scholarly journals Reverse-complement parameter sharing improves deep learning models for genomics

2017 ◽  
Author(s):  
Avanti Shrikumar ◽  
Peyton Greenside ◽  
Anshul Kundaje
Keyword(s):  
Computer Vision ◽  
Deep Learning ◽  
Dna Sequence ◽  
Language Processing ◽  
Learning Approaches ◽  
Learning Models ◽  
Network Layers ◽  
Reverse Complement ◽  
Improved Performance

Deep learning approaches that have produced breakthrough predictive models in computer vision, speech recognition and machine translation are now being successfully applied to problems in regulatory genomics. However, deep learning architectures used thus far in genomics are often directly ported from computer vision and natural language processing applications with few, if any, domain-specific modifications. In double-stranded DNA, the same pattern may appear identically on one strand and its reverse complement due to complementary base pairing. Here, we show that conventional deep learning models that do not explicitly model this property can produce substantially different predictions on forward and reverse-complement versions of the same DNA sequence. We present four new convolutional neural network layers that leverage the reverse-complement property of genomic DNA sequence by sharing parameters between forward and reverse-complement representations in the model. These layers guarantee that forward and reverse-complement sequences produce identical predictions within numerical precision. Using experiments on simulated and in vivo transcription factor binding data, we show that our proposed architectures lead to improved performance, faster learning and cleaner internal representations compared to conventional architectures trained on the same data.

scholarly journals Sequence-to-function deep learning frameworks for engineered riboregulators

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jacqueline A. Valeri ◽  
Katherine M. Collins ◽  
Pradeep Ramesh ◽  
Miguel A. Alcantar ◽  
Bianca A. Lepe ◽  
...  
Keyword(s):  
Computer Vision ◽  
Deep Learning ◽  
Nucleic Acid ◽  
Language Processing ◽  
Training Data ◽  
Design Rules ◽  
Improved Performance ◽  
Circuit Components ◽  
Learning Frameworks ◽  
Learning Architectures

Abstract While synthetic biology has revolutionized our approaches to medicine, agriculture, and energy, the design of completely novel biological circuit components beyond naturally-derived templates remains challenging due to poorly understood design rules. Toehold switches, which are programmable nucleic acid sensors, face an analogous design bottleneck; our limited understanding of how sequence impacts functionality often necessitates expensive, time-consuming screens to identify effective switches. Here, we introduce Sequence-based Toehold Optimization and Redesign Model (STORM) and Nucleic-Acid Speech (NuSpeak), two orthogonal and synergistic deep learning architectures to characterize and optimize toeholds. Applying techniques from computer vision and natural language processing, we ‘un-box’ our models using convolutional filters, attention maps, and in silico mutagenesis. Through transfer-learning, we redesign sub-optimal toehold sensors, even with sparse training data, experimentally validating their improved performance. This work provides sequence-to-function deep learning frameworks for toehold selection and design, augmenting our ability to construct potent biological circuit components and precision diagnostics.

scholarly journals Deep learning systems detect dysplasia with human-like accuracy using histopathology and probe-based confocal laser endomicroscopy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shan Guleria ◽  
Tilak U. Shah ◽  
J. Vincent Pulido ◽  
Matthew Fasullo ◽  
Lubaina Ehsan ◽  
...  
Keyword(s):  
Deep Learning ◽  
Diagnostic Accuracy ◽  
High Sensitivity ◽  
Confocal Laser Endomicroscopy ◽  
Confocal Laser ◽  
Learning Approaches ◽  
Learning Models ◽  
Whole Slide Image ◽  
Slide Image ◽  
Level Model

AbstractProbe-based confocal laser endomicroscopy (pCLE) allows for real-time diagnosis of dysplasia and cancer in Barrett’s esophagus (BE) but is limited by low sensitivity. Even the gold standard of histopathology is hindered by poor agreement between pathologists. We deployed deep-learning-based image and video analysis in order to improve diagnostic accuracy of pCLE videos and biopsy images. Blinded experts categorized biopsies and pCLE videos as squamous, non-dysplastic BE, or dysplasia/cancer, and deep learning models were trained to classify the data into these three categories. Biopsy classification was conducted using two distinct approaches—a patch-level model and a whole-slide-image-level model. Gradient-weighted class activation maps (Grad-CAMs) were extracted from pCLE and biopsy models in order to determine tissue structures deemed relevant by the models. 1970 pCLE videos, 897,931 biopsy patches, and 387 whole-slide images were used to train, test, and validate the models. In pCLE analysis, models achieved a high sensitivity for dysplasia (71%) and an overall accuracy of 90% for all classes. For biopsies at the patch level, the model achieved a sensitivity of 72% for dysplasia and an overall accuracy of 90%. The whole-slide-image-level model achieved a sensitivity of 90% for dysplasia and 94% overall accuracy. Grad-CAMs for all models showed activation in medically relevant tissue regions. Our deep learning models achieved high diagnostic accuracy for both pCLE-based and histopathologic diagnosis of esophageal dysplasia and its precursors, similar to human accuracy in prior studies. These machine learning approaches may improve accuracy and efficiency of current screening protocols.

