Autoencoders as Weight Initialization of Deep Classification Networks for Cancer versus Cancer Studies
University of Porto（波尔图大学）；Faculty of Engineering, University of Porto（波尔图大学工程学院）；INESC TEC - Institute for Systems and Computer Engineering, Technology and Science（INESC TEC——系统与计算机工程、技术与科学研究所）
Mafalda Falcao Ferreira, Rui Camacho, Luis F. Teixeira
备注：
5 pages, 2 figures (each one with 6 sub-figures), 2 tables. Special Session of Machine Learning in Healthcare Informatics and Medical Biology of the 16th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB2019)
Cancer is still one of the most devastating diseases of our time. One way of automatically classifying tumor samples is by analyzing its derived molecular information (i.e., its genes expression signatures). In this work, we aim to distinguish three different types of cancer: thyroid, skin, and stomach. For that, we compare the performance of a Denoising Autoencoder (DAE) used as weight initialization of a deep neural network. Although we address a different domain problem in this work, we have adopted the same methodology of Ferreira et al.. In our experiments, we assess two different approaches when training the classification model: (a) fixing the weights, after pre-training the DAE, and (b) allowing fine-tuning of the entire classification network. Additionally, we apply two different strategies for embedding the DAE into the classification network: (1) by only importing the encoding layers, and (2) by inserting the complete autoencoder. Our best result was the combination of unsupervised feature learning through a DAE, followed by its full import into the classification network, and subsequent fine-tuning through supervised training, achieving an F1 score of 98.04% +/- 1.09 when identifying cancerous thyroid samples.
Lawrence Livermore National Laboratory（劳伦斯利弗莫尔国家实验室）
Gene expression profiles have been widely used to characterize patterns of cellular responses to diseases. As data becomes available, scalable learning toolkits become essential to processing large datasets using deep learning models to model complex biological processes. We present an autoencoder to capture nonlinear relationships recovered from gene expression profiles. The autoencoder is a nonlinear dimension reduction technique using an artificial neural network, which learns hidden representations of unlabeled data. We train the autoencoder on a large collection of tumor samples from the …
Harbin Institute of Technology at Weihai（哈尔滨工业大学（威海））；University of Edinburgh（爱丁堡大学）；Sun Yat-sen University（中山大学）；University of Arizona（亚利桑那大学）
Cancer is a primary cause of human death, but discovering drugs and tailoring cancer therapies are expensive and time-consuming. We seek to facilitate the discovery of new drugs and treatment strategies for cancer using variational autoencoders (VAEs) and multi-layer perceptrons (MLPs) to predict anti-cancer drug responses. Our model takes as input gene expression data of cancer cell lines and anti-cancer drug molecular data and encodes these data with our {\sc {GeneVae}} model, which is an ordinary VAE model, and a rectified junction tree variational autoencoder ({\sc JTVae}) model, respectiv…
University of Kentucky（肯塔基大学）；Miami University（迈阿密大学）
With the increased affordability and availability of whole-genome sequencing, large-scale and high-throughput gene expression is widely used to characterize diseases, including cancers. However, establishing specificity in cancer diagnosis using gene expression data continues to pose challenges due to the high dimensionality and complexity of the data. Here we present models of deep learning (DL) and apply them to gene expression data for the diagnosis and categorization of cancer. In this study, we have developed two DL models using messenger ribonucleic acid (mRNA) datasets available from th…
Johns Hopkins University（约翰斯·霍普金斯大学）；Johns Hopkins University Applied Physics Lab（约翰斯·霍普金斯大学应用物理实验室）
In this paper, we investigate the evolution of autoencoders near their initialization. In particular, we study the distribution of the eigenvalues of the Jacobian matrices of autoencoders early in the training process, training on the MNIST data set. We find that autoencoders that have not been trained have eigenvalue distributions that are qualitatively different from those which have been trained for a long time ($>$100 epochs). Additionally, we find that even at early epochs, these eigenvalue distributions rapidly become qualitatively similar to those of the fully trained autoencoders. We a…
