11,568 research outputs found

    Machine learning in solar physics

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    The application of machine learning in solar physics has the potential to greatly enhance our understanding of the complex processes that take place in the atmosphere of the Sun. By using techniques such as deep learning, we are now in the position to analyze large amounts of data from solar observations and identify patterns and trends that may not have been apparent using traditional methods. This can help us improve our understanding of explosive events like solar flares, which can have a strong effect on the Earth environment. Predicting hazardous events on Earth becomes crucial for our technological society. Machine learning can also improve our understanding of the inner workings of the sun itself by allowing us to go deeper into the data and to propose more complex models to explain them. Additionally, the use of machine learning can help to automate the analysis of solar data, reducing the need for manual labor and increasing the efficiency of research in this field.Comment: 100 pages, 13 figures, 286 references, accepted for publication as a Living Review in Solar Physics (LRSP

    Defending Black-box Classifiers by Bayesian Boundary Correction

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    Classifiers based on deep neural networks have been recently challenged by Adversarial Attack, where the widely existing vulnerability has invoked the research in defending them from potential threats. Given a vulnerable classifier, existing defense methods are mostly white-box and often require re-training the victim under modified loss functions/training regimes. While the model/data/training specifics of the victim are usually unavailable to the user, re-training is unappealing, if not impossible for reasons such as limited computational resources. To this end, we propose a new black-box defense framework. It can turn any pre-trained classifier into a resilient one with little knowledge of the model specifics. This is achieved by new joint Bayesian treatments on the clean data, the adversarial examples and the classifier, for maximizing their joint probability. It is further equipped with a new post-train strategy which keeps the victim intact. We name our framework Bayesian Boundary Correction (BBC). BBC is a general and flexible framework that can easily adapt to different data types. We instantiate BBC for image classification and skeleton-based human activity recognition, for both static and dynamic data. Exhaustive evaluation shows that BBC has superior robustness and can enhance robustness without severely hurting the clean accuracy, compared with existing defense methods.Comment: arXiv admin note: text overlap with arXiv:2203.0471

    vONTSS: vMF based semi-supervised neural topic modeling with optimal transport

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    Recently, Neural Topic Models (NTM), inspired by variational autoencoders, have attracted a lot of research interest; however, these methods have limited applications in the real world due to the challenge of incorporating human knowledge. This work presents a semi-supervised neural topic modeling method, vONTSS, which uses von Mises-Fisher (vMF) based variational autoencoders and optimal transport. When a few keywords per topic are provided, vONTSS in the semi-supervised setting generates potential topics and optimizes topic-keyword quality and topic classification. Experiments show that vONTSS outperforms existing semi-supervised topic modeling methods in classification accuracy and diversity. vONTSS also supports unsupervised topic modeling. Quantitative and qualitative experiments show that vONTSS in the unsupervised setting outperforms recent NTMs on multiple aspects: vONTSS discovers highly clustered and coherent topics on benchmark datasets. It is also much faster than the state-of-the-art weakly supervised text classification method while achieving similar classification performance. We further prove the equivalence of optimal transport loss and cross-entropy loss at the global minimum.Comment: 24 pages, 12 figures, ACL findings 202

    Designing a Direct Feedback Loop between Humans and Convolutional Neural Networks through Local Explanations

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    The local explanation provides heatmaps on images to explain how Convolutional Neural Networks (CNNs) derive their output. Due to its visual straightforwardness, the method has been one of the most popular explainable AI (XAI) methods for diagnosing CNNs. Through our formative study (S1), however, we captured ML engineers' ambivalent perspective about the local explanation as a valuable and indispensable envision in building CNNs versus the process that exhausts them due to the heuristic nature of detecting vulnerability. Moreover, steering the CNNs based on the vulnerability learned from the diagnosis seemed highly challenging. To mitigate the gap, we designed DeepFuse, the first interactive design that realizes the direct feedback loop between a user and CNNs in diagnosing and revising CNN's vulnerability using local explanations. DeepFuse helps CNN engineers to systemically search "unreasonable" local explanations and annotate the new boundaries for those identified as unreasonable in a labor-efficient manner. Next, it steers the model based on the given annotation such that the model doesn't introduce similar mistakes. We conducted a two-day study (S2) with 12 experienced CNN engineers. Using DeepFuse, participants made a more accurate and "reasonable" model than the current state-of-the-art. Also, participants found the way DeepFuse guides case-based reasoning can practically improve their current practice. We provide implications for design that explain how future HCI-driven design can move our practice forward to make XAI-driven insights more actionable.Comment: 32 pages, 6 figures, 5 tables. Accepted for publication in the Proceedings of the ACM on Human-Computer Interaction (PACM HCI), CSCW 202

