Advancing Gene Selection in Oncology: A Fusion of Deep Learning and Sparsity for Precision Gene Selection

Gene selection plays a pivotal role in oncology research for improving outcome prediction accuracy and facilitating cost-effective genomic profiling for cancer patients. This paper introduces two gene selection strategies for deep learning-based survival prediction models. The first strategy uses a sparsity-inducing method while the second one uses importance based gene selection for identifying relevant genes. Our overall approach leverages the power of deep learning to model complex biological data structures, while sparsity-inducing methods ensure the selection process focuses on the most informative genes, minimizing noise and redundancy. Through comprehensive experimentation on diverse genomic and survival datasets, we demonstrate that our strategy not only identifies gene signatures with high predictive power for survival outcomes but can also streamlines the process for low-cost genomic profiling. The implications of this research are profound as it offers a scalable and effective tool for advancing personalized medicine and targeted cancer therapies. By pushing the boundaries of gene selection methodologies, our work contributes significantly to the ongoing efforts in cancer genomics, promising improved diagnostic and prognostic capabilities in clinical settings.

Heterogeneous graphs model spatial relationships between biological entities for breast cancer diagnosis

The heterogeneity of breast cancer presents considerable challenges for its early detection, prognosis, and treatment selection. Convolutional neural networks often neglect the spatial relationships within histopathological images, which can limit their accuracy. Graph neural networks (GNNs) offer a promising solution by coding the spatial relationships within images. Prior studies have investigated the modeling of histopathological images as cell and tissue graphs, but they have not fully tapped into the potential of extracting interrelationships between these biological entities. In this paper, we present a novel approach using a heterogeneous GNN that captures the spatial and hierarchical relations between cell and tissue graphs to enhance the extraction of useful information from histopathological images. We also compare the performance of a cross-attention-based network and a transformer architecture for modeling the intricate relationships within tissue and cell graphs. Our model demonstrates superior efficiency in terms of parameter count and achieves higher accuracy compared to the transformer-based state-of-the-art approach on three publicly available breast cancer datasets -- BRIGHT, BreakHis, and BACH.

WaveMixSR: A Resource-efficient Neural Network for Image Super-resolution

Image super-resolution research recently been dominated by transformer models which need higher computational resources than CNNs due to the quadratic complexity of self-attention. We propose a new neural network -- WaveMixSR -- for image super-resolution based on WaveMix architecture which uses a 2D-discrete wavelet transform for spatial token-mixing. Unlike transformer-based models, WaveMixSR does not unroll the image as a sequence of pixels/patches. It uses the inductive bias of convolutions along with the lossless token-mixing property of wavelet transform to achieve higher performance while requiring fewer resources and training data. We compare the performance of our network with other state-of-the-art methods for image super-resolution. Our experiments show that WaveMixSR achieves competitive performance in all datasets and reaches state-of-the-art performance in the BSD100 dataset on multiple super-resolution tasks. Our model is able to achieve this performance using less training data and computational resources while maintaining high parameter efficiency compared to current state-of-the-art models.

WavePaint: Resource-efficient Token-mixer for Self-supervised Inpainting

Image inpainting, which refers to the synthesis of missing regions in an image, can help restore occluded or degraded areas and also serve as a precursor task for self-supervision. The current state-of-the-art models for image inpainting are computationally heavy as they are based on transformer or CNN backbones that are trained in adversarial or diffusion settings. This paper diverges from vision transformers by using a computationally-efficient WaveMix-based fully convolutional architecture -- WavePaint. It uses a 2D-discrete wavelet transform (DWT) for spatial and multi-resolution token-mixing along with convolutional layers. The proposed model outperforms the current state-of-the-art models for image inpainting on reconstruction quality while also using less than half the parameter count and considerably lower training and evaluation times. Our model even outperforms current GAN-based architectures in CelebA-HQ dataset without using an adversarially trainable discriminator. Our work suggests that neural architectures that are modeled after natural image priors require fewer parameters and computations to achieve generalization comparable to transformers.

CHATTY: Coupled Holistic Adversarial Transport Terms with Yield for Unsupervised Domain Adaptation

We propose a new technique called CHATTY: Coupled Holistic Adversarial Transport Terms with Yield for Unsupervised Domain Adaptation. Adversarial training is commonly used for learning domain-invariant representations by reversing the gradients from a domain discriminator head to train the feature extractor layers of a neural network. We propose significant modifications to the adversarial head, its training objective, and the classifier head. With the aim of reducing class confusion, we introduce a sub-network which displaces the classifier outputs of the source and target domain samples in a learnable manner. We control this movement using a novel transport loss that spreads class clusters away from each other and makes it easier for the classifier to find the decision boundaries for both the source and target domains. The results of adding this new loss to a careful selection of previously proposed losses leads to improvement in UDA results compared to the previous state-of-the-art methods on benchmark datasets. We show the importance of the proposed loss term using ablation studies and visualization of the movement of target domain sample in representation space.

