GV-Rep: A Large-Scale Dataset for Genetic Variant Representation Learning

Genetic variants (GVs) are defined as differences in the DNA sequences among individuals and play a crucial role in diagnosing and treating genetic diseases. The rapid decrease in next generation sequencing cost has led to an exponential increase in patient-level GV data. This growth poses a challenge for clinicians who must efficiently prioritize patient-specific GVs and integrate them with existing genomic databases to inform patient management. To addressing the interpretation of GVs, genomic foundation models (GFMs) have emerged. However, these models lack standardized performance assessments, leading to considerable variability in model evaluations. This poses the question: How effectively do deep learning methods classify unknown GVs and align them with clinically-verified GVs? We argue that representation learning, which transforms raw data into meaningful feature spaces, is an effective approach for addressing both indexing and classification challenges. We introduce a large-scale Genetic Variant dataset, named GV-Rep, featuring variable-length contexts and detailed annotations, designed for deep learning models to learn GV representations across various traits, diseases, tissue types, and experimental contexts. Our contributions are three-fold: (i) Construction of a comprehensive dataset with 7 million records, each labeled with characteristics of the corresponding variants, alongside additional data from 17,548 gene knockout tests across 1,107 cell types, 1,808 variant combinations, and 156 unique clinically verified GVs from real-world patients. (ii) Analysis of the structure and properties of the dataset. (iii) Experimentation of the dataset with pre-trained GFMs. The results show a significant gap between GFMs current capabilities and accurate GV representation. We hope this dataset will help advance genomic deep learning to bridge this gap.

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.

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.

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}

$Δ$-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 $\Delta$-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 $\Delta$-Cache is proposed, which considers the inputs of the previous sampling image and reduces the bias in the inference. Extensive experiments on PIXART-$\alpha$ and DiT-XL demonstrate that the $\Delta$-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.

Locking Machine Learning Models into Hardware

Modern Machine Learning models are expensive IP and business competitiveness often depends on keeping this IP confidential. This in turn restricts how these models are deployed -- for example it is unclear how to deploy a model on-device without inevitably leaking the underlying model. At the same time, confidential computing technologies such as Multi-Party Computation or Homomorphic encryption remain impractical for wide adoption. In this paper we take a different approach and investigate feasibility of ML-specific mechanisms that deter unauthorized model use by restricting the model to only be usable on specific hardware, making adoption on unauthorized hardware inconvenient. That way, even if IP is compromised, it cannot be trivially used without specialised hardware or major model adjustment. In a sense, we seek to enable cheap locking of machine learning models into specific hardware. We demonstrate that locking mechanisms are feasible by either targeting efficiency of model representations, such making models incompatible with quantisation, or tie the model's operation on specific characteristics of hardware, such as number of cycles for arithmetic operations. We demonstrate that locking comes with negligible work and latency overheads, while significantly restricting usability of the resultant model on unauthorized hardware.

Enhancing Real-World Complex Network Representations with Hyperedge 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 that 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 Hyperedge Augmentation (HyperAug), a novel graph augmentation method that constructs virtual hyperedges directly form the raw data, and produces auxiliary node features by extracting from the virtual hyperedge information, which are used for enhancing GNN performances on downstream tasks. We design three diverse virtual hyperedge construction strategies to accompany the augmentation scheme: (1) via graph statistics, (2) from multiple data perspectives, and (3) utilising multi-modality. Furthermore, to facilitate HyperAug evaluation, we provide 23 novel real-world graph datasets across various domains including social media, biology, and e-commerce. Our empirical study shows that HyperAug 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 graph augmentation methods for real-world complex networks.

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.

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.

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 will open-source our framework once the paper is accepted.