A Deep Autoencoder based content retrieval algorithm is proposed for prediction and differentiation of cancer types based on the presence of epigenetic patterns of DNA methylation identified in genetic regions known as CpG islands. The developed deep learning system uses a CpG island state classification sub-system to complete sets of missing/incomplete island data in given human cell lines, and is then pipelined with an intricate set of statistical and signal processing methods to accurately predict the presence of cancer and further differentiate the type and cell of origin in the event of a…
University of Pisa（比萨大学）；University of Padova（帕多瓦大学）
Training RNNs to learn long-term dependencies is difficult due to vanishing gradients. We explore an alternative solution based on explicit memorization using linear autoencoders for sequences, which allows to maximize the short-term memory and that can be solved with a closed-form solution without backpropagation. We introduce an initialization schema that pretrains the weights of a recurrent neural network to approximate the linear autoencoder of the input sequences and we show how such pretraining can better support solving hard classification tasks with long sequences. We test our approach…
Cancer survival prediction is important for developing personalized treatments and inducing disease-causing mechanisms. Multi-omics data integration is attracting widespread interest in cancer research for providing information for understanding cancer progression at multiple genetic levels. Many works, however, are limited because of the high dimensionality and heterogeneity of multi-omics data. In this paper, we propose a novel method to integrate multi-omics data for cancer survival prediction, called Stacked AutoEncoder-based Survival Prediction Neural Network (SAEsurv-net). In the cancer …
We propose an unsupervised method using self-clustering convolutional adversarial autoencoders to classify prostate tissue as tumor or non-tumor without any labeled training data. The clustering method is integrated into the training of the autoencoder and requires only little post-processing. Our network trains on hematoxylin and eosin (H&E) input patches and we tested two different reconstruction targets, H&E and immunohistochemistry (IHC). We show that antibody-driven feature learning using IHC helps the network to learn relevant features for the clustering task. Our network achieves a F1 s…
University of Toronto（多伦多大学）；National Cancer Research Centre（国家癌症研究中心）；Institute for Oncology and Radiology（肿瘤与放射学研究所）
Accurate diagnosis of breast cancer in histopathology images is challenging due to the heterogeneity of cancer cell growth as well as of a variety of benign breast tissue proliferative lesions. In this paper, we propose a practical and self-interpretable invasive cancer diagnosis solution. With minimum annotation information, the proposed method mines contrast patterns between normal and malignant images in unsupervised manner and generates a probability map of abnormalities to verify its reasoning. Particularly, a fully convolutional autoencoder is used to learn the dominant structural patter…
Beyond Labels: A Self-Supervised Framework with Masked Autoencoders and Random Cropping for Breast Cancer Subtype Classification
DISIT, Computer Science Institute, University of Piemonte Orientale（DISIT计算机科学研究所，皮埃蒙特东方大学）；Center for Translational Research on Autoimmune and Allergic Diseases (CAAD), Department of Health Sciences, University of Piemonte Orientale（自身免疫和过敏疾病转化研究中心（CAAD），健康科学系，皮埃蒙特东方大学）；Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Department of Health Sciences, University of Piemonte Orientale（自身免疫疾病跨学科研究中心（IRCAD），健康科学系，皮埃蒙特东方大学）
提出一种基于 MAE 与随机裁剪的自监督框架，从 WSI 学习组织病理图像表示，并通过线性探针完成乳腺癌多亚型分类。
Australian e-Health Research Centre, CSIRO（澳大利亚联邦科学与工业研究组织电子健康研究中心）
Generative learning is a powerful tool for representation learning, and shows particular promise for problems in biomedical imaging. However, in this context, sampling from the distribution is secondary to finding representations of real images, which often come with labels and explicitly represent the content and quality of the target distribution. It remains difficult to faithfully reconstruct images from generative models, particularly those as complex as histological images. In this work, two existing methods (autoencoders and adversarial latent autoencoders) are combined in attempt to imp…
Data Science Institute, Imperial College London（伦敦帝国理工学院数据科学研究所）
