CPEM: Accurate cancer type classification based on somatic alterations using an ensemble of a random forest and a deep neural network

With recent advances in DNA sequencing technologies, fast acquisition of large-scale genomic data has become commonplace. For cancer studies, in particular, there is an increasing need for the classification of cancer type based on somatic alterations detected from sequencing analyses. However, the ever-increasing size and complexity of the data make the classification task extremely challenging. In this study, we evaluate the contributions of various input features, such as mutation profiles, mutation rates, mutation spectra and signatures, and somatic copy number alterations that can be derived from genomic data, and further utilize them for accurate cancer type classification. We introduce a novel ensemble of machine learning classifiers, called CPEM (Cancer Predictor using an Ensemble Model), which is tested on 7,002 samples representing over 31 different cancer types collected from The Cancer Genome Atlas (TCGA) database. We first systematically examined the impact of the input features. Features known to be associated with specific cancers had relatively high importance in our initial prediction model. We further investigated various machine learning classifiers and feature selection methods to derive the ensemble-based cancer type prediction model achieving up to 84% classification accuracy in the nested 10-fold cross-validation. Finally, we narrowed down the target cancers to the six most common types and achieved up to 94% accuracy

RAMP: response-aware multi-task learning with contrastive regularization for cancer drug response prediction

The accurate prediction of cancer drug sensitivity according to the multiomics profiles of individual patients is crucial for precision cancer medicine. However, the development of prediction models has been challenged by the complex crosstalk of input features and the resistance-dominant drug response information contained in public databases. In this study, we propose a novel multidrug response prediction framework, response-aware multitask prediction (RAMP), via a Bayesian neural network and restrict it by soft-supervised contrastive regularization. To utilize network embedding vectors as representation learning features for heterogeneous networks, we harness response-aware negative sampling, which applies cell line???drug response information to the training of network embeddings. RAMP overcomes the prediction accuracy limitation induced by the imbalance of trained response data based on the comprehensive selection and utilization of drug response features. When trained on the Genomics of Drug Sensitivity in Cancer dataset, RAMP achieved an area under the receiver operating characteristic curve > 89%, an area under the precision-recall curve > 59% and an F1 score > 52% and outperformed previously developed methods on both balanced and imbalanced datasets. Furthermore, RAMP predicted many missing drug responses that were not included in the public databases. Our results showed that RAMP will be suitable for the high-throughput prediction of cancer drug sensitivity and will be useful for guiding cancer drug selection processes. The Python implementation for RAMP is available at https://github.com/hvcl/RAMP

PAIP 2019: Liver cancer segmentation challenge

Pathology Artificial Intelligence Platform (PAIP) is a free research platform in support of pathological artificial intelligence (AI). The main goal of the platform is to construct a high-quality pathology learning data set that will allow greater accessibility. The PAIP Liver Cancer Segmentation Challenge, organized in conjunction with the Medical Image Computing and Computer Assisted Intervention Society (MICCAI 2019), is the first image analysis challenge to apply PAIP datasets. The goal of the challenge was to evaluate new and existing algorithms for automated detection of liver cancer in whole-slide images (WSIs). Additionally, the PAIP of this year attempted to address potential future problems of AI applicability in clinical settings. In the challenge, participants were asked to use analytical data and statistical metrics to evaluate the performance of automated algorithms in two different tasks. The participants were given the two different tasks: Task 1 involved investigating Liver Cancer Segmentation and Task 2 involved investigating Viable Tumor Burden Estimation. There was a strong correlation between high performance of teams on both tasks, in which teams that performed well on Task 1 also performed well on Task 2. After evaluation, we summarized the top 11 team's algorithms. We then gave pathological implications on the easily predicted images for cancer segmentation and the challenging images for viable tumor burden estimation. Out of the 231 participants of the PAIP challenge datasets, a total of 64 were submitted from 28 team participants. The submitted algorithms predicted the automatic segmentation on the liver cancer with WSIs to an accuracy of a score estimation of 0.78. The PAIP challenge was created in an effort to combat the lack of research that has been done to address Liver cancer using digital pathology. It remains unclear of how the applicability of AI algorithms created during the challenge can affect clinical diagnoses. However, the results of this dataset and evaluation metric provided has the potential to aid the development and benchmarking of cancer diagnosis and segmentation. (C) 2020 The Authors. Published by Elsevier B.V

