scholarly journals Crowdsourcing Image Analysis for Plant Phenomics to Generate Ground Truth Data for Machine Learning

2018 ◽  
Author(s):  
Naihui Zhou ◽  
Zachary D Siegel ◽  
Scott Zarecor ◽  
Nigel Lee ◽  
Darwin A Campbell ◽  
...  
Keyword(s):  
Machine Learning ◽  
Image Analysis ◽  
Best Practices ◽  
Ground Truth ◽  
Training Data ◽  
Quality Data ◽  
High Quality ◽  
Ground Truth Data ◽  
Plant Phenomics

AbstractThe accuracy of machine learning tasks critically depends on high quality ground truth data. Therefore, in many cases, producing good ground truth data typically involves trained professionals; however, this can be costly in time, effort, and money. Here we explore the use of crowdsourcing to generate a large number of training data of good quality. We explore an image analysis task involving the segmentation of corn tassels from images taken in a field setting. We investigate the accuracy, speed and other quality metrics when this task is performed by students for academic credit, Amazon MTurk workers, and Master Amazon MTurk workers. We conclude that the Amazon MTurk and Master Mturk workers perform significantly better than the for-credit students, but with no significant difference between the two MTurk worker types. Furthermore, the quality of the segmentation produced by Amazon MTurk workers rivals that of an expert worker. We provide best practices to assess the quality of ground truth data, and to compare data quality produced by different sources. We conclude that properly managed crowdsourcing can be used to establish large volumes of viable ground truth data at a low cost and high quality, especially in the context of high throughput plant phenotyping. We also provide several metrics for assessing the quality of the generated datasets.Author SummaryFood security is a growing global concern. Farmers, plant breeders, and geneticists are hastening to address the challenges presented to agriculture by climate change, dwindling arable land, and population growth. Scientists in the field of plant phenomics are using satellite and drone images to understand how crops respond to a changing environment and to combine genetics and environmental measures to maximize crop growth efficiency. However, the terabytes of image data require new computational methods to extract useful information. Machine learning algorithms are effective in recognizing select parts of images, butthey require high quality data curated by people to train them, a process that can be laborious and costly. We examined how well crowdsourcing works in providing training data for plant phenomics, specifically, segmenting a corn tassel – the male flower of the corn plant – from the often-cluttered images of a cornfield. We provided images to students, and to Amazon MTurkers, the latter being an on-demand workforce brokered by Amazon.com and paid on a task-by-task basis. We report on best practices in crowdsourcing image labeling for phenomics, and compare the different groups on measures such as fatigue and accuracy over time. We find that crowdsourcing is a good way of generating quality labeled data, rivaling that of experts.

scholarly journals Improving the Quality of Positive Datasets for the Establishment of Machine Learning Models for pre-microRNA Detection

2017 ◽  
Vol 14 (2) ◽  
Author(s):  
Müşerref Duygu Saçar Demirci ◽  
Jens Allmer
Keyword(s):  
Machine Learning ◽  
Training Data ◽  
Quality Data ◽  
Virus Infections ◽  
High Quality ◽  
Disease States ◽  
Positive Data ◽  
Mirna Detection ◽  
Post Transcriptional Regulation

AbstractMicroRNAs (miRNAs) are involved in the post-transcriptional regulation of protein abundance and thus have a great impact on the resulting phenotype. It is, therefore, no wonder that they have been implicated in many diseases ranging from virus infections to cancer. This impact on the phenotype leads to a great interest in establishing the miRNAs of an organism. Experimental methods are complicated which led to the development of computational methods for pre-miRNA detection. Such methods generally employ machine learning to establish models for the discrimination between miRNAs and other sequences. Positive training data for model establishment, for the most part, stems from miRBase, the miRNA registry. The quality of the entries in miRBase has been questioned, though. This unknown quality led to the development of filtering strategies in attempts to produce high quality positive datasets which can lead to a scarcity of positive data. To analyze the quality of filtered data we developed a machine learning model and found it is well able to establish data quality based on intrinsic measures. Additionally, we analyzed which features describing pre-miRNAs could discriminate between low and high quality data. Both models are applicable to data from miRBase and can be used for establishing high quality positive data. This will facilitate the development of better miRNA detection tools which will make the prediction of miRNAs in disease states more accurate. Finally, we applied both models to all miRBase data and provide the list of high quality hairpins.

scholarly journals “Garbage In, Garbage Out” Revisited: What Do Machine Learning Application Papers Report About Human-Labeled Training Data?