Different aspects of a clinical sample can be revealed by multiple types of omics data. Integrated analysis of multi-omics data provides a comprehensive view of patients, which has the potential to facilitate more accurate clinical decision making. However, omics data are normally high dimensional with large number of molecular features and relatively small number of available samples with clinical labels. The "dimensionality curse" makes it challenging to train a machine learning model using high dimensional omics data like DNA methylation and gene expression profiles. Here we propose an end-…
Osaka University（大阪大学）；Nara Institute of Science and Technology（奈良先端科学技术大学院大学）；Yunnan University（云南大学）
Defining and separating cancer subtypes is essential for facilitating personalized therapy modality and prognosis of patients. The definition of subtypes has been constantly recalibrated as a result of our deepened understanding. During this recalibration, researchers often rely on clustering of cancer data to provide an intuitive visual reference that could reveal the intrinsic characteristics of subtypes. The data being clustered are often omics data such as transcriptomics that have strong correlations to the underlying biological mechanism. However, while existing studies have shown promis…
SELECTOR: Heterogeneous graph network with convolutional masked autoencoder for multimodal robust prediction of cancer survival
College of Computer Science and Electronic Engineering, Hunan University（湖南大学计算机与通信工程学院）；The Second Xiangya Hospital, Central South University（中南大学湘雅二医院）
University of Zanjan（赞詹大学）；Zanjan University of Medical Sciences（赞詹医科大学）
Non-synonymous single nucleotide polymorphisms (nsSNPs) are single nucleotide substitution occurring in the coding region of a gene and leads to a change in amino-acid sequence of protein. The studies have shown these variations may be associated with disease. Thus, investigating the effects of nsSNPs on protein function will give a greater insight on how nsSNPs can lead into disease. Breast cancer is the most common cancer among women causing highest cancer death every year. BRCA1 and BRCA2 tumor suppressor genes are two main candidates of which, mutations in them can increase the risk of dev…
Iowa State University（爱荷华州立大学）；Texas A&M University（得克萨斯农工大学）
We provide a series of results for unsupervised learning with autoencoders. Specifically, we study shallow two-layer autoencoder architectures with shared weights. We focus on three generative models for data that are common in statistical machine learning: (i) the mixture-of-gaussians model, (ii) the sparse coding model, and (iii) the sparsity model with non-negative coefficients. For each of these models, we prove that under suitable choices of hyperparameters, architectures, and initialization, autoencoders learned by gradient descent can successfully recover the parameters of the correspon…
University of Delhi（德里大学）；All India Institute of Medical Sciences（全印医学科学学院）；Hans Raj College（汉斯拉吉学院）
Breast cancer has long been a prominent cause of mortality among women. Diagnosis, therapy, and prognosis are now possible, thanks to the availability of RNA sequencing tools capable of recording gene expression data. Molecular subtyping being closely related to devising clinical strategy and prognosis, this paper focuses on the use of gene expression data for the classification of breast cancer into four subtypes, namely, Basal, Her2, LumA, and LumB. In stage 1, we suggested a deep learning-based model that uses an autoencoder to reduce dimensionality. The size of the feature set is reduced f…
Recently, a number of works have studied clustering strategies that combine classical clustering algorithms and deep learning methods. These approaches follow either a sequential way, where a deep representation is learned using a deep autoencoder before obtaining clusters with k-means, or a simultaneous way, where deep representation and clusters are learned jointly by optimizing a single objective function. Both strategies improve clustering performance, however the robustness of these approaches is impeded by several deep autoencoder setting issues, among which the weights initialization, t…
Predicting gene essentiality and drug response from perturbation screens in preclinical cancer models with LEAP: Layered Ensemble of Autoencoders and Predictors
Fraunhofer ITWM（弗劳恩霍夫工业数学研究所）；Technical University of Kaiserslautern（凯泽斯劳滕工业大学）
We consider a variational autoencoder (VAE) for binary data. Our main innovations are an interpretable lower bound for its training objective, a modified initialization and architecture of such a VAE that leads to faster training, and a decision support for finding the appropriate dimension of the latent space via using a PCA. Numerical examples illustrate our theoretical result and the performance of the new architecture.
