scholarly journals DeepIsoFun: a deep domain adaptation approach to predict isoform functions

2018 ◽  
Vol 35 (15) ◽  
pp. 2535-2544 ◽  
Author(s):  
Dipan Shaw ◽  
Hao Chen ◽  
Tao Jiang
Keyword(s):  
Network Architecture ◽  
Domain Adaptation ◽  
Multiple Instance Learning ◽  
Training Data ◽  
Supplementary Information ◽  
Operating Characteristics ◽  
Neural Network Architecture ◽  
Receiver Operating Characteristics Curve ◽  
Gene Functions ◽  
Better Than

AbstractMotivationIsoforms are mRNAs produced from the same gene locus by alternative splicing and may have different functions. Although gene functions have been studied extensively, little is known about the specific functions of isoforms. Recently, some computational approaches based on multiple instance learning have been proposed to predict isoform functions from annotated gene functions and expression data, but their performance is far from being desirable primarily due to the lack of labeled training data. To improve the performance on this problem, we propose a novel deep learning method, DeepIsoFun, that combines multiple instance learning with domain adaptation. The latter technique helps to transfer the knowledge of gene functions to the prediction of isoform functions and provides additional labeled training data. Our model is trained on a deep neural network architecture so that it can adapt to different expression distributions associated with different gene ontology terms.ResultsWe evaluated the performance of DeepIsoFun on three expression datasets of human and mouse collected from SRA studies at different times. On each dataset, DeepIsoFun performed significantly better than the existing methods. In terms of area under the receiver operating characteristics curve, our method acquired at least 26% improvement and in terms of area under the precision-recall curve, it acquired at least 10% improvement over the state-of-the-art methods. In addition, we also study the divergence of the functions predicted by our method for isoforms from the same gene and the overall correlation between expression similarity and the similarity of predicted functions.Availability and implementationhttps://github.com/dls03/DeepIsoFun/Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals Fighting Together against the Pandemic: Learning Multiple Models on Tomography Images for COVID-19 Diagnosis

AI ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 261-273
Author(s):  
Mario Manzo ◽  
Simone Pellino
Keyword(s):  
Network Architecture ◽  
State Of The Art ◽  
Ensemble Classification ◽  
Effective Vaccine ◽  
Rt Pcr ◽  
Neural Network Architecture ◽  
Experimental Phase ◽  
Different Types ◽  
Polymerase Chain ◽  
Better Than

COVID-19 has been a great challenge for humanity since the year 2020. The whole world has made a huge effort to find an effective vaccine in order to save those not yet infected. The alternative solution is early diagnosis, carried out through real-time polymerase chain reaction (RT-PCR) tests or thorax Computer Tomography (CT) scan images. Deep learning algorithms, specifically convolutional neural networks, represent a methodology for image analysis. They optimize the classification design task, which is essential for an automatic approach with different types of images, including medical. In this paper, we adopt a pretrained deep convolutional neural network architecture in order to diagnose COVID-19 disease from CT images. Our idea is inspired by what the whole of humanity is achieving, as the set of multiple contributions is better than any single one for the fight against the pandemic. First, we adapt, and subsequently retrain for our assumption, some neural architectures that have been adopted in other application domains. Secondly, we combine the knowledge extracted from images by the neural architectures in an ensemble classification context. Our experimental phase is performed on a CT image dataset, and the results obtained show the effectiveness of the proposed approach with respect to the state-of-the-art competitors.

scholarly journals Deep learning of stochastic contagion dynamics on complex networks

2020 ◽  
Author(s):  
Charles Murphy ◽  
Edward Laurence ◽  
Antoine Allard
Keyword(s):  
Deep Learning ◽  
Network Architecture ◽  
Time Series Data ◽  
Training Data ◽  
Series Data ◽  
Neural Network Architecture ◽  
Complementary Approach ◽  
Quantitative Accuracy ◽  
Simplifying Assumptions ◽  
Effective Models