Towards Self-Supervised Learning for Image Restoration

Department of Computer Science and Engineeringclos

Noise2Kernel: Adaptive Self-Supervised Blind Denoising Using a Dilated Convolutional Kernel Architecture

With the advent of unsupervised learning, efficient training of a deep network for image denoising without pairs of noisy and clean images has become feasible. Most current unsupervised denoising methods are built on self-supervised loss with the assumption of zero-mean noise under the signal-independent condition, which causes brightness-shifting artifacts on unconventional noise statistics (i.e., different from commonly used noise models). Moreover, most blind denoising methods require a random masking scheme for training to ensure the invariance of the denoising process. In this study, we propose a dilated convolutional network that satisfies an invariant property, allowing efficient kernel-based training without random masking. We also propose an adaptive self-supervision loss to increase the tolerance for unconventional noise, which is specifically effective in removing salt-and-pepper or hybrid noise where prior knowledge of noise statistics is not readily available. We demonstrate the efficacy of the proposed method by comparing it with state-of-the-art denoising methods using various examples

ISCL: Interdependent Self-Cooperative Learning for Unpaired Image Denoising

With the advent of advances in self-supervised learning, paired clean-noisy data are no longer required in deep learning-based image denoising. However, existing blind denoising methods still require the assumption with regard to noise characteristics, such as zero-mean noise distribution and pixel-wise noise-signal independence; this hinders wide adaptation of the method in the medical domain. On the other hand, unpaired learning can overcome limitations related to the assumption on noise characteristics, which makes it more feasible for collecting the training data in real-world scenarios. In this paper, we propose a novel image denoising scheme, Interdependent Self-Cooperative Learning (ISCL), that leverages unpaired learning by combining cyclic adversarial learning with self-supervised residual learning. Unlike the existing unpaired image denoising methods relying on matching data distributions in different domains, the two architectures in ISCL, designed for different tasks, complement each other and boost the learning process. To assess the performance of the proposed method, we conducted extensive experiments in various biomedical image degradation scenarios, such as noise caused by physical characteristics of electron microscopy (EM) devices (film and charging noise), and structural noise found in low-dose computer tomography (CT). We demonstrate that the image quality of our method is superior to conventional and current state-of-the-art deep learning-based unpaired image denoising methods

Improving the Accuracy of Intrahepatic Cholangiocarcinoma Subtype Classification by Hidden Class Detection via Label Smoothing

Obtaining ground-truth labels for supervised training is a labor-intensive and time-consuming task. Owning to their large size, only slide-level labels or a handful of coarse annotations are usually provided for pathology images, which makes the training of the classifier challenging. In this study, we propose a conceptually simple, two-stage approach to classify small and large duct types in intrahepatic chalongiocarcinoma using only slide-level labels. Unlike conventional pathology image analysis methods employ multiple instance learning (MTh) applied to overcome the problem of the slide-level label, we introduce a novel label smoothing method to progressively refine the training labels to improve the classification accuracy. The main idea is that we introduce the hidden class, which is assumed to be mutually inclusive of all ground-truth classes and less confident for classification. By iteratively refining (i.e., smoothing) per-patch labels, we can extract and discard the hidden class from the training data. We demonstrate that the proposed label filtering scheme improves the classification accuracy by up to 30% compared to the baseline MTh method and 10% compared to the state-of-the-art noisy label cleaning method. In addition, we demonstrate the effectiveness of gene mutation prior information in the classification of two different duct types. The experimental results suggest that the proposed method may provide pathologists insight into the study of correlations between genetic and histologic subtypes.N