Washington University School of Medicine, Washington University in St. Louis（圣路易斯华盛顿大学医学院）；Dalian University of Technology（大连理工大学）
Drug resistance is still a major challenge in cancer therapy. Drug combination is expected to overcome drug resistance. However, the number of possible drug combinations is enormous, and thus it is infeasible to experimentally screen all effective drug combinations considering the limited resources. Therefore, computational models to predict and prioritize effective drug combinations is important for combinatory therapy discovery in cancer. In this study, we proposed a novel deep learning model, AuDNNsynergy, to prediction drug combinations by integrating multi-omics data and chemical structur…
King’s College London（伦敦国王学院）；Institute for Infocomm Research, A*STAR（新加坡科技研究局资讯通信研究院）
Cancer is a complex disease with significant social and economic impact. Advancements in high-throughput molecular assays and the reduced cost for performing high-quality multi-omics measurements have fuelled insights through machine learning . Previous studies have shown promise on using multiple omic layers to predict survival and stratify cancer patients. In this paper, we developed a Supervised Autoencoder (SAE) model for survival-based multi-omic integration which improves upon previous work, and report a Concrete Supervised Autoencoder model (CSAE), which uses feature selection to jointl…
Deep linear networks trained with gradient descent yield low rank solutions, as is typically studied in matrix factorization. In this paper, we take a step further and analyze implicit rank regularization in autoencoders. We show greedy learning of low-rank latent codes induced by a linear sub-network at the autoencoder bottleneck. We further propose orthogonal initialization and principled learning rate adjustment to mitigate sensitivity of training dynamics to spectral prior and linear depth. With linear autoencoders on synthetic data, our method converges stably to ground-truth latent code …
One of the challenges of using machine learning techniques with medical data is the frequent dearth of source image data on which to train. A representative example is automated lung cancer diagnosis, where nodule images need to be classified as suspicious or benign. In this work we propose an automatic synthetic lung nodule image generator. Our 3D shape generator is designed to augment the variety of 3D images. Our proposed system takes root in autoencoder techniques, and we provide extensive experimental characterization that demonstrates its ability to produce quality synthetic images.
Hyperspectral unmixing involves separating a pixel as a weighted combination of its constituent endmembers and corresponding fractional abundances, with the current state of the art results achieved by neural models on benchmark datasets. However, these networks are severely over-parameterized and consequently, the invariant endmember spectra extracted as decoder weights have a high variance over multiple runs. These approaches perform substantial post-processing while requiring an exact specification of the number of endmembers and specialized initialization of weights from other algorithms l…
Institute of Information and Communication Technology, Bangladesh University of Engineering and Technology（孟加拉工程技术大学信息与通信技术学院）
Breast cancer is a common fatal disease for women. Early diagnosis and detection is necessary in order to improve the prognosis of breast cancer affected people. For predicting breast cancer, several automated systems are already developed using different medical imaging modalities. This paper provides a systematic review of the literature on artificial neural network (ANN) based models for the diagnosis of breast cancer via mammography. The advantages and limitations of different ANN models including spiking neural network (SNN), deep belief network (DBN), convolutional neural network (CNN), …
Multi-omic data provides multiple views of the same patients. Integrative analysis of multi-omic data is crucial to elucidate the molecular underpinning of disease etiology. However, multi-omic data has the "big p, small N" problem (the number of features is large, but the number of samples is small), it is challenging to train a complicated machine learning model from the multi-omic data alone and make it generalize well. Here we propose a framework termed Multi-view Factorization AutoEncoder with network constraints to integrate multi-omic data with domain knowledge (biological interactions …
School of Information Systems, Science and Engineering Faculty of Queensland University of Technology（昆士兰科技大学科学与工程学院信息系统学院）；Department of Computer Science and Engineering, Instituto Superior Técnico / INESC-ID, University of Lisbon（里斯本大学高等技术学院/INESC-ID计算机科学与工程系）
This paper explores interpretability techniques for two of the most successful learning algorithms in medical decision-making literature: deep neural networks and random forests. We applied these algorithms in a real-world medical dataset containing information about patients with cancer, where we learn models that try to predict the type of cancer of the patient, given their set of medical activity records. We explored different algorithms based on neural network architectures using long short term deep neural networks, and random forests. Since there is a growing need to provide decision-mak…
