Joint multi-task learning improves weakly-supervised biomarker prediction in computational pathology
Deep Learning (DL) can predict biomarkers directly from digitized cancer histology in a weakly-supervised setting. Recently, the prediction of continuous biomarkers through regression-based DL has seen an increasing interest. Nonetheless, clinical decision making often requires a categorical outcome. Consequently, we developed a weakly-supervised joint multi-task Transformer architecture which has been trained and evaluated on four public patient cohorts for the prediction of two key predictive biomarkers, microsatellite instability (MSI) and homologous recombination deficiency (HRD), trained with auxiliary regression tasks related to the tumor microenvironment. Moreover, we perform a comprehensive benchmark of 16 approaches of task balancing for weakly-supervised joint multi-task learning in computational pathology. Using our novel approach, we improve over the state-of-the-art area under the receiver operating characteristic by +7.7% and +4.1%, as well as yielding better clustering of latent embeddings by +8% and +5% for the prediction of MSI and HRD in external cohorts, respectively.
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We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, Princeton ModelNet40, and NVIDIA Dynamic Hand Gesture.
The Evidential regression network (ENet) estimates a continuous target and its predictive uncertainty without costly Bayesian model averaging. However, it is possible that the target is inaccurately predicted due to the gradient shrinkage problem of the original loss function of the ENet, the negative log marginal likelihood (NLL) loss. In this paper, the objective is to improve the prediction accuracy of the ENet while maintaining its efficient uncertainty estimation by resolving the gradient shrinkage problem. A multi-task learning (MTL) framework, referred to as MT-ENet, is proposed to accomplish this aim. In the MTL, we define the Lipschitz modified mean squared error (MSE) loss function as another loss and add it to the existing NLL loss. The Lipschitz modified MSE loss is designed to mitigate the gradient conflict with the NLL loss by dynamically adjusting its Lipschitz constant. By doing so, the Lipschitz MSE loss does not disturb the uncertainty estimation of the NLL loss. The MT-ENet enhances the predictive accuracy of the ENet without losing uncertainty estimation capability on the synthetic dataset and real-world benchmarks, including drug-target affinity (DTA) regression. Furthermore, the MT-ENet shows remarkable calibration and out-of-distribution detection capability on the DTA benchmarks.
Deep Learning (DL) is the most widely used tool in the contemporary field of computer vision. Its ability to accurately solve complex problems is employed in vision research to learn deep neural models for a variety of tasks, including security critical applications. However, it is now known that DL is vulnerable to adversarial attacks that can manipulate its predictions by introducing visually imperceptible perturbations in images and videos. Since the discovery of this phenomenon in 2013~[1], it has attracted significant attention of researchers from multiple sub-fields of machine intelligence. In [2], we reviewed the contributions made by the computer vision community in adversarial attacks on deep learning (and their defenses) until the advent of year 2018. Many of those contributions have inspired new directions in this area, which has matured significantly since witnessing the first generation methods. Hence, as a legacy sequel of [2], this literature review focuses on the advances in this area since 2018. To ensure authenticity, we mainly consider peer-reviewed contributions published in the prestigious sources of computer vision and machine learning research. Besides a comprehensive literature review, the article also provides concise definitions of technical terminologies for non-experts in this domain. Finally, this article discusses challenges and future outlook of this direction based on the literature reviewed herein and [2].
We present ResMLP, an architecture built entirely upon multi-layer perceptrons for image classification. It is a simple residual network that alternates (i) a linear layer in which image patches interact, independently and identically across channels, and (ii) a two-layer feed-forward network in which channels interact independently per patch. When trained with a modern training strategy using heavy data-augmentation and optionally distillation, it attains surprisingly good accuracy/complexity trade-offs on ImageNet. We will share our code based on the Timm library and pre-trained models.
Artificial neural networks thrive in solving the classification problem for a particular rigid task, acquiring knowledge through generalized learning behaviour from a distinct training phase. The resulting network resembles a static entity of knowledge, with endeavours to extend this knowledge without targeting the original task resulting in a catastrophic forgetting. Continual learning shifts this paradigm towards networks that can continually accumulate knowledge over different tasks without the need to retrain from scratch. We focus on task incremental classification, where tasks arrive sequentially and are delineated by clear boundaries. Our main contributions concern 1) a taxonomy and extensive overview of the state-of-the-art, 2) a novel framework to continually determine the stability-plasticity trade-off of the continual learner, 3) a comprehensive experimental comparison of 11 state-of-the-art continual learning methods and 4 baselines. We empirically scrutinize method strengths and weaknesses on three benchmarks, considering Tiny Imagenet and large-scale unbalanced iNaturalist and a sequence of recognition datasets. We study the influence of model capacity, weight decay and dropout regularization, and the order in which the tasks are presented, and qualitatively compare methods in terms of required memory, computation time, and storage.
The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.
Meta-learning, or learning to learn, has gained renewed interest in recent years within the artificial intelligence community. However, meta-learning is incredibly prevalent within nature, has deep roots in cognitive science and psychology, and is currently studied in various forms within neuroscience. The aim of this review is to recast previous lines of research in the study of biological intelligence within the lens of meta-learning, placing these works into a common framework. More recent points of interaction between AI and neuroscience will be discussed, as well as interesting new directions that arise under this perspective.
Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
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