2021 ◽  
pp. 1-32
Author(s):  
R. Stuart Geiger ◽  
Dominique Cope ◽  
Jamie Ip ◽  
Marsha Lotosh ◽  
Aayush Shah ◽  
...  
Keyword(s):  
Machine Learning ◽  
Best Practices ◽  
Ground Truth ◽  
Training Data ◽  
Supervised Machine Learning ◽  
Social Media Platforms ◽  
Learning Research ◽  
Research And Education ◽  
Application Fields

Abstract Supervised machine learning, in which models are automatically derived from labeled training data, is only as good as the quality of that data. This study builds on prior work that investigated to what extent ‘best practices’ around labeling training data were followed in applied ML publications within a single domain (social media platforms). In this paper, we expand by studying publications that apply supervised ML in a far broader spectrum of disciplines, focusing on human-labeled data. We report to what extent a random sample of ML application papers across disciplines give specific details about whether best practices were followed, while acknowledging that a greater range of application fields necessarily produces greater diversity of labeling and annotation methods. Because much of machine learning research and education only focuses on what is done once a “ground truth” or “gold standard” of training data is available, it is especially relevant to discuss issues around the equally-important aspect of whether such data is reliable in the first place. This determination becomes increasingly complex when applied to a variety of specialized fields, as labeling can range from a task requiring little-to-no background knowledge to one that must be performed by someone with career expertise. Peer Review https://publons.com/publon/10.1162/qss_a_00144

scholarly journals Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning

2018 ◽  
Vol 14 (7) ◽  
pp. e1006337 ◽  
Author(s):  
Naihui Zhou ◽  
Zachary D. Siegel ◽  
Scott Zarecor ◽  
Nigel Lee ◽  
Darwin A. Campbell ◽  
...  
Keyword(s):  
Machine Learning ◽  
Image Analysis ◽  
Ground Truth ◽  
Ground Truth Data ◽  
Plant Phenomics

Glean

2021 ◽  
Vol 14 (6) ◽  
pp. 997-1005
Author(s):  
Sandeep Tata ◽  
Navneet Potti ◽  
James B. Wendt ◽  
Lauro Beltrão Costa ◽  
Marc Najork ◽  
...  
Keyword(s):  
Machine Learning ◽  
Data Management ◽  
Real World ◽  
Empirical Studies ◽  
Ground Truth ◽  
Training Data ◽  
Ground Truth Data ◽  
Document Type ◽  
Machine Learning Model ◽  
Structured Information

Extracting structured information from templatic documents is an important problem with the potential to automate many real-world business workflows such as payment, procurement, and payroll. The core challenge is that such documents can be laid out in virtually infinitely different ways. A good solution to this problem is one that generalizes well not only to known templates such as invoices from a known vendor, but also to unseen ones. We developed a system called Glean to tackle this problem. Given a target schema for a document type and some labeled documents of that type, Glean uses machine learning to automatically extract structured information from other documents of that type. In this paper, we describe the overall architecture of Glean, and discuss three key data management challenges : 1) managing the quality of ground truth data, 2) generating training data for the machine learning model using labeled documents, and 3) building tools that help a developer rapidly build and improve a model for a given document type. Through empirical studies on a real-world dataset, we show that these data management techniques allow us to train a model that is over 5 F1 points better than the exact same model architecture without the techniques we describe. We argue that for such information-extraction problems, designing abstractions that carefully manage the training data is at least as important as choosing a good model architecture.