Open-set recognition generalizes a classification task by classifying test samples as one of the known classes from training or "unknown." As novel cancer drug cocktails with improved treatment are continually discovered, predicting cancer treatments can naturally be formulated in terms of an open-set recognition problem. Drawbacks, due to modeling unknown samples during training, arise from straightforward implementations of prior work in healthcare open-set learning. Accordingly, we reframe the problem methodology and apply a recent existing Gaussian mixture variational autoencoder model, wh…
Stable and Steerable Sparse Autoencoders with Weight Regularization
Department of Biology, University of Oxford, Oxford, UK（牛津大学生物学系）；Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK（牛津大学纳科学发现研究所）；Department of Chemistry, University of Oxford, Oxford, UK（牛津大学化学系）
Biologically Informed Deep Neural Networks for Multi-Omic Integration, Pathway Activity Inference and Risk Stratification in Cancer
King’s College London（伦敦国王学院）；Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR)（科技研究局信息与通信研究所）；Shenzhen University（深圳大学）；University of Manchester（曼彻斯特大学）
Instituto de Investigación e Innovación en Bioingeniería, I3B, Universitat Politècnica de València（瓦伦西亚理工大学生物工程研究与创新学院（I3B））；Hospital Clínico Universitario de Valencia, Universidad de Valencia（瓦伦西亚大学附属临床医院）
Epigenetic alterations have an important role in the development of several types of cancer. Epigenetic studies generate a large amount of data, which makes it essential to develop novel models capable of dealing with large-scale data. In this work, we propose a deep embedded refined clustering method for breast cancer differentiation based on DNA methylation. In concrete, the deep learning system presented here uses the levels of CpG island methylation between 0 and 1. The proposed approach is composed of two main stages. The first stage consists in the dimensionality reduction of the methyla…
Cambridge Cancer Genomics（剑桥癌症基因组学公司）；University of Lancaster（兰卡斯特大学）；University of Cambridge（剑桥大学）
Analysis of somatic mutation profiles from cancer patients is essential in the development of cancer research. However, the low frequency of most mutations and the varying rates of mutations across patients makes the data extremely challenging to statistically analyze as well as difficult to use in classification problems, for clustering, visualization or for learning useful information. Thus, the creation of low dimensional representations of somatic mutation profiles that hold useful information about the DNA of cancer cells will facilitate the use of such data in applications that will prog…
$Γ$-VAE: Curvature regularized variational autoencoders for uncovering emergent low dimensional geometric structure in high dimensional data
Cornell University（康奈尔大学）；Sorbonne Université（索邦大学）；Institut Curie Research Center（居里研究所）；PSL University（巴黎文理研究大学）；Inserm（法国国家健康与医学研究院）；Center for Advanced Computing, Cornell University（康奈尔大学高级计算中心）；Kavli Institute at Cornell for Nanoscale Science, Cornell University（康奈尔大学卡夫利纳米科学研究所）
International initiatives such as METABRIC (Molecular Taxonomy of Breast Cancer International Consortium) have collected several multigenomic and clinical data sets to identify the undergoing molecular processes taking place throughout the evolution of various cancers. Numerous Machine Learning and statistical models have been designed and trained to analyze these types of data independently, however, the integration of such differently shaped and sourced information streams has not been extensively studied. To better integrate these data sets and generate meaningful representations that can u…
School of Computer Science, The University of Sydney（悉尼大学计算机科学学院）；School of Computer Science, University of Technology Sydney（悉尼科技大学计算机科学学院）
Class imbalance occurs in many real-world applications, including image classification, where the number of images in each class differs significantly. With imbalanced data, the generative adversarial networks (GANs) leans to majority class samples. The two recent methods, Balancing GAN (BAGAN) and improved BAGAN (BAGAN-GP), are proposed as an augmentation tool to handle this problem and restore the balance to the data. The former pre-trains the autoencoder weights in an unsupervised manner. However, it is unstable when the images from different categories have similar features. The latter is …
Indian Institute of Technology Kharagpur（印度理工学院克勒格布尔分校）
Various screening and diagnostic methods have led to a large reduction of cervical cancer death rates in developed countries. However, cervical cancer is the leading cause of cancer related deaths in women in India and other low and middle income countries (LMICs) especially among the urban poor and slum dwellers. Several sophisticated techniques such as cytology tests, HPV tests etc. have been widely used for screening of cervical cancer. These tests are inherently time consuming. In this paper, we propose a convolutional autoencoder based framework, having an architecture similar to SegNet w…