scholarly journals Deep Learning with Neuroimaging and Genomics in Alzheimer’s Disease

2021 ◽  
Vol 22 (15) ◽  
pp. 7911
Author(s):  
Eugene Lin ◽  
Chieh-Hsin Lin ◽  
Hsien-Yuan Lane
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Deep Learning ◽  
Future Research ◽  
Learning Approaches ◽  
Learning Models ◽  
Learning Techniques ◽  
Neuroimaging Data ◽  
Similarities And Differences ◽  
Normal Controls

A growing body of evidence currently proposes that deep learning approaches can serve as an essential cornerstone for the diagnosis and prediction of Alzheimer’s disease (AD). In light of the latest advancements in neuroimaging and genomics, numerous deep learning models are being exploited to distinguish AD from normal controls and/or to distinguish AD from mild cognitive impairment in recent research studies. In this review, we focus on the latest developments for AD prediction using deep learning techniques in cooperation with the principles of neuroimaging and genomics. First, we narrate various investigations that make use of deep learning algorithms to establish AD prediction using genomics or neuroimaging data. Particularly, we delineate relevant integrative neuroimaging genomics investigations that leverage deep learning methods to forecast AD on the basis of incorporating both neuroimaging and genomics data. Moreover, we outline the limitations as regards to the recent AD investigations of deep learning with neuroimaging and genomics. Finally, we depict a discussion of challenges and directions for future research. The main novelty of this work is that we summarize the major points of these investigations and scrutinize the similarities and differences among these investigations.

scholarly journals Generation of Cross-Lingual Word Vectors for Low-Resourced Languages Using Deep Learning and Topological Metrics in a Data-Efficient Way

Electronics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1372
Author(s):  
Sanjanasri JP ◽  
Vijay Krishna Menon ◽  
Soman KP ◽  
Rajendran S ◽  
Agnieszka Wolk
Keyword(s):  
Deep Learning ◽  
Language Processing ◽  
Semantic Space ◽  
Semantic Interpretation ◽  
Learning Approaches ◽  
Qualitative Comparison ◽  
Bilingual Dictionary ◽  
Pos Tagging ◽  
Part Of Speech ◽  
Cross Lingual

Linguists have been focused on a qualitative comparison of the semantics from different languages. Evaluation of the semantic interpretation among disparate language pairs like English and Tamil is an even more formidable task than for Slavic languages. The concept of word embedding in Natural Language Processing (NLP) has enabled a felicitous opportunity to quantify linguistic semantics. Multi-lingual tasks can be performed by projecting the word embeddings of one language onto the semantic space of the other. This research presents a suite of data-efficient deep learning approaches to deduce the transfer function from the embedding space of English to that of Tamil, deploying three popular embedding algorithms: Word2Vec, GloVe and FastText. A novel evaluation paradigm was devised for the generation of embeddings to assess their effectiveness, using the original embeddings as ground truths. Transferability across other target languages of the proposed model was assessed via pre-trained Word2Vec embeddings from Hindi and Chinese languages. We empirically prove that with a bilingual dictionary of a thousand words and a corresponding small monolingual target (Tamil) corpus, useful embeddings can be generated by transfer learning from a well-trained source (English) embedding. Furthermore, we demonstrate the usability of generated target embeddings in a few NLP use-case tasks, such as text summarization, part-of-speech (POS) tagging, and bilingual dictionary induction (BDI), bearing in mind that those are not the only possible applications.

scholarly journals PlotMI: visualization of pairwise interactions and positional preferences learned by a deep learning model from sequence data

2021 ◽  
Author(s):  
Tuomo Hartonen ◽  
Teemu Kivioja ◽  
Jussi Taipale
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Sequence Data ◽  
Predictive Performance ◽  
Learning Model ◽  
Biological Research ◽  
Learning Approaches ◽  
Learning Models ◽  
Model Interpretation ◽  
Pairwise Interactions

Deep learning models have in recent years gained success in various tasks related to understanding information coded in the DNA sequence. Rapidly developing genome-wide measurement technologies provide large quantities of data ideally suited for modeling using deep learning or other powerful machine learning approaches. Although offering state-of-the art predictive performance, the predictions made by deep learning models can be difficult to understand. In virtually all biological research, the understanding of how a predictive model works is as important as the raw predictive performance. Thus interpretation of deep learning models is an emerging hot topic especially in context of biological research. Here we describe plotMI, a mutual information based model interpretation strategy that can intuitively visualize positional preferences and pairwise interactions learned by any machine learning model trained on sequence data with a defined alphabet as input. PlotMI is freely available at https://github.com/hartonen/plotMI.