Abstract Forecasting the evolution of contagion dynamics is still an open problem to which mechanistic models only offer a partial answer. To remain mathematically and/or computationally tractable, these models must rely on simplifying assumptions, thereby limiting the quantitative accuracy of their predictions and the complexity of the dynamics they can model. Here, we propose a complementary approach based on deep learning where the effective local mechanisms governing a dynamic are learned automatically from time series data. Our graph neural network architecture makes very few assumptions about the dynamics, and we demonstrate its accuracy using stochastic contagion dynamics of increasing complexity on static and temporal networks. By allowing simulations on arbitrary network structures, our approach makes it possible to explore the properties of the learned dynamics beyond the training data. Our results demonstrate how deep learning offers a new and complementary perspective to build effective models of contagion dynamics on networks.

scholarly journals Weakly supervised semantic segmentation of tomographic images in the diagnosis of stroke

2021 ◽  
Vol 2099 (1) ◽  
pp. 012021
Author(s):  
A V Dobshik ◽  
A A Tulupov ◽  
V B Berikov
Keyword(s):  
Computed Tomography ◽  
Network Architecture ◽  
Semantic Segmentation ◽  
Training Data ◽  
Neural Network Architecture ◽  
Brain Images ◽  
Tomographic Images ◽  
Computed Tomography Images ◽  
Segmentation Accuracy ◽  
Weakly Supervised

Abstract This paper presents an automatic algorithm for the segmentation of areas affected by an acute stroke in the non-contrast computed tomography brain images. The proposed algorithm is designed for learning in a weakly supervised scenario when some images are labeled accurately, and some images are labeled inaccurately. Wrong labels appear as a result of inaccuracy made by a radiologist in the process of manual annotation of computed tomography images. We propose methods for solving the segmentation problem in the case of inaccurately labeled training data. We use the U-Net neural network architecture with several modifications. Experiments on real computed tomography scans show that the proposed methods increase the segmentation accuracy.

scholarly journals Varmole: a biologically drop-connect deep neural network model for prioritizing disease risk variants and genes

2020 ◽  
Author(s):  
Nam D Nguyen ◽  
Ting Jin ◽  
Daifeng Wang
Keyword(s):  
Neural Network ◽  
Network Architecture ◽  
Deep Neural Network ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Disease Risk ◽  
Supplementary Information ◽  
Neural Network Architecture ◽  
Risk Variants ◽  
Genome Wide

Abstract Summary Population studies such as genome-wide association study have identified a variety of genomic variants associated with human diseases. To further understand potential mechanisms of disease variants, recent statistical methods associate functional omic data (e.g. gene expression) with genotype and phenotype and link variants to individual genes. However, how to interpret molecular mechanisms from such associations, especially across omics, is still challenging. To address this problem, we developed an interpretable deep learning method, Varmole, to simultaneously reveal genomic functions and mechanisms while predicting phenotype from genotype. In particular, Varmole embeds multi-omic networks into a deep neural network architecture and prioritizes variants, genes and regulatory linkages via biological drop-connect without needing prior feature selections. Availability and implementation Varmole is available as a Python tool on GitHub at https://github.com/daifengwanglab/Varmole. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation

2020 ◽  
Author(s):  
Hong-Dong Li ◽  
Changhuo Yang ◽  
Zhimin Zhang ◽  
Mengyun Yang ◽  
Fang-Xiang Wu ◽  
...  
Keyword(s):  
Latent Variables ◽  
Functional Annotation ◽  
Latent Variable ◽  
Prediction Models ◽  
Domain Adaptation ◽  
Single Gene ◽  
Function Prediction ◽  
Supplementary Information ◽  
Similar Distribution ◽  
Gene Functions

Abstract Motivation High resolution annotation of gene functions is a central goal in functional genomics. A single gene may produce multiple isoforms with different functions through alternative splicing. Conventional approaches, however, consider a gene as a single entity without differentiating these functionally different isoforms. Towards understanding gene functions at higher resolution, recent efforts have focused on predicting the functions of isoforms. However, the performance of existing methods is far from satisfactory mainly because of the lack of isoform-level functional annotation. Results We present IsoResolve, a novel approach for isoform function prediction, which leverages the information from gene function prediction models with domain adaptation (DA). IsoResolve treats gene-level and isoform-level features as source and target domains, respectively. It uses DA to project the two domains into a latent variable space in such a way that the latent variables from the two domains have similar distribution, which enables the gene domain information to be leveraged for isoform function prediction. We systematically evaluated the performance of IsoResolve in predicting functions. Compared with five state-of-the-art methods, IsoResolve achieved significantly better performance. IsoResolve was further validated by case studies of genes with isoform-level functional annotation. Availability and implementation IsoResolve is freely available at https://github.com/genemine/IsoResolve. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Accurate diagnosis of colorectal cancer based on histopathology images using artificial intelligence

