Self-supervised Chinese ontology learning from online encyclopedias.
Ontology highlight
ABSTRACT:
SUBMITTER: Hu F
PROVIDER: S-EPMC3970055 | biostudies-other | 2014
REPOSITORIES: biostudies-other
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Project description:Machine learning analysis of longitudinal neuroimaging data is typically based on supervised learning, which requires large number of ground-truth labels to be informative. As ground-truth labels are often missing or expensive to obtain in neuroscience, we avoid them in our analysis by combing factor disentanglement with self-supervised learning to identify changes and consistencies across the multiple MRIs acquired of each individual over time. Specifically, we propose a new definition of disentanglement by formulating a multivariate mapping between factors (e.g., brain age) associated with an MRI and a latent image representation. Then, factors that evolve across acquisitions of longitudinal sequences are disentangled from that mapping by self-supervised learning in such a way that changes in a single factor induce change along one direction in the representation space. We implement this model, named Longitudinal Self-Supervised Learning (LSSL), via a standard autoencoding structure with a cosine loss to disentangle brain age from the image representation. We apply LSSL to two longitudinal neuroimaging studies to highlight its strength in extracting the brain-age information from MRI and revealing informative characteristics associated with neurodegenerative and neuropsychological disorders. Moreover, the representations learned by LSSL facilitate supervised classification by recording faster convergence and higher (or similar) prediction accuracy compared to several other representation learning techniques.
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Project description:Backgrounds & Aims: Transcriptomic classification of intrahepatic cholangiocarcinoma (iCCA) has been recently improved from two classes to five classes, associated with pathological features, targetable genetic alterations and survival. Despite its prognostic and therapeutic value, the classification is not routinely performed due to technical limits such as insufficient material or the cost of molecular analyses. Our aim was to predict iCCA transcriptomic classes on whole-slide digital histological images (WSI) using a self-supervised learning (SSL) model. Methods: Gene expression was investigated using RNA sequencing to class samples in the five transcriptomic classes. We then used a SSL method called GigaSSL. We first trained our model on a discovery set of 769 slides (biopsy and surgical samples, 246 patients) in a 5-fold cross-validation scheme. We then validated the model in a TCGA (n= 29) and a French external validation set (n=32). Results: Our model showed good performance for predicting each transcriptomic class in the discovery set (Area under the curve, AUC: 0.55-0.81), particularly for the Hepatic stem-like class (most frequent group, 37% of cases), with AUC 0.81. The model generalised well for the prediction of four on five of the transcriptomic classes into the two validation sets with AUCs ranging from 0.76 to 0.80 in the TCGA set and from 0.62 to 0.92 in the French external set. Conclusion: We have developed and validated a SSL based model able to predict iCCA transcriptomic classes on routine histological slides (biopsy and surgical samples), which could have an impact on the management of patients.
2023-11-01 | GSE244807 | GEO
Project description:PurposeVirtual reality-based simulators have the potential to become an essential part of surgical education. To make full use of this potential, they must be able to automatically recognize activities performed by users and assess those. Since annotations of trajectories by human experts are expensive, there is a need for methods that can learn to recognize surgical activities in a data-efficient way.MethodsWe use self-supervised training of deep encoder-decoder architectures to learn representations of surgical trajectories from video data. These representations allow for semi-automatic extraction of features that capture information about semantically important events in the trajectories. Such features are processed as inputs of an unsupervised surgical activity recognition pipeline.ResultsOur experiments document that the performance of hidden semi-Markov models used for recognizing activities in a simulated myomectomy scenario benefits from using features extracted from representations learned while training a deep encoder-decoder network on the task of predicting the remaining surgery progress.ConclusionOur work is an important first step in the direction of making efficient use of features obtained from deep representation learning for surgical activity recognition in settings where only a small fraction of the existing data is annotated by human domain experts and where those annotations are potentially incomplete.
