software and hardware optimizations with new data formats. Second, MASE achieves LLM inference at an average precision of 4-bits, with minimal to no accuracy degradation. To our knowledge, MASE represents the first effort to harness fine-grain multi-precision MX formats in the design of LLM hardware accelerators. Over a range of LLMs and datasets, MASE achieves an average improvement of 24% in $Δ$ accuracy with an overhead of only 3% in energy efficiency compared to designs using 8-bit fixed-point numbers.

cs.AR↗

arXiv2024

DiscDiff: Latent Diffusion Model for DNA Sequence Generation

This paper introduces a novel framework for DNA sequence generation, comprising two key components: DiscDiff, a Latent Diffusion Model (LDM) tailored for generating discrete DNA sequences, and Absorb-Escape, a post-training algorithm designed to refine these sequences. Absorb-Escape enhances the realism of the generated sequences by correcting `round errors' inherent in the conversion process between latent and input spaces. Our approach not only sets new standards in DNA sequence generation but also demonstrates superior performance over existing diffusion models, in generating both short and long DNA sequences. Additionally, we introduce EPD-GenDNA, the first comprehensive, multi-species dataset for DNA generation, encompassing 160,000 unique sequences from 15 species. We hope this study will advance the generative modelling of DNA, with potential implications for gene therapy and protein production.

q-bio.GN↗

arXiv2024

The Curse of Recursion: Training on Generated Data Makes Models Forget

Stable Diffusion revolutionised image creation from descriptive text. GPT-2, GPT-3(.5) and GPT-4 demonstrated astonishing performance across a variety of language tasks. ChatGPT introduced such language models to the general public. It is now clear that large language models (LLMs) are here to stay, and will bring about drastic change in the whole ecosystem of online text and images. In this paper we consider what the future might hold. What will happen to GPT-{n} once LLMs contribute much of the language found online? We find that use of model-generated content in training causes irreversible defects in the resulting models, where tails of the original content distribution disappear. We refer to this effect as Model Collapse and show that it can occur in Variational Autoencoders, Gaussian Mixture Models and LLMs. We build theoretical intuition behind the phenomenon and portray its ubiquity amongst all learned generative models. We demonstrate that it has to be taken seriously if we are to sustain the benefits of training from large-scale data scraped from the web. Indeed, the value of data collected about genuine human interactions with systems will be increasingly valuable in the presence of content generated by LLMs in data crawled from the Internet.

cs.LG↗

arXiv2024

ImpNet: Imperceptible and blackbox-undetectable backdoors in compiled neural networks

Early backdoor attacks against machine learning set off an arms race in attack and defence development. Defences have since appeared demonstrating some ability to detect backdoors in models or even remove them. These defences work by inspecting the training data, the model, or the integrity of the training procedure. In this work, we show that backdoors can be added during compilation, circumventing any safeguards in the data preparation and model training stages. The attacker can not only insert existing weight-based backdoors during compilation, but also a new class of weight-independent backdoors, such as ImpNet. These backdoors are impossible to detect during the training or data preparation processes, because they are not yet present. Next, we demonstrate that some backdoors, including ImpNet, can only be reliably detected at the stage where they are inserted and removing them anywhere else presents a significant challenge. We conclude that ML model security requires assurance of provenance along the entire technical pipeline, including the data, model architecture, compiler, and hardware specification.

cs.LG↗

arXiv2024

Hybrid Graph: A Unified Graph Representation with Datasets and Benchmarks for Complex Graphs