Magnification Invariant Medical Image Analysis: A Comparison of Convolutional Networks, Vision Transformers, and Token Mixers

Convolution Neural Networks (CNNs) are widely used in medical image analysis, but their performance degrade when the magnification of testing images differ from the training images. The inability of CNNs to generalize across magnification scales can result in sub-optimal performance on external datasets. This study aims to evaluate the robustness of various deep learning architectures in the analysis of breast cancer histopathological images with varying magnification scales at training and testing stages. Here we explore and compare the performance of multiple deep learning architectures, including CNN-based ResNet and MobileNet, self-attention-based Vision Transformers and Swin Transformers, and token-mixing models, such as FNet, ConvMixer, MLP-Mixer, and WaveMix. The experiments are conducted using the BreakHis dataset, which contains breast cancer histopathological images at varying magnification levels. We show that performance of WaveMix is invariant to the magnification of training and testing data and can provide stable and good classification accuracy. These evaluations are critical in identifying deep learning architectures that can robustly handle changes in magnification scale, ensuring that scale changes across anatomical structures do not disturb the inference results.

WaveMix-Lite: A Resource-efficient Neural Network for Image Analysis

Gains in the ability to generalize on image analysis tasks for neural networks have come at the cost of increased number of parameters and layers, dataset sizes, training and test computations, and GPU RAM. We introduce a new architecture -- WaveMix-Lite -- that can generalize on par with contemporary transformers and convolutional neural networks (CNNs) while needing fewer resources. WaveMix-Lite uses 2D-discrete wavelet transform to efficiently mix spatial information from pixels. WaveMix-Lite seems to be a versatile and scalable architectural framework that can be used for multiple vision tasks, such as image classification and semantic segmentation, without requiring significant architectural changes, unlike transformers and CNNs. It is able to meet or exceed several accuracy benchmarks while training on a single GPU. For instance, it achieves state-of-the-art accuracy on five EMNIST datasets, outperforms CNNs and transformers in ImageNet-1K (64$\times$64 images), and achieves an mIoU of 75.32 % on Cityscapes validation set, while using less than one-fifth the number parameters and half the GPU RAM of comparable CNNs or transformers. Our experiments show that while the convolutional elements of neural architectures exploit the shift-invariance property of images, new types of layers (e.g., wavelet transform) can exploit additional properties of images, such as scale-invariance and finite spatial extents of objects.

WaveMix: Resource-efficient Token Mixing for Images

Although certain vision transformer (ViT) and CNN architectures generalize well on vision tasks, it is often impractical to use them on green, edge, or desktop computing due to their computational requirements for training and even testing. We present WaveMix as an alternative neural architecture that uses a multi-scale 2D discrete wavelet transform (DWT) for spatial token mixing. Unlike ViTs, WaveMix neither unrolls the image nor requires self-attention of quadratic complexity. Additionally, DWT introduces another inductive bias -- besides convolutional filtering -- to utilize the 2D structure of an image to improve generalization. The multi-scale nature of the DWT also reduces the requirement for a deeper architecture compared to the CNNs, as the latter relies on pooling for partial spatial mixing. WaveMix models show generalization that is competitive with ViTs, CNNs, and token mixers on several datasets while requiring lower GPU RAM (training and testing), number of computations, and storage. WaveMix have achieved State-of-the-art (SOTA) results in EMNIST Byclass and EMNIST Balanced datasets.

Convolutional Xformers for Vision

Vision transformers (ViTs) have found only limited practical use in processing images, in spite of their state-of-the-art accuracy on certain benchmarks. The reason for their limited use include their need for larger training datasets and more computational resources compared to convolutional neural networks (CNNs), owing to the quadratic complexity of their self-attention mechanism. We propose a linear attention-convolution hybrid architecture -- Convolutional X-formers for Vision (CXV) -- to overcome these limitations. We replace the quadratic attention with linear attention mechanisms, such as Performer, Nystr\"omformer, and Linear Transformer, to reduce its GPU usage. Inductive prior for image data is provided by convolutional sub-layers, thereby eliminating the need for class token and positional embeddings used by the ViTs. We also propose a new training method where we use two different optimizers during different phases of training and show that it improves the top-1 image classification accuracy across different architectures. CXV outperforms other architectures, token mixers (e.g. ConvMixer, FNet and MLP Mixer), transformer models (e.g. ViT, CCT, CvT and hybrid Xformers), and ResNets for image classification in scenarios with limited data and GPU resources (cores, RAM, power).

"So You Think You're Funny?": Rating the Humour Quotient in Standup Comedy

Computational Humour (CH) has attracted the interest of Natural Language Processing and Computational Linguistics communities. Creating datasets for automatic measurement of humour quotient is difficult due to multiple possible interpretations of the content. In this work, we create a multi-modal humour-annotated dataset ($\sim$40 hours) using stand-up comedy clips. We devise a novel scoring mechanism to annotate the training data with a humour quotient score using the audience's laughter. The normalized duration (laughter duration divided by the clip duration) of laughter in each clip is used to compute this humour coefficient score on a five-point scale (0-4). This method of scoring is validated by comparing with manually annotated scores, wherein a quadratic weighted kappa of 0.6 is obtained. We use this dataset to train a model that provides a "funniness" score, on a five-point scale, given the audio and its corresponding text. We compare various neural language models for the task of humour-rating and achieve an accuracy of $0.813$ in terms of Quadratic Weighted Kappa (QWK). Our "Open Mic" dataset is released for further research along with the code.