BMC Medicine ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
K. S. Wang ◽  
G. Yu ◽  
C. Xu ◽  
X. H. Meng ◽  
J. Zhou ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Colorectal Cancer ◽  
Kappa Statistic ◽  
Cancer Tissue ◽  
Operating Characteristics ◽  
Receiver Operating Characteristics Curve ◽  
Slide Image ◽  
The Usa ◽  
Knowledge Intensive ◽  
Better Than

Abstract Background Accurate and robust pathological image analysis for colorectal cancer (CRC) diagnosis is time-consuming and knowledge-intensive, but is essential for CRC patients’ treatment. The current heavy workload of pathologists in clinics/hospitals may easily lead to unconscious misdiagnosis of CRC based on daily image analyses. Methods Based on a state-of-the-art transfer-learned deep convolutional neural network in artificial intelligence (AI), we proposed a novel patch aggregation strategy for clinic CRC diagnosis using weakly labeled pathological whole-slide image (WSI) patches. This approach was trained and validated using an unprecedented and enormously large number of 170,099 patches, > 14,680 WSIs, from > 9631 subjects that covered diverse and representative clinical cases from multi-independent-sources across China, the USA, and Germany. Results Our innovative AI tool consistently and nearly perfectly agreed with (average Kappa statistic 0.896) and even often better than most of the experienced expert pathologists when tested in diagnosing CRC WSIs from multicenters. The average area under the receiver operating characteristics curve (AUC) of AI was greater than that of the pathologists (0.988 vs 0.970) and achieved the best performance among the application of other AI methods to CRC diagnosis. Our AI-generated heatmap highlights the image regions of cancer tissue/cells. Conclusions This first-ever generalizable AI system can handle large amounts of WSIs consistently and robustly without potential bias due to fatigue commonly experienced by clinical pathologists. It will drastically alleviate the heavy clinical burden of daily pathology diagnosis and improve the treatment for CRC patients. This tool is generalizable to other cancer diagnosis based on image recognition.

scholarly journals Accurate Diagnosis of Colorectal Cancer Based on Histopathology Images Using Artificial Intelligence

2020 ◽  
Author(s):  
Kuan-Song Wang ◽  
Gang Yu ◽  
Chao Xu ◽  
Xiang-He Meng ◽  
Jianhua Zhou ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Colorectal Cancer ◽  
Kappa Statistic ◽  
Cancer Tissue ◽  
Operating Characteristics ◽  
Receiver Operating Characteristics Curve ◽  
Slide Image ◽  
Knowledge Intensive ◽  
Pathological Image ◽  
Better Than

AbstractBackgroundAccurate and robust pathological image analysis for colorectal cancer (CRC) diagnosis is time-consuming and knowledge-intensive, but is essential for CRC patients’ treatment. The current heavy workload of pathologists in clinics/hospitals may easily lead to unconscious misdiagnosis of CRC based on their daily image analyses.MethodsBased on a state-of-the-art transfer-learned deep convolutional neural network in artificial intelligence (AI), we proposed a novel patch aggregation strategy for clinic CRC prediction/diagnosis using weakly labeled pathological whole slide image (WSI) patches. This approach was trained and validated using an unprecedented and enormously large number of 170,099 patches, >14,680 WSIs, from >9,631 subjects that covered diverse and representative clinical cases from multi-independent-sources across China, U.S., and Germany.ResultsOur innovative AI tool was consistently nearly perfectly agreed with (average Kappa-statistic 0.896) and even often better than most of the experienced expert pathologists when tested in diagnosing CRC WSIs from multi-centers. The average area under the receiver operating characteristics curve (AUC) of AI was greater than that of the pathologists (0.981 vs 0.970) and achieved the best performance among the application of other AI methods to CRC diagnosis. Our AI-generated heatmap highlights the image regions of cancer tissue/cells.ConclusionsThis first-ever generalizable AI system can handle large amounts of WSIs consistently and robustly without potential bias due to fatigue commonly experienced by clinical pathologists. Hence, it will drastically alleviate the heavy clinical burden of daily pathology diagnosis, and improve the treatment for CRC patients. This tool is generalizable to other cancer diagnosis based on image recognition.

