HEALNet -- Hybrid Multi-Modal Fusion for Heterogeneous Biomedical Data

Technological advances in medical data collection such as high-resolution histopathology and high-throughput genomic sequencing have contributed to the rising requirement for multi-modal biomedical modelling, specifically for image, tabular, and graph data. Most multi-modal deep learning approaches use modality-specific architectures that are trained separately and cannot capture the crucial cross-modal information that motivates the integration of different data sources. This paper presents the Hybrid Early-fusion Attention Learning Network (HEALNet): a flexible multi-modal fusion architecture, which a) preserves modality-specific structural information, b) captures the cross-modal interactions and structural information in a shared latent space, c) can effectively handle missing modalities during training and inference, and d) enables intuitive model inspection by learning on the raw data input instead of opaque embeddings. We conduct multi-modal survival analysis on Whole Slide Images and Multi-omic data on four cancer cohorts of The Cancer Genome Atlas (TCGA). HEALNet achieves state-of-the-art performance, substantially improving over both uni-modal and recent multi-modal baselines, whilst being robust in scenarios with missing modalities.Comment: 7 pages body, 5 pages appendi

Constraining Variational Inference with Geometric Jensen-Shannon Divergence.

We examine the problem of controlling divergences for latent space regularisation in variational autoencoders. Specifically, when aiming to reconstruct example $x\in\mathbb{R}^{m}$ via latent space $z\in\mathbb{R}^{n}$ ($n\leq m$), while balancing this against the need for generalisable latent representations. We present a regularisation mechanism based on the skew-geometric Jensen-Shannon divergence $\left(\textrm{JS}^{\textrm{G}_{\alpha}}\right)$. We find a variation in $\textrm{JS}^{\textrm{G}_{\alpha}}$, motivated by limiting cases, which leads to an intuitive interpolation between forward and reverse KL in the space of both distributions and divergences. We motivate its potential benefits for VAEs through low-dimensional examples, before presenting quantitative and qualitative results. Our experiments demonstrate that skewing our variant of $\textrm{JS}^{\textrm{G}_{\alpha}}$, in the context of $\textrm{JS}^{\textrm{G}_{\alpha}}$-VAEs, leads to better reconstruction and generation when compared to several baseline VAEs. Our approach is entirely unsupervised and utilises only one hyperparameter which can be easily interpreted in latent space.Comment: Camera-ready version, accepted at NeurIPS 202

GCondNet: A Novel Method for Improving Neural Networks on Small High-Dimensional Tabular Data

Neural network models often struggle with high-dimensional but small sample-size tabular datasets. One reason is that current weight initialisation methods assume independence between weights, which can be problematic when there are insufficient samples to estimate the model's parameters accurately. In such small data scenarios, leveraging additional structures can improve the model's training stability and performance. To address this, we propose GCondNet, a general approach to enhance neural networks by leveraging implicit structures present in tabular data. We create a graph between samples for each data dimension, and utilise Graph Neural Networks (GNNs) for extracting this implicit structure, and for conditioning the parameters of the first layer of an underlying predictor MLP network. By creating many small graphs, GCondNet exploits the data's high-dimensionality, and thus improves the performance of an underlying predictor network. We demonstrate the effectiveness of our method on nine real-world datasets, where GCondNet outperforms 14 standard and state-of-the-art methods. The results show that GCondNet is robust and can be applied to any small sample-size and high-dimensional tabular learning task.Comment: Early version presented at the 17th Machine Learning in Computational Biology (MLCB) meeting, 202

In-Domain Self-Supervised Learning Can Lead to Improvements in Remote Sensing Image Classification

Self-supervised learning (SSL) has emerged as a promising approach for remote sensing image classification due to its ability to leverage large amounts of unlabeled data. In contrast to traditional supervised learning, SSL aims to learn representations of data without the need for explicit labels. This is achieved by formulating auxiliary tasks that can be used to create pseudo-labels for the unlabeled data and learn pre-trained models. The pre-trained models can then be fine-tuned on downstream tasks such as remote sensing image scene classification. The paper analyzes the effectiveness of SSL pre-training using Million AID - a large unlabeled remote sensing dataset on various remote sensing image scene classification datasets as downstream tasks. More specifically, we evaluate the effectiveness of SSL pre-training using the iBOT framework coupled with Vision transformers (ViT) in contrast to supervised pre-training of ViT using the ImageNet dataset. The comprehensive experimental work across 14 datasets with diverse properties reveals that in-domain SSL leads to improved predictive performance of models compared to the supervised counterparts

Current Trends in Deep Learning for Earth Observation: An Open-source Benchmark Arena for Image Classification

We present 'AiTLAS: Benchmark Arena' -- an open-source benchmark framework for evaluating state-of-the-art deep learning approaches for image classification in Earth Observation (EO). To this end, we present a comprehensive comparative analysis of more than 400 models derived from nine different state-of-the-art architectures, and compare them to a variety of multi-class and multi-label classification tasks from 22 datasets with different sizes and properties. In addition to models trained entirely on these datasets, we also benchmark models trained in the context of transfer learning, leveraging pre-trained model variants, as it is typically performed in practice. All presented approaches are general and can be easily extended to many other remote sensing image classification tasks not considered in this study. To ensure reproducibility and facilitate better usability and further developments, all of the experimental resources including the trained models, model configurations and processing details of the datasets (with their corresponding splits used for training and evaluating the models) are publicly available on the repository: https://github.com/biasvariancelabs/aitlas-arena

Enhancing Representation Learning on High-Dimensional, Small-Size Tabular Data: A Divide and Conquer Method with Ensembled VAEs

Variational Autoencoders and their many variants have displayed impressive ability to perform dimensionality reduction, often achieving state-of-the-art performance. Many current methods however, struggle to learn good representations in High Dimensional, Low Sample Size (HDLSS) tasks, which is an inherently challenging setting. We address this challenge by using an ensemble of lightweight VAEs to learn posteriors over subsets of the feature-space, which get aggregated into a joint posterior in a novel divide-and-conquer approach. Specifically, we present an alternative factorisation of the joint posterior that induces a form of implicit data augmentation that yields greater sample efficiency. Through a series of experiments on eight real-world datasets, we show that our method learns better latent representations in HDLSS settings, which leads to higher accuracy in a downstream classification task. Furthermore, we verify that our approach has a positive effect on disentanglement and achieves a lower estimated Total Correlation on learnt representations. Finally, we show that our approach is robust to partial features at inference, exhibiting little performance degradation even with most features missing