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.

Flareon: Stealthy any2any Backdoor Injection via Poisoned Augmentation

Open software supply chain attacks, once successful, can exact heavy costs in mission-critical applications. As open-source ecosystems for deep learning flourish and become increasingly universal, they present attackers previously unexplored avenues to code-inject malicious backdoors in deep neural network models. This paper proposes Flareon, a small, stealthy, seemingly harmless code modification that specifically targets the data augmentation pipeline with motion-based triggers. Flareon neither alters ground-truth labels, nor modifies the training loss objective, nor does it assume prior knowledge of the victim model architecture, training data, and training hyperparameters. Yet, it has a surprisingly large ramification on training -- models trained under Flareon learn powerful target-conditional (or "any2any") backdoors. The resulting models can exhibit high attack success rates for any target choices and better clean accuracies than backdoor attacks that not only seize greater control, but also assume more restrictive attack capabilities. We also demonstrate the effectiveness of Flareon against recent defenses. Flareon is fully open-source and available online to the deep learning community: https://github.com/lafeat/flareon.

Revisiting Structured Dropout

Large neural networks are often overparameterised and prone to overfitting, Dropout is a widely used regularization technique to combat overfitting and improve model generalization. However, unstructured Dropout is not always effective for specific network architectures and this has led to the formation of multiple structured Dropout approaches to improve model performance and, sometimes, reduce the computational resources required for inference. In this work, we revisit structured Dropout comparing different Dropout approaches to natural language processing and computer vision tasks for multiple state-of-the-art networks. Additionally, we devise an approach to structured Dropout we call \textbf{\emph{ProbDropBlock}} which drops contiguous blocks from feature maps with a probability given by the normalized feature salience values. We find that with a simple scheduling strategy the proposed approach to structured Dropout consistently improved model performance compared to baselines and other Dropout approaches on a diverse range of tasks and models. In particular, we show \textbf{\emph{ProbDropBlock}} improves RoBERTa finetuning on MNLI by $0.22\%$, and training of ResNet50 on ImageNet by $0.28\%$.

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. As an illustration, the attacker can insert weight-based backdoors during the hardware compilation step that will not be detected by any training or data-preparation process. Next, we demonstrate that some backdoors, such as 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 machine-learning model security requires assurance of provenance along the entire technical pipeline, including the data, model architecture, compiler, and hardware specification.