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 Fr\'echet 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.

LLM4DV: Using Large Language Models for Hardware Test Stimuli Generation

Test stimuli generation has been a crucial but labor-intensive task in hardware design verification. In this paper, we revolutionize this process by harnessing the power of large language models (LLMs) and present a novel benchmarking framework, LLM4DV. This framework introduces a prompt template for interactively eliciting test stimuli from the LLM, along with four innovative prompting improvements to support the pipeline execution and further enhance its performance. We compare LLM4DV to traditional constrained-random testing (CRT), using three self-designed design-under-test (DUT) modules. Experiments demonstrate that LLM4DV excels in efficiently handling straightforward DUT scenarios, leveraging its ability to employ basic mathematical reasoning and pre-trained knowledge. While it exhibits reduced efficiency in complex task settings, it still outperforms CRT in relative terms. The proposed framework and the DUT modules used in our experiments will be open-sourced upon publication.

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.

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 (GCPN and GraphAF), 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 and GraphAF 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.

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.

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/.

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.

Revisiting Automated Prompting: Are We Actually Doing Better?

Current literature demonstrates that Large Language Models (LLMs) are great few-shot learners, and prompting significantly increases their performance on a range of downstream tasks in a few-shot learning setting. An attempt to automate human-led prompting followed, with some progress achieved. In particular, subsequent work demonstrates automation can outperform fine-tuning in certain K-shot learning scenarios. In this paper, we revisit techniques for automated prompting on six different downstream tasks and a larger range of K-shot learning settings. We find that automated prompting does not consistently outperform simple manual prompts. Our work suggests that, in addition to fine-tuning, manual prompts should be used as a baseline in this line of research.

Dynamic Stashing Quantization for Efficient Transformer Training

Large Language Models (LLMs) have demonstrated impressive performance on a range of Natural Language Processing (NLP) tasks. Unfortunately, the immense amount of computations and memory accesses required for LLM training makes them prohibitively expensive in terms of hardware cost, and thus challenging to deploy in use cases such as on-device learning. In this paper, motivated by the observation that LLM training is memory-bound, we propose a novel dynamic quantization strategy, termed Dynamic Stashing Quantization (DSQ), that puts a special focus on reducing the memory operations, but also enjoys the other benefits of low precision training, such as the reduced arithmetic cost. We conduct a thorough study on two translation tasks (trained-from-scratch) and three classification tasks (fine-tuning). DSQ reduces the amount of arithmetic operations by $20.95\times$ and the number of DRAM operations by $2.55\times$ on IWSLT17 compared to the standard 16-bit fixed-point, which is widely used in on-device learning.

Task-Agnostic Graph Neural Network Evaluation via Adversarial Collaboration

It has been increasingly demanding to develop reliable Graph Neural Network (GNN) evaluation methods to quantify the progress of the rapidly expanding GNN research. Existing GNN benchmarking methods focus on comparing the GNNs with respect to their performances on some node/graph classification/regression tasks in certain datasets. There lacks a principled, task-agnostic method to directly compare two GNNs. Moreover, most of the existing graph self-supervised learning (SSL) works incorporate handcrafted augmentations to the graph, which has several severe difficulties due to the unique characteristics of graph-structured data. To address the aforementioned issues, we propose GraphAC (Graph Adversarial Collaboration) -- a conceptually novel, principled, task-agnostic, and stable framework for evaluating GNNs through contrastive self-supervision. GraphAC succeeds in distinguishing GNNs of different expressiveness across various aspects, and has been proven to be a principled and reliable GNN evaluation method, eliminating the need for handcrafted augmentations for stable SSL.