University of California, San Diego（加州大学圣地亚哥分校）；Pacific Northwest National Laboratory（太平洋西北国家实验室）
Physics-constrained data-driven computing is an emerging computational paradigm that allows simulation of complex materials directly based on material database and bypass the classical constitutive model construction. However, it remains difficult to deal with high-dimensional applications and extrapolative generalization. This paper introduces deep learning techniques under the data-driven framework to address these fundamental issues in nonlinear materials modeling. To this end, an autoencoder neural network architecture is introduced to learn the underlying low-dimensional representation (e…
Reusability report: Prostate cancer stratification with diverse biologically-informed neural architectures
Courant Institute of Mathematical Sciences, New York University（纽约大学库朗数学科学研究所）；Center for Data Science, New York University（纽约大学数据科学中心）；Center for Computational Astrophysics, Flatiron Institute（弗拉蒂隆研究所计算天体物理中心）；Center for Computational Neuroscience, Flatiron Institute（弗拉蒂隆研究所计算神经科学中心）；Cedars-Sinai Medical Center（西达赛奈医疗中心）；Department of Applied Mathematics and Theoretical Physics, University of Cambridge（剑桥大学应用数学与理论物理系）；Institute of Astronomy, University of Cambridge（剑桥大学天文研究所）；Department of Astrophysical Sciences, Princeton University（普林斯顿大学天体物理科学系）；Center for Computational Biology, Flatiron Institute（弗拉蒂隆研究所计算生物学中心）
Imperial College London（帝国理工学院）；University College London（伦敦大学学院）；Hong Kong Baptist University（香港浸会大学）
The lack of explainability is one of the most prominent disadvantages of deep learning applications in omics. This "black box" problem can undermine the credibility and limit the practical implementation of biomedical deep learning models. Here we present XOmiVAE, a variational autoencoder (VAE) based interpretable deep learning model for cancer classification using high-dimensional omics data. XOmiVAE is capable of revealing the contribution of each gene and latent dimension for each classification prediction, and the correlation between each gene and each latent dimension. It is also demonst…
One of the main problems with biomedical signals is the limited amount of patient-specific data and the significant amount of time needed to record the sufficient number of samples needed for diagnostic and treatment purposes. In this study, we present a framework to simultaneously generate and classify biomedical time series based on a modified Adversarial Autoencoder (AAE) algorithm and one-dimensional convolutions. Our work is based on breathing time series, with specific motivation to capture breathing motion during radiotherapy lung cancer treatments. First, we explore the potential in us…
Pathway-Guided Optimization of Deep Generative Molecular Design Models for Cancer Therapy
Texas A&M University（德克萨斯农工大学）；Frederick National Laboratory for Cancer Research（弗雷德里克国家癌症研究所）；Leidos Biomedical Research（莱多斯生物医学研究所）；Brookhaven National Laboratory（布鲁克海文国家实验室）
University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心）
Deep Learning can significantly benefit cancer proteomics and genomics. In this study, we attempt to determine a set of critical proteins that are associated with the FLT3-ITD mutation in newly-diagnosed acute myeloid leukemia patients. A Deep Learning network consisting of autoencoders forming a hierarchical model from which high-level features are extracted without labeled training data. Dimensional reduction reduced the number of critical proteins from 231 to 20. Deep Learning found an excellent correlation between FLT3-ITD mutation with the levels of these 20 critical proteins (accuracy 97…
Pattern Recognition Lab, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)（埃尔朗根-纽伦堡大学模式识别实验室）；Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)（埃尔朗根-纽伦堡大学埃尔朗根医院病理学研究所）；Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN)（埃尔朗根-欧洲大都会区综合癌症中心）；Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)（埃尔朗根-纽伦堡大学生物医学工程人工智能系）；Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)（埃尔朗根-纽伦堡大学埃尔朗根医院妇产科）
Supervised deep learning has shown state-of-the-art performance for medical image segmentation across different applications, including histopathology and cancer research; however, the manual annotation of such data is extremely laborious. In this work, we explore the use of superpixel approaches to compute a pre-segmentation of HER2 stained images for breast cancer diagnosis that facilitates faster manual annotation and correction in a second step. Four methods are compared: Standard Simple Linear Iterative Clustering (SLIC) as a baseline, a domain adapted SLIC, and superpixels based on featu…
IgCONDA-PET: Weakly-Supervised PET Anomaly Detection using Implicitly-Guided Attention-Conditional Counterfactual Diffusion Modeling -- a Multi-Center, Multi-Cancer, and Multi-Tracer Study
organization= Department of Physics \& Astronomy, University of British Columbia , city= Vancouver , state= BC , country= Canada；organization= Department of Integrative Oncology, BC Cancer Research Institute , city= Vancouver , state= BC , country= Canada；organization= Department of Radiology, University of British Columbia , city= Vancouver , state= BC , country= Canada