Collective annotation patterns in learning from crowds

2020 ◽  
Vol 24 ◽  
pp. 63-86
Author(s):  
Francisco Mena ◽  
Ricardo Ñanculef ◽  
Carlos Valle
Keyword(s):  
Machine Learning ◽  
Large Scale ◽  
Ground Truth ◽  
Experimental Results ◽  
Ground Truth Data ◽  
Satisfactory Performance ◽  
Machine Learning Applications ◽  
Data Points ◽  
Confusion Matrices

The lack of annotated data is one of the major barriers facing machine learning applications today. Learning from crowds, i.e. collecting ground-truth data from multiple inexpensive annotators, has become a common method to cope with this issue. It has been recently shown that modeling the varying quality of the annotations obtained in this way, is fundamental to obtain satisfactory performance in tasks where inexpert annotators may represent the majority but not the most trusted group. Unfortunately, existing techniques represent annotation patterns for each annotator individually, making the models difficult to estimate in large-scale scenarios. In this paper, we present two models to address these problems. Both methods are based on the hypothesis that it is possible to learn collective annotation patterns by introducing confusion matrices that involve groups of data point annotations or annotators. The first approach clusters data points with a common annotation pattern, regardless the annotators from which the labels have been obtained. Implicitly, this method attributes annotation mistakes to the complexity of the data itself and not to the variable behavior of the annotators. The second approach explicitly maps annotators to latent groups that are collectively parametrized to learn a common annotation pattern. Our experimental results show that, compared with other methods for learning from crowds, both methods have advantages in scenarios with a large number of annotators and a small number of annotations per annotator.

scholarly journals From Village to Globe: A Dynamic Real-Time Map of African Fields Through PlantVillage

2021 ◽  
Vol 5 ◽  
Author(s):  
Annalyse Kehs ◽  
Peter McCloskey ◽  
John Chelal ◽  
Derek Morr ◽  
Stellah Amakove ◽  
...  
Keyword(s):  
Real Time ◽  
Ground Truth ◽  
Cost Effective ◽  
Quality Data ◽  
Learning Tools ◽  
High Quality ◽  
Ground Truth Data ◽  
Cost Effective Method ◽  
High Throughput Method ◽  
Major Bottleneck

A major bottleneck to the application of machine learning tools to satellite data of African farms is the lack of high-quality ground truth data. Here we describe a high throughput method using youth in Kenya that results in a cost-effective method for high-quality data in near real-time. This data is presented to the global community, as a public good and is linked to other data sources that will inform our understanding of crop stress, particularly in the context of climate change.

scholarly journals DeepSatData: Building large scale datasets of satellite images for training machine learning models

2021 ◽  
Author(s):  
Michael Tarasiou
Keyword(s):  
Machine Learning ◽  
Large Scale ◽  
Ground Truth ◽  
Semantic Segmentation ◽  
Point Of View ◽  
Learning Models ◽  
Ground Truth Data ◽  
Machine Learning Models ◽  
Sentinel 2

This paper presents DeepSatData a pipeline for automatically generating satellite imagery datasets for training machine learning models. We also discuss design considerations with emphasis on dense classification tasks, e.g. semantic segmentation. The implementation presented makes use of freely available Sentinel-2 data which allows the generation of large scale datasets required for training deep neural networks (DNN). We discuss issues faced from the point of view of DNN training and evaluation such as checking the quality of ground truth data and comment on the scalability of the approach.

scholarly journals DeepSatData: Building large scale datasets of satellite images for training machine learning models

2021 ◽  
Author(s):  
Michael Tarasiou
Keyword(s):  
Machine Learning ◽  
Large Scale ◽  
Ground Truth ◽  
Semantic Segmentation ◽  
Point Of View ◽  
Learning Models ◽  
Ground Truth Data ◽  
Machine Learning Models ◽  
Sentinel 2

This paper presents DeepSatData a pipeline for automatically generating satellite imagery datasets for training machine learning models. We also discuss design considerations with emphasis on dense classification tasks, e.g. semantic segmentation. The implementation presented makes use of freely available Sentinel-2 data which allows the generation of large scale datasets required for training deep neural networks (DNN). We discuss issues faced from the point of view of DNN training and evaluation such as checking the quality of ground truth data and comment on the scalability of the approach.