Graphs are widely used to encapsulate a variety of data formats, but real-world networks often involve complex node relations beyond only being pairwise. While hypergraphs and hierarchical graphs have been developed and employed to account for the complex node relations, they cannot fully represent these complexities in practice. Additionally, though many Graph Neural Networks (GNNs) have been proposed for representation learning on higher-order graphs, they are usually only evaluated on simple graph datasets. Therefore, there is a need for a unified modelling of higher-order graphs, and a collection of comprehensive datasets with an accessible evaluation framework to fully understand the performance of these algorithms on complex graphs. In this paper, we introduce the concept of hybrid graphs, a unified definition for higher-order graphs, and present the Hybrid Graph Benchmark (HGB). HGB contains 23 real-world hybrid graph datasets across various domains such as biology, social media, and e-commerce. Furthermore, we provide an extensible evaluation framework and a supporting codebase to facilitate the training and evaluation of GNNs on HGB. Our empirical study of existing GNNs on HGB reveals various research opportunities and gaps, including (1) evaluating the actual performance improvement of hypergraph GNNs over simple graph GNNs; (2) comparing the impact of different sampling strategies on hybrid graph learning methods; and (3) exploring ways to integrate simple graph and hypergraph information. We make our source code and full datasets publicly available at https://zehui127.github.io/hybrid-graph-benchmark/.

cs.LG↗

arXiv2024

Will More Expressive Graph Neural Networks do Better on Generative Tasks?

Graph generation poses a significant challenge as it involves predicting a complete graph with multiple nodes and edges based on simply a given label. This task also carries fundamental importance to numerous real-world applications, including de-novo drug and molecular design. In recent years, several successful methods have emerged in the field of graph generation. However, these approaches suffer from two significant shortcomings: (1) the underlying Graph Neural Network (GNN) architectures used in these methods are often underexplored; and (2) these methods are often evaluated on only a limited number of metrics. To fill this gap, we investigate the expressiveness of GNNs under the context of the molecular graph generation task, by replacing the underlying GNNs of graph generative models with more expressive GNNs. Specifically, we analyse the performance of six GNNs in two different generative frameworks -- autoregressive generation models, such as GCPN and GraphAF, and one-shot generation models, such as GraphEBM -- on six different molecular generative objectives on the ZINC-250k dataset. Through our extensive experiments, we demonstrate that advanced GNNs can indeed improve the performance of GCPN, GraphAF, and GraphEBM on molecular generation tasks, but GNN expressiveness is not a necessary condition for a good GNN-based generative model. Moreover, we show that GCPN and GraphAF with advanced GNNs can achieve state-of-the-art results across 17 other non-GNN-based graph generative approaches, such as variational autoencoders and Bayesian optimisation models, on the proposed molecular generative objectives (DRD2, Median1, Median2), which are important metrics for de-novo molecular design.

cs.LG↗

arXiv2024

Architectural Neural Backdoors from First Principles

While previous research backdoored neural networks by changing their parameters, recent work uncovered a more insidious threat: backdoors embedded within the definition of the network's architecture. This involves injecting common architectural components, such as activation functions and pooling layers, to subtly introduce a backdoor behavior that persists even after (full re-)training. However, the full scope and implications of architectural backdoors have remained largely unexplored. Bober-Irizar et al. [2023] introduced the first architectural backdoor; they showed how to create a backdoor for a checkerboard pattern, but never explained how to target an arbitrary trigger pattern of choice. In this work we construct an arbitrary trigger detector which can be used to backdoor an architecture with no human supervision. This leads us to revisit the concept of architecture backdoors and taxonomise them, describing 12 distinct types. To gauge the difficulty of detecting such backdoors, we conducted a user study, revealing that ML developers can only identify suspicious components in common model definitions as backdoors in 37% of cases, while they surprisingly preferred backdoored models in 33% of cases. To contextualize these results, we find that language models outperform humans at the detection of backdoors. Finally, we discuss defenses against architectural backdoors, emphasizing the need for robust and comprehensive strategies to safeguard the integrity of ML systems.

