Deep machine learning provides state-of-the-art performance in image-based plant phenotyping

AbstractDeep learning is an emerging field that promises unparalleled results on many data analysis problems. We show the success offered by such techniques when applied to the challenging problem of image-based plant phenotyping, and demonstrate state-of-the-art results for root and shoot feature identification and localisation. We predict a paradigm shift in image-based phenotyping thanks to deep learning approaches.

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Erratum to: Deep machine learning provides state-of-the-art performance in image-based plant phenotyping

GigaScience ◽

10.1093/gigascience/giy042 ◽

2018 ◽

Vol 7 (7) ◽

Cited By ~ 2

Author(s):

Michael P Pound ◽

Jonathan A Atkinson ◽

Alexandra J Townsend ◽

Michael H Wilson ◽

Marcus Griffiths ◽

...

Keyword(s):

Machine Learning ◽

State Of The Art ◽

Plant Phenotyping ◽

Art Performance

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A Graph-based Evolutionary Algorithm for Automated Machine Learning

10.37686/ser.v1i2.77 ◽

2020 ◽

Author(s):

Fei Qi ◽

Zhaohui Xia ◽

Gaoyang Tang ◽

Hang Yang ◽

Yu Song ◽

...

Keyword(s):

Machine Learning ◽

Evolutionary Algorithm ◽

Parameter Optimization ◽

State Of The Art ◽

The State ◽

Complex Structures ◽

Architecture Evolution ◽

Automated Machine Learning ◽

Art Performance

As an emerging field, Automated Machine Learning (AutoML) aims to reduce or eliminate manual operations that require expertise in machine learning. In this paper, a graph-based architecture is employed to represent flexible combinations of ML models, which provides a large searching space compared to tree-based and stacking-based architectures. Based on this, an evolutionary algorithm is proposed to search for the best architecture, where the mutation and heredity operators are the key for architecture evolution. With Bayesian hyper-parameter optimization, the proposed approach can automate the workflow of machine learning. On the PMLB dataset, the proposed approach shows the state-of-the-art performance compared with TPOT, Autostacker, and auto-sklearn. Some of the optimized models are with complex structures which are difficult to obtain in manual design.

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Attentive deep learning-based tumor-only somatic mutation classifier achieves high accuracy agnostic of tissue type and capture kit.

10.1101/2021.12.07.471513 ◽

2021 ◽

Author(s):

R. Tyler McLaughlin ◽

Maansi Asthana ◽

Marc Di Meo ◽

Michele Ceccarelli ◽

Howard J. Jacob ◽

...

Keyword(s):

Machine Learning ◽

Deep Learning ◽

State Of The Art ◽

Variant Calling ◽

Learning Model ◽

Tissue Type ◽

Germline Variants ◽

Art Performance ◽

Deep Learning Model ◽

Tumor Dna

In precision oncology, reliable identification of tumor-specific DNA mutations requires sequencing tumor DNA and non-tumor DNA (so-called "matched normal") from the same patient. The normal sample allows researchers to distinguish acquired (somatic) and hereditary (germline) variants. The ability to distinguish somatic and germline variants facilitates estimation of tumor mutation burden (TMB), which is a recently FDA-approved pan-cancer marker for highly successful cancer immunotherapies; in tumor-only variant calling (i.e., without a matched normal), the difficulty in discriminating germline and somatic variants results in inflated and unreliable TMB estimates. We apply machine learning to the task of somatic vs germline classification in tumor-only samples using TabNet, a recently developed attentive deep learning model for tabular data that has achieved state of the art performance in multiple classification tasks (Arik and Pfister 2019). We constructed a training set for supervised classification using features derived from tumor-only variant calling and drawing somatic and germline truth-labels from an independent pipeline incorporating the patient-matched normal samples. Our trained model achieved state-of-the-art performance on two hold-out test datasets: a TCGA dataset including sarcoma, breast adenocarcinoma, and endometrial carcinoma samples (F1-score: 88.3), and a metastatic melanoma dataset, (F1-score 79.8). Concordance between matched-normal and tumor-only TMB improves from R2 = 0.006 to 0.705 with the addition of our classifier. And importantly, this approach generalizes across tumor tissue types and capture kits and has a call rate of 100%. The interpretable feature masks of the attentive deep learning model explain the reasons for misclassified variants. We reproduce the recent finding that tumor-only TMB estimates for Black patients are extremely inflated relative to that of White patients due to the racial biases of germline databases. We show that our machine learning approach appreciably reduces this racial bias in tumor-only variant-calling.

