5,452 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

    UNCOVERING THE MENTAL WORLD OF CHILDREN: ATTACHMENT QUALITY, MENTALIZATION, AND CHILDREN’S DRAWINGS

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    Although we have long been aware of the widespread benefits of drawing for children (Goodenough, 1926), there is much to learn from a clinical perspective about children’s attachment patterns and mentalization capacities in analyzing their drawings. The present study utilized archival data to uncover trends associated with children’s drawing characteristics, attachment qualities, and mentalization capacities. This study further explored the extent to which mentalization mediates the relationship between attachment quality and Formal Elements (FE) scores as well as the relationship between attachment quality and Content scores of children’s drawings. Two samples of 5–12-year-old children and their caregivers were recruited: one child sample from a public elementary school in White Plains, NY (n = 54), and the other child sample recruited consecutively following admission to a child psychiatric inpatient unit in White Plains, NY (n = 45). Each of the 99 children, including both the inpatient and nonpatient samples, completed three drawings: a drawing of family, primary caregiver, and self, totaling 297 drawings. These drawings were coded using the Formal Elements and Content rating scales (Tuman, 1998, 1999a). Attachment quality and mentalization data for these samples were obtained from previous studies, using the Attachment Story-Completion Task (ASCT) and Children’s Apperception Test (CAT). Attachment quality was found to have a significant positive relationship with the Content scores of family drawings within the inpatient sample. Attachment quality was also found to have a significant positive relationship with mentalization in both the nonpatient and inpatient samples. Mentalization was found to have a significant positive relationship with the Content and FE scores of children’s drawings. This relationship held true for Content scores of caregiver drawings and FE scores of family drawings within the nonpatient sample, and for both the Content and FE scores of family drawings within the inpatient sample. In general, drawings appear to hold promise as tools to access both psychiatrically compromised and nonpatient children’s internal working models and mental states. Gender differences and clinical implications are discussed

    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

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

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    GeschĂ€tzt mehr als 6.000 Erkrankungen werden durch VerĂ€nderungen 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 begĂŒnstigen. All diese Prozesse mĂŒssen ĂŒberprĂŒft werden, um die zum beschriebenen PhĂ€notyp 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 PathogenitĂ€t. Die Entwicklung eines Varianteneffektmodells erfordert eine Reihe von Schritten: Annotation der Trainingsdaten, Auswahl von Features, Training verschiedener Modelle und Selektion eines Modells. Hier prĂ€sentiere 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 fĂŒr 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 AllelhĂ€ufigkeit 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 verfĂŒgbar.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

    Machine Learning Meets Mental Training -- A Proof of Concept Applied to Memory Sports

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    This work aims to combine these two fields together by presenting a practical implementation of machine learning to the particular form of mental training that is the art of memory, taken in its competitive version called "Memory Sports". Such a fusion, on the one hand, strives to raise awareness about both realms, while on the other it seeks to encourage research in this mixed field as a way to, ultimately, drive forward the development of this seemingly underestimated sport.Comment: 75 pages, 47 figures, 2 tables, 26 code excerpt

    Endogenous measures for contextualising large-scale social phenomena: a corpus-based method for mediated public discourse

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    This work presents an interdisciplinary methodology for developing endogenous measures of group membership through analysis of pervasive linguistic patterns in public discourse. Focusing on political discourse, this work critiques the conventional approach to the study of political participation, which is premised on decontextualised, exogenous measures to characterise groups. Considering the theoretical and empirical weaknesses of decontextualised approaches to large-scale social phenomena, this work suggests that contextualisation using endogenous measures might provide a complementary perspective to mitigate such weaknesses. This work develops a sociomaterial perspective on political participation in mediated discourse as affiliatory action performed through language. While the affiliatory function of language is often performed consciously (such as statements of identity), this work is concerned with unconscious features (such as patterns in lexis and grammar). This work argues that pervasive patterns in such features that emerge through socialisation are resistant to change and manipulation, and thus might serve as endogenous measures of sociopolitical contexts, and thus of groups. In terms of method, the work takes a corpus-based approach to the analysis of data from the Twitter messaging service whereby patterns in users’ speech are examined statistically in order to trace potential community membership. The method is applied in the US state of Michigan during the second half of 2018—6 November having been the date of midterm (i.e. non-Presidential) elections in the United States. The corpus is assembled from the original posts of 5,889 users, who are nominally geolocalised to 417 municipalities. These users are clustered according to pervasive language features. Comparing the linguistic clusters according to the municipalities they represent finds that there are regular sociodemographic differentials across clusters. This is understood as an indication of social structure, suggesting that endogenous measures derived from pervasive patterns in language may indeed offer a complementary, contextualised perspective on large-scale social phenomena