cs.CR↗

arXiv2023

Latent Diffusion Model for DNA Sequence Generation

The harnessing of machine learning, especially deep generative models, has opened up promising avenues in the field of synthetic DNA sequence generation. Whilst Generative Adversarial Networks (GANs) have gained traction for this application, they often face issues such as limited sample diversity and mode collapse. On the other hand, Diffusion Models are a promising new class of generative models that are not burdened with these problems, enabling them to reach the state-of-the-art in domains such as image generation. In light of this, we propose a novel latent diffusion model, DiscDiff, tailored for discrete DNA sequence generation. By simply embedding discrete DNA sequences into a continuous latent space using an autoencoder, we are able to leverage the powerful generative abilities of continuous diffusion models for the generation of discrete data. Additionally, we introduce Fréchet Reconstruction Distance (FReD) as a new metric to measure the sample quality of DNA sequence generations. Our DiscDiff model demonstrates an ability to generate synthetic DNA sequences that align closely with real DNA in terms of Motif Distribution, Latent Embedding Distribution (FReD), and Chromatin Profiles. Additionally, we contribute a comprehensive cross-species dataset of 150K unique promoter-gene sequences from 15 species, enriching resources for future generative modelling in genomics. We will make our code public upon publication.

cs.LG↗

arXiv2023

MiliPoint: A Point Cloud Dataset for mmWave Radar

Millimetre-wave (mmWave) radar has emerged as an attractive and cost-effective alternative for human activity sensing compared to traditional camera-based systems. mmWave radars are also non-intrusive, providing better protection for user privacy. However, as a Radio Frequency (RF) based technology, mmWave radars rely on capturing reflected signals from objects, making them more prone to noise compared to cameras. This raises an intriguing question for the deep learning community: Can we develop more effective point set-based deep learning methods for such attractive sensors? To answer this question, our work, termed MiliPoint, delves into this idea by providing a large-scale, open dataset for the community to explore how mmWave radars can be utilised for human activity recognition. Moreover, MiliPoint stands out as it is larger in size than existing datasets, has more diverse human actions represented, and encompasses all three key tasks in human activity recognition. We have also established a range of point-based deep neural networks such as DGCNN, PointNet++ and PointTransformer, on MiliPoint, which can serve to set the ground baseline for further development.

cs.LG↗

arXiv2023

Revisiting Block-based Quantisation: What is Important for Sub-8-bit LLM Inference?

The inference of Large language models (LLMs) requires immense computation and memory resources. To curtail these costs, quantisation has merged as a promising solution, but existing LLM quantisation mainly focuses on 8-bit. In this work, we explore the statistical and learning properties of the LLM layer and attribute the bottleneck of LLM quantisation to numerical scaling offsets. To address this, we adapt block quantisations for LLMs, a family of methods that share scaling factors across packed numbers. Block quantisations efficiently reduce the numerical scaling offsets solely from an arithmetic perspective, without additional treatments in the computational path. Our nearly-lossless quantised 6-bit LLMs achieve a $19\times$ higher arithmetic density and $5\times$ memory density than the float32 baseline, surpassing the prior art 8-bit quantisation by $2.5\times$ in arithmetic density and $1.2\times$ in memory density, without requiring any data calibration or re-training. We also share our insights into sub-8-bit LLM quantisation, including the mismatch between activation and weight distributions, optimal fine-tuning strategies, and a lower quantisation granularity inherent in the statistical properties of LLMs. The latter two tricks enable nearly-lossless 4-bit LLMs on downstream tasks. Our code is open-sourced.

cs.LG↗

arXiv2023

Genomic Interpreter: A Hierarchical Genomic Deep Neural Network with 1D Shifted Window Transformer

Given the increasing volume and quality of genomics data, extracting new insights requires interpretable machine-learning models. This work presents Genomic Interpreter: a novel architecture for genomic assay prediction. This model outperforms the state-of-the-art models for genomic assay prediction tasks. Our model can identify hierarchical dependencies in genomic sites. This is achieved through the integration of 1D-Swin, a novel Transformer-based block designed by us for modelling long-range hierarchical data. Evaluated on a dataset containing 38,171 DNA segments of 17K base pairs, Genomic Interpreter demonstrates superior performance in chromatin accessibility and gene expression prediction and unmasks the underlying `syntax' of gene regulation.

cs.LG↗