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Project description:Traffic sign recognition is a classification problem that poses challenges for computer vision and machine learning algorithms. Although both computer vision and machine learning techniques have constantly been improved to solve this problem, the sudden rise in the number of unlabeled traffic signs has become even more challenging. Large data collation and labeling are tedious and expensive tasks that demand much time, expert knowledge, and fiscal resources to satisfy the hunger of deep neural networks. Aside from that, the problem of having unbalanced data also poses a greater challenge to computer vision and machine learning algorithms to achieve better performance. These problems raise the need to develop algorithms that can fully exploit a large amount of unlabeled data, use a small amount of labeled samples, and be robust to data imbalance to build an efficient and high-quality classifier. In this work, we propose a novel semi-supervised classification technique that is robust to small and unbalanced data. The framework integrates weakly-supervised learning and self-training with self-paced learning to generate attention maps to augment the training set and utilizes a novel pseudo-label generation and selection algorithm to generate and select pseudo-labeled samples. The method improves the performance by: (1) normalizing the class-wise confidence levels to prevent the model from ignoring hard-to-learn samples, thereby solving the imbalanced data problem; (2) jointly learning a model and optimizing pseudo-labels generated on unlabeled data; and (3) enlarging the training set to satisfy the hunger of deep learning models. Extensive evaluations on two public traffic sign recognition datasets demonstrate the effectiveness of the proposed technique and provide a potential solution for practical applications.
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Project description:Learning from limited exemplars (few-shot learning) is a fundamental, unsolved problem that has been laboriously explored in the machine learning community. However, current few-shot learners are mostly supervised and rely heavily on a large amount of labeled examples. Unsupervised learning is a more natural procedure for cognitive mammals and has produced promising results in many machine learning tasks. In this paper, we propose an unsupervised feature learning method for few-shot learning. The proposed model consists of two alternate processes, progressive clustering and episodic training. The former generates pseudo-labeled training examples for constructing episodic tasks; and the later trains the few-shot learner using the generated episodic tasks which further optimizes the feature representations of data. The two processes facilitate each other, and eventually produce a high quality few-shot learner. In our experiments, our model achieves good generalization performance in a variety of downstream few-shot learning tasks on Omniglot and MiniImageNet. We also construct a new few-shot person re-identification dataset FS-Market1501 to demonstrate the feasibility of our model to a real-world application.
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Project description:An individual's B cell receptor (BCR) repertoire encodes information about past immune responses and potential for future disease protection. Deciphering the information stored in BCR sequence datasets will transform our understanding of disease and enable discovery of novel diagnostics and antibody therapeutics. A key challenge of BCR sequence analysis is the prediction of BCR properties from their amino acid sequence alone. Here, we present an antibody-specific language model, Antibody-specific Bidirectional Encoder Representation from Transformers (AntiBERTa), which provides a contextualized representation of BCR sequences. Following pre-training, we show that AntiBERTa embeddings capture biologically relevant information, generalizable to a range of applications. As a case study, we fine-tune AntiBERTa to predict paratope positions from an antibody sequence, outperforming public tools across multiple metrics. To our knowledge, AntiBERTa is the deepest protein-family-specific language model, providing a rich representation of BCRs. AntiBERTa embeddings are primed for multiple downstream tasks and can improve our understanding of the language of antibodies.
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Project description:In recent years, several deep learning models recommend first to represent Magnetic Resonance Imaging (MRI) as latent features before performing a downstream task of interest (such as classification or regression). The performance of the downstream task generally improves when these latent representations are explicitly associated with factors of interest. For example, we derived such a representation for capturing brain aging by applying self-supervised learning to longitudinal MRIs and then used the resulting encoding to automatically identify diseases accelerating the aging of the brain. We now propose a refinement of this representation by replacing the linear modeling of brain aging with one that is consistent in local neighborhoods in the latent space. Called Longitudinal Neighborhood Embedding (LNE), we derive an encoding so that neighborhoods are age-consistent (i.e., brain MRIs of different subjects with similar brain ages are in close proximity of each other) and progression-consistent, i.e., the latent space is defined by a smooth trajectory field where each trajectory captures changes in brain ages between a pair of MRIs extracted from a longitudinal sequence. To make the problem computationally tractable, we further propose a strategy for mini-batch sampling so that the resulting local neighborhoods accurately approximate the ones that would be defined based on the whole cohort. We evaluate LNE on three different downstream tasks: (1) to predict chronological age from T1-w MRI of 274 healthy subjects participating in a study at SRI International; (2) to distinguish Normal Control (NC) from Alzheimer's Disease (AD) and stable Mild Cognitive Impairment (sMCI) from progressive Mild Cognitive Impairment (pMCI) based on T1-w MRI of 632 participants of the Alzheimer's Disease Neuroimaging Initiative (ADNI); and (3) to distinguish no-to-low from moderate-to-heavy alcohol drinkers based on fractional anisotropy derived from diffusion tensor MRIs of 764 adolescents recruited by the National Consortium on Alcohol and NeuroDevelopment in Adolescence (NCANDA). Across the three data sets, the visualization of the smooth trajectory vector fields and superior accuracy on downstream tasks demonstrate the strength of the proposed method over existing self-supervised methods in extracting information related to brain aging, which could help study the impact of substance use and neurodegenerative disorders. The code is available at https://github.com/ouyangjiahong/longitudinal-neighbourhood-embedding.