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OnionMHC: A deep learning model for peptide — HLA-A*02:01 binding predictions using both structure and sequence feature sets

Journal of Micromechanics and Molecular Physics ◽

10.1142/s2424913020500095 ◽

2021 ◽

pp. 2050009

Author(s):

Shikhar Saxena ◽

Sambhavi Animesh ◽

Melissa J. Fullwood ◽

Yuguang Mu

Keyword(s):

Machine Learning ◽

Deep Learning ◽

Binding Affinity ◽

State Of The Art ◽

Learning Model ◽

Peptide Sequence ◽

Sequencing Analysis ◽

Art Performance ◽

Deep Learning Model ◽

Human Receptor

Abstract The peptide binding to Major Histocompatibility Complex (MHC) proteins is an important step in the antigen-presentation pathway. Thus, predicting the binding potential of peptides with MHC is essential for the design of peptide-based therapeutics. Most of the available machine learning-based models predict the peptide-MHC binding based on the sequence of amino acids alone. Given the importance of structural information in determining the stability of the complex, here we have utilized both the complex structure and the peptide sequence features to predict the binding affinity of peptides to human receptor HLA-A*02:01. To our knowledge, no such model has been developed for the human HLA receptor before that incorporates both structure and sequence-based features. Results: We have applied machine learning techniques through the natural language processing (NLP) and convolutional neural network to design a model that performs comparably with the existing state-of-the-art models. Our model shows that the information from both sequence and structure domains results in enhanced performance in the binding prediction compared to the information from one domain alone. The testing results in 18 weekly benchmark datasets provided by the Immune Epitope Database (IEDB) as well as experimentally validated peptides from the whole-exome sequencing analysis of the breast cancer patients indicate that our model has achieved state-of-the-art performance. Conclusion: We have developed a deep-learning model (OnionMHC) that incorporates both structure as well as sequence-based features to predict the binding affinity of peptides with human receptor HLA-A*02:01. The model demonstrates state-of-the-art performance on the IEDB benchmark dataset as well as the experimentally validated peptides. The model can be used in the screening of potential neo-epitopes for the development of cancer vaccines or designing peptides for peptide-based therapeutics. OnionMHC is freely available at https://github.com/shikhar249/OnionMHC .

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OnionMHC: A Deep Learning Model for Peptide - HLA-A*02:01 Binding Predictions using both Structure and Sequence Feature Sets

10.21203/rs.3.rs-124695/v1 ◽

2020 ◽

Author(s):

Shikhar Saxena ◽

Sambhavi Animesh ◽

Melissa Fullwood ◽

Yuguang Mu

Keyword(s):

Machine Learning ◽

Deep Learning ◽

Binding Affinity ◽

State Of The Art ◽

Learning Model ◽

Peptide Sequence ◽

Sequencing Analysis ◽

Art Performance ◽

Deep Learning Model ◽

Human Receptor

Abstract Background:The peptide binding to Major Histocompatibility Complex (MHC) proteins is an important step in the antigen-presentation pathway. Thus, predicting the binding potential of peptides with MHC is essential for the design of peptide-based therapeutics. Most of the available machine learning-based models predict the peptide-MHC binding based on the sequence of amino acids alone. Given the importance of structural information in determining the stability of the complex, here we have utilized both the complex structure and the peptide sequence features to predict the binding affinity of peptides to human receptor HLA-A*02:01. To our knowledge, no such model has been developed for the human HLA receptor before that incorporates both structure and sequence-based features.Results:We have applied machine learning techniques through the natural language processing (NLP) and convolutional neural network to design a model that performs comparably with the existing state-of-the-art models. Our model shows that the information from both sequence and structure domains results in enhanced performance in the binding prediction compared to the information from one domain alone. The testing results in 18 weekly benchmark datasets provided by the Immune Epitope Database (IEDB) as well as experimentally validated peptides from the whole-exome sequencing analysis of the breast cancer patients indicate that our model has achieved state-of-the-art performance.Conclusion: We have developed a deep-learning model (OnionMHC) that incorporates both structure as well as sequence-based features to predict the binding affinity of peptides with human receptor HLA-A*02:01. The model demonstrates state-of-the-art performance on the IEDB benchmark dataset as well as the experimentally validated peptides. The model can be used in the screening of potential neo-epitopes for the development of cancer vaccines or designing peptides for peptide-based therapeutics. OnionMHC is freely available at https://github.com/shikhar249/OnionMHC

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Data science in economics: comprehensive review of advanced machine learning and deep learning methods

10.31232/osf.io/4pxq2 ◽

2020 ◽

Author(s):

Saeed Nosratabadi ◽

Amir Mosavi ◽

Puhong Duan ◽

Pedram Ghamisi ◽

Ferdinand Filip ◽

...