scholarly journals Covid-19 detection via deep neural network and occlusion sensitivity maps

2021 ◽  
Author(s):  
Noor Ahmad ◽  
Muhammad Aminu ◽  
Mohd Halim Mohd Noor
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
State Of The Art ◽  
Color Images ◽  
Fine Tuning ◽  
Training Dataset ◽  
Learning Approaches ◽  
Learning Models ◽  
Sensitivity Maps

Deep learning approaches have attracted a lot of attention in the automatic detection of Covid-19 and transfer learning is the most common approach. However, majority of the pre-trained models are trained on color images, which can cause inefficiencies when fine-tuning the models on Covid-19 images which are often grayscale. To address this issue, we propose a deep learning architecture called CovidNet which requires a relatively smaller number of parameters. CovidNet accepts grayscale images as inputs and is suitable for training with limited training dataset. Experimental results show that CovidNet outperforms other state-of-the-art deep learning models for Covid-19 detection.

Leveraging Natural Language Processing Applications Using Machine Learning

2020 ◽  
pp. 338-360
Author(s):  
Janjanam Prabhudas ◽  
C. H. Pradeep Reddy
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Text Summarization ◽  
Feature Representation ◽  
Learning Models ◽  
Primary Focus ◽  
And Performance

The enormous increase of information along with the computational abilities of machines created innovative applications in natural language processing by invoking machine learning models. This chapter will project the trends of natural language processing by employing machine learning and its models in the context of text summarization. This chapter is organized to make the researcher understand technical perspectives regarding feature representation and their models to consider before applying on language-oriented tasks. Further, the present chapter revises the details of primary models of deep learning, its applications, and performance in the context of language processing. The primary focus of this chapter is to illustrate the technical research findings and gaps of text summarization based on deep learning along with state-of-the-art deep learning models for TS.

scholarly journals A Review of Deep Learning Methods for Antibodies

Antibodies ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 12 ◽  
Author(s):  
Jordan Graves ◽  
Jacob Byerly ◽  
Eduardo Priego ◽  
Naren Makkapati ◽  
S. Vince Parish ◽  
...  
Keyword(s):  
Computer Vision ◽  
Deep Learning ◽  
Drug Discovery ◽  
Small Molecules ◽  
Language Processing ◽  
Protein Design ◽  
Therapeutic Drug ◽  
Major Goal ◽  
Antibody Design ◽  
Antibody Drug

Driven by its successes across domains such as computer vision and natural language processing, deep learning has recently entered the field of biology by aiding in cellular image classification, finding genomic connections, and advancing drug discovery. In drug discovery and protein engineering, a major goal is to design a molecule that will perform a useful function as a therapeutic drug. Typically, the focus has been on small molecules, but new approaches have been developed to apply these same principles of deep learning to biologics, such as antibodies. Here we give a brief background of deep learning as it applies to antibody drug development, and an in-depth explanation of several deep learning algorithms that have been proposed to solve aspects of both protein design in general, and antibody design in particular.

scholarly journals Machine Learning Models for Abnormality Detection in Musculoskeletal Radiographs

Reports ◽  
2019 ◽  
Vol 2 (4) ◽  
pp. 26 ◽  
Author(s):  
Govind Chada
Keyword(s):  
Machine Learning ◽  
Primary Care ◽  
Deep Learning ◽  
Transfer Learning ◽  
Primary Care Physicians ◽  
Screening Tools ◽  
Learning Approaches ◽  
Limited Data ◽  
Learning Models ◽  
High Recognition Accuracy

Increasing radiologist workloads and increasing primary care radiology services make it relevant to explore the use of artificial intelligence (AI) and particularly deep learning to provide diagnostic assistance to radiologists and primary care physicians in improving the quality of patient care. This study investigates new model architectures and deep transfer learning to improve the performance in detecting abnormalities of upper extremities while training with limited data. DenseNet-169, DenseNet-201, and InceptionResNetV2 deep learning models were implemented and evaluated on the humerus and finger radiographs from MURA, a large public dataset of musculoskeletal radiographs. These architectures were selected because of their high recognition accuracy in a benchmark study. The DenseNet-201 and InceptionResNetV2 models, employing deep transfer learning to optimize training on limited data, detected abnormalities in the humerus radiographs with 95% CI accuracies of 83–92% and high sensitivities greater than 0.9, allowing for these models to serve as useful initial screening tools to prioritize studies for expedited review. The performance in the case of finger radiographs was not as promising, possibly due to the limitations of large inter-radiologist variation. It is suggested that the causes of this variation be further explored using machine learning approaches, which may lead to appropriate remediation.

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