    Segmentation of Pathology Images: A Deep Learning Strategy with Annotated Data

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    Cancer has significantly threatened human life and health for many years. In the clinic, histopathology image segmentation is the golden stand for evaluating the prediction of patient prognosis and treatment outcome. Generally, manually labelling tumour regions in hundreds of high-resolution histopathological images is time-consuming and expensive for pathologists. Recently, the advancements in hardware and computer vision have allowed deep-learning-based methods to become mainstream to segment tumours automatically, significantly reducing the workload of pathologists. However, most current methods rely on large-scale labelled histopathological images. Therefore, this research studies label-effective tumour segmentation methods using deep-learning paradigms to relieve the annotation limitations. Chapter 3 proposes an ensemble framework for fully-supervised tumour segmentation. Usually, the performance of an individual-trained network is limited by significant morphological variances in histopathological images. We propose a fully-supervised learning ensemble fusion model that uses both shallow and deep U-Nets, trained with images of different resolutions and subsets of images, for robust predictions of tumour regions. Noise elimination is achieved with Convolutional Conditional Random Fields. Two open datasets are used to evaluate the proposed method: the ACDC@LungHP challenge at ISBI2019 and the DigestPath challenge at MICCAI2019. With a dice coefficient of 79.7 %, the proposed method takes third place in ACDC@LungHP. In DigestPath 2019, the proposed method achieves a dice coefficient 77.3 %. Well-annotated images are an indispensable part of training fully-supervised segmentation strategies. However, large-scale histopathology images are hardly annotated finely in clinical practice. It is common for labels to be of poor quality or for only a few images to be manually marked by experts. Consequently, fully-supervised methods cannot perform well in these cases. Chapter 4 proposes a self-supervised contrast learning for tumour segmentation. A self-supervised cancer segmentation framework is proposed to reduce label dependency. An innovative contrastive learning scheme is developed to represent tumour features based on unlabelled images. Unlike a normal U-Net, the backbone is a patch-based segmentation network. Additionally, data augmentation and contrastive losses are applied to improve the discriminability of tumour features. A convolutional Conditional Random Field is used to smooth and eliminate noise. Three labelled, and fourteen unlabelled images are collected from a private skin cancer dataset called BSS. Experimental results show that the proposed method achieves better tumour segmentation performance than other popular self-supervised methods. However, by evaluated on the same public dataset as chapter 3, the proposed self-supervised method is hard to handle fine-grained segmentation around tumour boundaries compared to the supervised method we proposed. Chapter 5 proposes a sketch-based weakly-supervised tumour segmentation method. To segment tumour regions precisely with coarse annotations, a sketch-supervised method is proposed, containing a dual CNN-Transformer network and a global normalised class activation map. CNN-Transformer networks simultaneously model global and local tumour features. With the global normalised class activation map, a gradient-based tumour representation can be obtained from the dual network predictions. We invited experts to mark fine and coarse annotations in the private BSS and the public PAIP2019 datasets to facilitate reproducible performance comparisons. Using the BSS dataset, the proposed method achieves 76.686 % IOU and 86.6 % Dice scores, outperforming state-of-the-art methods. Additionally, the proposed method achieves a Dice gain of 8.372 % compared with U-Net on the PAIP2019 dataset. The thesis presents three approaches to segmenting cancers from histology images: fully-supervised, unsupervised, and weakly supervised methods. This research effectively segments tumour regions based on histopathological annotations and well-designed modules. Our studies comprehensively demonstrate label-effective automatic histopathological image segmentation. Experimental results prove that our works achieve state-of-the-art segmentation performances on private and public datasets. In the future, we plan to integrate more tumour feature representation technologies with other medical modalities and apply them to clinical research