scholarly journals Establishment of a prognostic model for patients with sepsis based on SOFA: a retrospective cohort study

2021 ◽  
Vol 49 (9) ◽  
pp. 030006052110448
Author(s):  
Hui Liu ◽  
Luming Zhang ◽  
Fengshuo Xu ◽  
Shaojin Li ◽  
Zichen Wang ◽  
...  
Keyword(s):  
Mortality Risk ◽  
Medical Information ◽  
Cox Regression ◽  
Metastatic Cancer ◽  
Operating Characteristics ◽  
Distribution Width ◽  
Net Reclassification Improvement ◽  
Receiver Operating Characteristics Curve ◽  
Failure Assessment ◽  
Better Than

Objective To construct a nomogram based on the Sequential Organ Failure Assessment (SOFA) that is more accurate in predicting 30-, 60-, and 90-day mortality risk in patients with sepsis. Methods Data from patients with sepsis were retrospectively collected from the Medical Information Mart for Intensive Care (MIMIC) database. Included patients were randomly divided into training and validation cohorts. Variables were selected using a backward stepwise selection method with Cox regression, then used to construct a prognostic nomogram. The nomogram was compared with the SOFA model using the concordance index (C-index), area under the time-dependent receiver operating characteristics curve (AUC), net reclassification improvement (NRI), integrated discrimination improvement (IDI), calibration plotting, and decision-curve analysis (DCA). Results A total of 5240 patients were included in the study. Patient’s age, SOFA score, metastatic cancer, SpO2, lactate, body temperature, albumin, and red blood cell distribution width were included in the nomogram. The C-index, AUC, NRI, IDI, and DCA of the nomogram showed that it performs better than the SOFA alone. Conclusion A nomogram was established that performed better than the SOFA in predicting 30-, 60-, and 90-day mortality risk in patients with sepsis.

scholarly journals Automatically Paraphrasing via Sentence Reconstruction and Round-trip Translation

2021 ◽  
Author(s):  
Zilu Guo ◽  
Zhongqiang Huang ◽  
Kenny Q. Zhu ◽  
Guandan Chen ◽  
Kaibo Zhang ◽  
...  
Keyword(s):  
Machine Translation ◽  
Question Answering ◽  
Domain Adaptation ◽  
State Of The Art ◽  
Training Data ◽  
Round Trip ◽  
Previous State ◽  
Supervised Methods ◽  
Paraphrase Generation ◽  
Better Than

Paraphrase generation plays key roles in NLP tasks such as question answering, machine translation, and information retrieval. In this paper, we propose a novel framework for paraphrase generation. It simultaneously decodes the output sentence using a pretrained wordset-to-sequence model and a round-trip translation model. We evaluate this framework on Quora, WikiAnswers, MSCOCO and Twitter, and show its advantage over previous state-of-the-art unsupervised methods and distantly-supervised methods by significant margins on all datasets. For Quora and WikiAnswers, our framework even performs better than some strongly supervised methods with domain adaptation. Further, we show that the generated paraphrases can be used to augment the training data for machine translation to achieve substantial improvements.

FIR and IIR Synapses, a New Neural Network Architecture for Time Series Modeling

1991 ◽  
Vol 3 (3) ◽  
pp. 375-385 ◽  
Author(s):  
A. D. Back ◽  
A. C. Tsoi
Keyword(s):  
Neural Network ◽  
Time Series ◽  
Mean Square Error ◽  
Network Architecture ◽  
Learning Rule ◽  
Mean Square ◽  
Time Series Modeling ◽  
Neural Network Architecture ◽  
Mean Square Error Criterion ◽  
Better Than

A new neural network architecture involving either local feedforward global feedforward, and/or local recurrent global feedforward structure is proposed. A learning rule minimizing a mean square error criterion is derived. The performance of this algorithm (local recurrent global feedforward architecture) is compared with a local-feedforward global-feedforward architecture. It is shown that the local-recurrent global-feedforward model performs better than the local-feedforward global-feedforward model.

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