Keyword(s):

Machine Learning ◽

Deep Learning ◽

Data Science ◽

State Of The Art ◽

Science Methods ◽

Learning Models ◽

Diverse Range ◽

Hybrid Machine ◽

Economics Research

This paper provides a state-of-the-art investigation of advances in data science in emerging economic applications. The analysis was performed on novel data science methods in four individual classes of deep learning models, hybrid deep learning models, hybrid machine learning, and ensemble models. Application domains include a wide and diverse range of economics research from the stock market, marketing, and e-commerce to corporate banking and cryptocurrency. Prisma method, a systematic literature review methodology, was used to ensure the quality of the survey. The findings reveal that the trends follow the advancement of hybrid models, which, based on the accuracy metric, outperform other learning algorithms. It is further expected that the trends will converge toward the advancements of sophisticated hybrid deep learning models.

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Deep Learning for text in limted data settings

10.36227/techrxiv.12100692 ◽

2020 ◽

Author(s):

Pathikkumar Patel ◽

Bhargav Lad ◽

Jinan Fiaidhi

Keyword(s):

Machine Learning ◽

Time Series ◽

Deep Learning ◽

Sentiment Analysis ◽

Transfer Learning ◽

Text Classification ◽

State Of The Art ◽

Time Series Forecasting ◽

Text Data ◽

Performance Levels

During the last few years, RNN models have been extensively used and they have proven to be better for sequence and text data. RNNs have achieved state-of-the-art performance levels in several applications such as text classification, sequence to sequence modelling and time series forecasting. In this article we will review different Machine Learning and Deep Learning based approaches for text data and look at the results obtained from these methods. This work also explores the use of transfer learning in NLP and how it affects the performance of models on a specific application of sentiment analysis.

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Multi-hop assortativities for network classification

Journal of Complex Networks ◽

10.1093/comnet/cny034 ◽

2018 ◽

Vol 7 (4) ◽

pp. 603-622 ◽

Cited By ~ 1

Author(s):

Leonardo Gutiérrez-Gómez ◽

Jean-Charles Delvenne

Keyword(s):

Machine Learning ◽

Scientific Collaboration ◽

State Of The Art ◽

Medical Engineering ◽

Research Field ◽

Classification Task ◽

Collaboration Network ◽

Structural Patterns ◽

Art Methods

Abstract Several social, medical, engineering and biological challenges rely on discovering the functionality of networks from their structure and node metadata, when it is available. For example, in chemoinformatics one might want to detect whether a molecule is toxic based on structure and atomic types, or discover the research field of a scientific collaboration network. Existing techniques rely on counting or measuring structural patterns that are known to show large variations from network to network, such as the number of triangles, or the assortativity of node metadata. We introduce the concept of multi-hop assortativity, that captures the similarity of the nodes situated at the extremities of a randomly selected path of a given length. We show that multi-hop assortativity unifies various existing concepts and offers a versatile family of ‘fingerprints’ to characterize networks. These fingerprints allow in turn to recover the functionalities of a network, with the help of the machine learning toolbox. Our method is evaluated empirically on established social and chemoinformatic network benchmarks. Results reveal that our assortativity based features are competitive providing highly accurate results often outperforming state of the art methods for the network classification task.

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Advances in the Application of Machine Learning Techniques for Power System Analytics: A Survey

Energies ◽

10.3390/en14164776 ◽

2021 ◽

Vol 14 (16) ◽

pp. 4776

Author(s):

Seyed Mahdi Miraftabzadeh ◽

Michela Longo ◽

Federica Foiadelli ◽

Marco Pasetti ◽

Raul Igual

Keyword(s):

Machine Learning ◽

Power Systems ◽

Smart Grids ◽

State Of The Art ◽

Smart Cities ◽

Power Grids ◽

Machine Learning Techniques ◽

Learning Techniques ◽

New Research ◽

Traditional Approaches

The recent advances in computing technologies and the increasing availability of large amounts of data in smart grids and smart cities are generating new research opportunities in the application of Machine Learning (ML) for improving the observability and efficiency of modern power grids. However, as the number and diversity of ML techniques increase, questions arise about their performance and applicability, and on the most suitable ML method depending on the specific application. Trying to answer these questions, this manuscript presents a systematic review of the state-of-the-art studies implementing ML techniques in the context of power systems, with a specific focus on the analysis of power flows, power quality, photovoltaic systems, intelligent transportation, and load forecasting. The survey investigates, for each of the selected topics, the most recent and promising ML techniques proposed by the literature, by highlighting their main characteristics and relevant results. The review revealed that, when compared to traditional approaches, ML algorithms can handle massive quantities of data with high dimensionality, by allowing the identification of hidden characteristics of (even) complex systems. In particular, even though very different techniques can be used for each application, hybrid models generally show better performances when compared to single ML-based models.

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