    Deep learning for unsupervised domain adaptation in medical imaging: Recent advancements and future perspectives

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    Deep learning has demonstrated remarkable performance across various tasks in medical imaging. However, these approaches primarily focus on supervised learning, assuming that the training and testing data are drawn from the same distribution. Unfortunately, this assumption may not always hold true in practice. To address these issues, unsupervised domain adaptation (UDA) techniques have been developed to transfer knowledge from a labeled domain to a related but unlabeled domain. In recent years, significant advancements have been made in UDA, resulting in a wide range of methodologies, including feature alignment, image translation, self-supervision, and disentangled representation methods, among others. In this paper, we provide a comprehensive literature review of recent deep UDA approaches in medical imaging from a technical perspective. Specifically, we categorize current UDA research in medical imaging into six groups and further divide them into finer subcategories based on the different tasks they perform. We also discuss the respective datasets used in the studies to assess the divergence between the different domains. Finally, we discuss emerging areas and provide insights and discussions on future research directions to conclude this survey.Comment: Under Revie

    Using machine learning to predict pathogenicity of genomic variants throughout the human genome

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    Geschätzt mehr als 6.000 Erkrankungen werden durch Veränderungen im Genom verursacht. Ursachen gibt es viele: Eine genomische Variante kann die Translation eines Proteins stoppen, die Genregulation stören oder das Spleißen der mRNA in eine andere Isoform begünstigen. All diese Prozesse müssen überprüft werden, um die zum beschriebenen Phänotyp passende Variante zu ermitteln. Eine Automatisierung dieses Prozesses sind Varianteneffektmodelle. Mittels maschinellem Lernen und Annotationen aus verschiedenen Quellen bewerten diese Modelle genomische Varianten hinsichtlich ihrer Pathogenität. Die Entwicklung eines Varianteneffektmodells erfordert eine Reihe von Schritten: Annotation der Trainingsdaten, Auswahl von Features, Training verschiedener Modelle und Selektion eines Modells. Hier präsentiere ich ein allgemeines Workflow dieses Prozesses. Dieses ermöglicht es den Prozess zu konfigurieren, Modellmerkmale zu bearbeiten, und verschiedene Annotationen zu testen. Der Workflow umfasst außerdem die Optimierung von Hyperparametern, Validierung und letztlich die Anwendung des Modells durch genomweites Berechnen von Varianten-Scores. Der Workflow wird in der Entwicklung von Combined Annotation Dependent Depletion (CADD), einem Varianteneffektmodell zur genomweiten Bewertung von SNVs und InDels, verwendet. Durch Etablierung des ersten Varianteneffektmodells für das humane Referenzgenome GRCh38 demonstriere ich die gewonnenen Möglichkeiten Annotationen aufzugreifen und neue Modelle zu trainieren. Außerdem zeige ich, wie Deep-Learning-Scores als Feature in einem CADD-Modell die Vorhersage von RNA-Spleißing verbessern. Außerdem werden Varianteneffektmodelle aufgrund eines neuen, auf Allelhäufigkeit basierten, Trainingsdatensatz entwickelt. Diese Ergebnisse zeigen, dass der entwickelte Workflow eine skalierbare und flexible Möglichkeit ist, um Varianteneffektmodelle zu entwickeln. Alle entstandenen Scores sind unter cadd.gs.washington.edu und cadd.bihealth.org frei verfügbar.More than 6,000 diseases are estimated to be caused by genomic variants. This can happen in many possible ways: a variant may stop the translation of a protein, interfere with gene regulation, or alter splicing of the transcribed mRNA into an unwanted isoform. It is necessary to investigate all of these processes in order to evaluate which variant may be causal for the deleterious phenotype. A great help in this regard are variant effect scores. Implemented as machine learning classifiers, they integrate annotations from different resources to rank genomic variants in terms of pathogenicity. Developing a variant effect score requires multiple steps: annotation of the training data, feature selection, model training, benchmarking, and finally deployment for the model's application. Here, I present a generalized workflow of this process. It makes it simple to configure how information is converted into model features, enabling the rapid exploration of different annotations. The workflow further implements hyperparameter optimization, model validation and ultimately deployment of a selected model via genome-wide scoring of genomic variants. The workflow is applied to train Combined Annotation Dependent Depletion (CADD), a variant effect model that is scoring SNVs and InDels genome-wide. I show that the workflow can be quickly adapted to novel annotations by porting CADD to the genome reference GRCh38. Further, I demonstrate the integration of deep-neural network scores as features into a new CADD model, improving the annotation of RNA splicing events. Finally, I apply the workflow to train multiple variant effect models from training data that is based on variants selected by allele frequency. In conclusion, the developed workflow presents a flexible and scalable method to train variant effect scores. All software and developed scores are freely available from cadd.gs.washington.edu and cadd.bihealth.org