Improving Data Quality Using Amazon Mechanical Turk Through Platform Setup

2021 ◽  
pp. 193896552110254
Author(s):  
Lu Lu ◽  
Nathan Neale ◽  
Nathaniel D. Line ◽  
Mark Bonn
Keyword(s):  
Best Practices ◽  
Data Quality ◽  
Mechanical Turk ◽  
Amazon Mechanical Turk ◽  
Quality Data ◽  
High Quality ◽  
High Quality Data ◽  
Amazon's Mechanical Turk ◽  
Associated Data

As the use of Amazon’s Mechanical Turk (MTurk) has increased among social science researchers, so, too, has research into the merits and drawbacks of the platform. However, while many endeavors have sought to address issues such as generalizability, the attentiveness of workers, and the quality of the associated data, there has been relatively less effort concentrated on integrating the various strategies that can be used to generate high-quality data using MTurk samples. Accordingly, the purpose of this research is twofold. First, existing studies are integrated into a set of strategies/best practices that can be used to maximize MTurk data quality. Second, focusing on task setup, selected platform-level strategies that have received relatively less attention in previous research are empirically tested to further enhance the contribution of the proposed best practices for MTurk usage.

scholarly journals Survey of Public Assay Data: Opportunities and Challenges to Understanding Antimicrobial Resistance

2019 ◽  
Author(s):  
Akshay Agarwal ◽  
Gowri Nayar ◽  
James Kaufman
Keyword(s):  
Machine Learning ◽  
Antimicrobial Resistance ◽  
Pathogen Detection ◽  
Ground Truth ◽  
Training Data ◽  
Learning Models ◽  
Learning Methods ◽  
Ground Truth Data ◽  
Specificity And Sensitivity ◽  
Machine Learning Models

ABSTRACTComputational learning methods allow researchers to make predictions, draw inferences, and automate generation of mathematical models. These models are crucial to solving real world problems, such as antimicrobial resistance, pathogen detection, and protein evolution. Machine learning methods depend upon ground truth data to achieve specificity and sensitivity. Since the data is limited in this case, as we will show during the course of this paper, and as the size of available data increases super-linearly, it is of paramount importance to understand the distribution of ground truth data and the analyses it is suited and where it may have limitations that bias downstream learning methods. In this paper, we focus on training data required to model antimicrobial resistance (AR). We report an analysis of bacterial biochemical assay data associated with whole genome sequencing (WGS) from the National Center for Biotechnology Information (NCBI), and discuss important implications when making use of assay data, utilizing genetic features as training data for machine learning models. Complete discussion of machine learning model implementation is outside the scope of this paper and the subject to a later publication.The antimicrobial assay data was obtained from NCBI BioSample, which contains descriptive information about the physical biological specimen from which experimental data is obtained and the results of those experiments themselves.[1] Assay data includes minimum inhibitory concentrations (MIC) of antibiotics, links to associated microbial WGS data, and treatment of a particular microorganism with antibiotics.We observe that there is minimal microbial data available for many antibiotics and for targeted taxonomic groups. The antibiotics with the highest number of assays have less than 1500 measurements each. Corresponding bias in available assays makes machine learning problematic for some important microbes and for building more advanced models that can work across microbial genera. In this study we focus, therefore, on the antibiotic with most assay data (tetracycline) and the corresponding genus with the most available sequence (Acinetobacter with 14000 measurements across 49 antibiotic compounds). Using this data for training and testing, we observed contradictions in the distribution of assay outcomes and report methods to identify and resolve such conflicts. Per antibiotic, we find that there can be up to 30% of (resolvable) conflicting measurements. As more data becomes available, automated training data curation will be an important part of creating useful machine learning models to predict antibiotic resistance.CCS CONCEPTS• Applied computing → Computational biology; Computational genomics; Bioinformatics;

Sign in / Sign up

Export Citation Format

Share Document