    Object Segmentation and Reconstruction Using Infrastructure Sensor Nodes for Autonomous Mobility

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    This thesis focuses on the Lidar point cloud processing for the infrastructure sensor node that serves as the perception system for autonomous robots with general mobility in indoor applications. Compared with typical schemes mounting sensors on the robots, the method acquires data from infrastructure sensor nodes, providing a more comprehensive view of the environment, which benefits the robot's navigation. The number of sensors would not need to be increased even for multiple robots, significantly reducing costs. In addition, with a central perception system using the infrastructure sensor nodes navigating every robot, a more comprehensive understanding of the current environment and all the robots' locations can be obtained for the control and operation of the autonomous robots. For a robot in the detection range of the sensor node, the sensor node can detect and segment obstacles in its driveable area and reconstruct the incomplete, sparse point cloud of objects upon their movement. The complete shape by the reconstruction benefits the localization and path planning which follows the perception part of the robot's system. Considering the sparse Lidar data and the variety of object categories in the environment, a model-free scheme is selected for object segmentation. Point segmentation starts with background filtering. Considering the complexity of the indoor environment, a depth-matching-based background removal approach is first proposed. However, later tests imply that the method is adequate but not time-efficient. Therefore, based on the depth matching-based method, a process that only focuses on the drive-able area of the robot is proposed, and the computational complexity is significantly reduced. With optimization, the computation time for processing one frame of data can be greatly increased, from 0.2 second by the first approach to 0.01 second by the second approach. After background filtering, the remaining points for occurring objects are segmented as separate clusters using an object clustering algorithm. With independent clusters of objects, an object tracking algorithm is followed to allocate the point clusters with IDs and arrange the clusters in a time sequence. With a stream of clusters for a specific object in a time sequence, point registration is deployed to aggregate the clusters into a complete shape. And as noticed during the experiment, one of the differences between indoor and outdoor environments is that contact between objects in the indoor environment is much more common. The objects in contact are likely to be segmented as a single cluster by the model-free clustering algorithm, which needs to be avoided in the reconstruction process. Therefore an improvement is made in the tracking algorithm when contact happens. The algorithms in this thesis have been experimentally evaluated and presented

    DataComp: In search of the next generation of multimodal datasets

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    Multimodal datasets are a critical component in recent breakthroughs such as Stable Diffusion and GPT-4, yet their design does not receive the same research attention as model architectures or training algorithms. To address this shortcoming in the ML ecosystem, we introduce DataComp, a testbed for dataset experiments centered around a new candidate pool of 12.8 billion image-text pairs from Common Crawl. Participants in our benchmark design new filtering techniques or curate new data sources and then evaluate their new dataset by running our standardized CLIP training code and testing the resulting model on 38 downstream test sets. Our benchmark consists of multiple compute scales spanning four orders of magnitude, which enables the study of scaling trends and makes the benchmark accessible to researchers with varying resources. Our baseline experiments show that the DataComp workflow leads to better training sets. In particular, our best baseline, DataComp-1B, enables training a CLIP ViT-L/14 from scratch to 79.2% zero-shot accuracy on ImageNet, outperforming OpenAI's CLIP ViT-L/14 by 3.7 percentage points while using the same training procedure and compute. We release DataComp and all accompanying code at www.datacomp.ai

    2023-2024 Boise State University Undergraduate Catalog

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    This catalog is primarily for and directed at students. However, it serves many audiences, such as high school counselors, academic advisors, and the public. In this catalog you will find an overview of Boise State University and information on admission, registration, grades, tuition and fees, financial aid, housing, student services, and other important policies and procedures. However, most of this catalog is devoted to describing the various programs and courses offered at Boise State
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