    Reinforced Learning for Label-Efficient 3D Face Reconstruction

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    3D face reconstruction plays a major role in many human-robot interaction systems, from automatic face authentication to human-computer interface-based entertainment. To improve robustness against occlusions and noise, 3D face reconstruction networks are often trained on a set of in-the-wild face images preferably captured along different viewpoints of the subject. However, collecting the required large amounts of 3D annotated face data is expensive and time-consuming. To address the high annotation cost and due to the importance of training on a useful set, we propose an Active Learning (AL) framework that actively selects the most informative and representative samples to be labeled. To the best of our knowledge, this paper is the first work on tackling active learning for 3D face reconstruction to enable a label-efficient training strategy. In particular, we propose a Reinforcement Active Learning approach in conjunction with a clustering-based pooling strategy to select informative view-points of the subjects. Experimental results on 300W-LP and AFLW2000 datasets demonstrate that our proposed method is able to 1) efficiently select the most influencing view-points for labeling and outperforms several baseline AL techniques and 2) further improve the performance of a 3D Face Reconstruction network trained on the full dataset

    Discriminative Multimodal Learning via Conditional Priors in Generative Models

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    Deep generative models with latent variables have been used lately to learn joint representations and generative processes from multi-modal data. These two learning mechanisms can, however, conflict with each other and representations can fail to embed information on the data modalities. This research studies the realistic scenario in which all modalities and class labels are available for model training, but where some modalities and labels required for downstream tasks are missing. We show, in this scenario, that the variational lower bound limits mutual information between joint representations and missing modalities. We, to counteract these problems, introduce a novel conditional multi-modal discriminative model that uses an informative prior distribution and optimizes a likelihood-free objective function that maximizes mutual information between joint representations and missing modalities. Extensive experimentation demonstrates the benefits of our proposed model, empirical results show that our model achieves state-of-the-art results in representative problems such as downstream classification, acoustic inversion, and image and annotation generation

    RainDiffusion:When Unsupervised Learning Meets Diffusion Models for Real-world Image Deraining

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    What will happen when unsupervised learning meets diffusion models for real-world image deraining? To answer it, we propose RainDiffusion, the first unsupervised image deraining paradigm based on diffusion models. Beyond the traditional unsupervised wisdom of image deraining, RainDiffusion introduces stable training of unpaired real-world data instead of weakly adversarial training. RainDiffusion consists of two cooperative branches: Non-diffusive Translation Branch (NTB) and Diffusive Translation Branch (DTB). NTB exploits a cycle-consistent architecture to bypass the difficulty in unpaired training of standard diffusion models by generating initial clean/rainy image pairs. DTB leverages two conditional diffusion modules to progressively refine the desired output with initial image pairs and diffusive generative prior, to obtain a better generalization ability of deraining and rain generation. Rain-Diffusion is a non adversarial training paradigm, serving as a new standard bar for real-world image deraining. Extensive experiments confirm the superiority of our RainDiffusion over un/semi-supervised methods and show its competitive advantages over fully-supervised ones.Comment: 9 page
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