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Project description:SummaryThe biological functions of proteins are determined by the chemical and geometric properties of their surfaces. Recently, with the booming progress of deep learning, a series of learning-based surface descriptors have been proposed and achieved inspirational performance in many tasks such as protein design, protein-protein interaction prediction, etc. However, they are still limited by the problem of label scarcity, since the labels are typically obtained through wet experiments. Inspired by the great success of self-supervised learning in natural language processing and computer vision, we introduce ProteinMAE, a self-supervised framework specifically designed for protein surface representation to mitigate label scarcity. Specifically, we propose an efficient network and utilize a large number of accessible unlabeled protein data to pre-train it by self-supervised learning. Then we use the pre-trained weights as initialization and fine-tune the network on downstream tasks. To demonstrate the effectiveness of our method, we conduct experiments on three different downstream tasks including binding site identification in protein surface, ligand binding protein pocket classification, and protein-protein interaction prediction. The extensive experiments show that our method not only successfully improves the network's performance on all downstream tasks and enables it to achieve competitive performance with state-of-the-art methods. Moreover, our proposed network also exhibits significant advantages in terms of computational cost, which only requires less than a tenth of memory cost of previous methods.Availability and implementationhttps://github.com/phdymz/ProteinMAE.Supplementary informationWe provide supplementary material following the manuscript.
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Project description:With a spatial resolution of tens of microns, ultrasound localization microscopy (ULM) reconstructs microvascular structures and measures intravascular flows by tracking microbubbles (1-5 μm) in contrast enhanced ultrasound (CEUS) images. Since the size of CEUS bubble traces, e.g. 0.5-1 mm for ultrasound with a wavelength λ = 280 μm, is typically two orders of magnitude larger than the bubble diameter, accurately localizing microbubbles in noisy CEUS data is vital to the fidelity of the ULM results. In this paper, we introduce a residual learning based supervised super-resolution blind deconvolution network (SupBD-net), and a new loss function for a self-supervised blind deconvolution network (SelfBD-net), for detecting bubble centers at a spatial resolution finer than λ/10. Our ultimate purpose is to improve the ability to distinguish closely located microvessels and the accuracy of the velocity profile measurements in macrovessels. Using realistic synthetic data, the performance of these methods is calibrated and compared against several recently introduced deep learning and blind deconvolution techniques. For bubble detection, errors in bubble center location increase with the trace size, noise level, and bubble concentration. For all cases, SupBD-net yields the least error, keeping it below 0.1 λ. For unknown bubble trace morphology, where all the supervised learning methods fail, SelfBD-net can still maintain an error of less than 0.15 λ. SupBD-net also outperforms the other methods in separating closely located bubbles and parallel microvessels. In macrovessels, SupBD-net maintains the least errors in the vessel radius and velocity profile after introducing a procedure that corrects for terminated tracks caused by overlapping traces. Application of these methods is demonstrated by mapping the cerebral microvasculature of a neonatal pig, where neighboring microvessels separated by 0.15 λ can be readily distinguished by SupBD-net and SelfBD-net, but not by the other techniques. Hence, the newly proposed residual learning based methods improve the spatial resolution and accuracy of ULM in micro- and macro-vessels.
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