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1. Improving Crowdsourcing-Based Image Classification Through Expanded Input Elicitation and Machine Learning

   https://doi.org/10.3389/frai.2022.848056  

   Yasmin, Romena ; Hassan, Md Mahmudulla ; Grassel, Joshua T. ; Bhogaraju, Harika ; Escobedo, Adolfo R. ; Fuentes, Olac ( June 2022 , Frontiers in Artificial Intelligence)

   This work investigates how different forms of input elicitation obtained from crowdsourcing can be utilized to improve the quality of inferred labels for image classification tasks, where an image must be labeled as either positive or negative depending on the presence/absence of a specified object. Five types of input elicitation methods are tested: binary classification (positive or negative); the ( x, y )-coordinate of the position participants believe a target object is located; level of confidence in binary response (on a scale from 0 to 100%); what participants believe the majority of the other participants' binary classification is; and participant's perceived difficulty level of the task (on a discrete scale). We design two crowdsourcing studies to test the performance of a variety of input elicitation methods and utilize data from over 300 participants. Various existing voting and machine learning (ML) methods are applied to make the best use of these inputs. In an effort to assess their performance on classification tasks of varying difficulty, a systematic synthetic image generation process is developed. Each generated image combines items from the MPEG-7 Core Experiment CE-Shape-1 Test Set into a single image using multiple parameters (e.g., density, transparency, etc.) and may or may not contain a target object. The difficulty of these images is validated by the performance of an automated image classification method. Experiment results suggest that more accurate results can be achieved with smaller training datasets when both the crowdsourced binary classification labels and the average of the self-reported confidence values in these labels are used as features for the ML classifiers. Moreover, when a relatively larger properly annotated dataset is available, in some cases augmenting these ML algorithms with the results (i.e., probability of outcome) from an automated classifier can achieve even higher performance than what can be obtained by using any one of the individual classifiers. Lastly, supplementary analysis of the collected data demonstrates that other performance metrics of interest, namely reduced false-negative rates, can be prioritized through special modifications of the proposed aggregation methods. 

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2. The Temple University Digital Pathology Corpus: The Breast Tissue Subset

   https://doi.org/10.1109/SPMB52430.2021.9672275  

   Wevodau, Z. ; Doshna, B. ; Jhala, N. ; Akhtar, I. ; Obeid, I. ; Picone, J. ( December 2021 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue. It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do not have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools. The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”). This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels. Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA. 

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3. A Machine Learning Framework for Detecting COVID-19 Infection Using Surface-Enhanced Raman Scattering

   https://doi.org/10.3390/bios12080589  

   Ikponmwoba, Eloghosa ; Ukorigho, Okezzi ; Moitra, Parikshit ; Pan, Dipanjan ; Gartia, Manas Ranjan ; Owoyele, Opeoluwa ( August 2022 , Biosensors)

   In this study, we explored machine learning approaches for predictive diagnosis using surface-enhanced Raman scattering (SERS), applied to the detection of COVID-19 infection in biological samples. To do this, we utilized SERS data collected from 20 patients at the University of Maryland Baltimore School of Medicine. As a preprocessing step, the positive-negative labels are obtained using Polymerase Chain Reaction (PCR) testing. First, we compared the performance of linear and nonlinear dimensionality techniques for projecting the high-dimensional Raman spectra to a low-dimensional space where a smaller number of variables defines each sample. The appropriate number of reduced features used was obtained by comparing the mean accuracy from a 10-fold cross-validation. Finally, we employed Gaussian process (GP) classification, a probabilistic machine learning approach, to correctly predict the occurrence of a negative or positive sample as a function of the low-dimensional space variables. As opposed to providing rigid class labels, the GP classifier provides a probability (ranging from zero to one) that a given sample is positive or negative. In practice, the proposed framework can be used to provide high-throughput rapid testing, and a follow-up PCR can be used for confirmation in cases where the model’s uncertainty is unacceptably high. 

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4. A Machine-Learning Approach for Semantically-Enriched Building-Code Sentence Generation for Automatic Semantic Analysis

   https://doi.org/10.1061/9780784482865.133  

   Zhang, Ruichuan ; El-Gohary, Nora ( November 2020 , Construction Research Congress 2020)

   Tang, P. ; Grau, D. ; El Asmar, M. (Ed.)

   Existing automated code checking (ACC) systems require the extraction of requirements from regulatory textual documents into computer-processable rule representations. The information extraction processes in those ACC systems are based on either human interpretation, manual annotation, or predefined automated information extraction rules. Despite the high performance they showed, rule-based information extraction approaches, by nature, lack sufficient scalability—the rules typically need some level of adaptation if the characteristics of the text change. Machine learning-based methods, instead of relying on hand-crafted rules, automatically capture the underlying patterns of the existing training text and have a great capability of generalizing to a variety of texts. A more scalable, machine learning-based approach is thus needed to achieve a more robust performance across different types of codes/documents for automatically generating semantically-enriched building-code sentences for the purpose of ACC. To address this need, this paper proposes a machine learning-based approach for generating semantically-enriched building-code sentences, which are annotated syntactically and semantically, for supporting IE. For improved robustness and scalability, the proposed approach uses transfer learning strategies to train deep neural network models on both general-domain and domain-specific data. The proposed approach consists of four steps: (1) data preparation and preprocessing; (2) development of a base deep neural network model for generating semantically-enriched building-code sentences; (3) model training using transfer learning strategies; and (4) model evaluation. The proposed approach was evaluated on a corpus of sentences from the 2009 International Building Code (IBC) and the Champaign 2015 IBC Amendments. The preliminary results show that the proposed approach achieved an optimal precision of 88%, recall of 86%, and F1-measure of 87%, indicating good performance. 

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5. Skin Cancer Diagnostics with an All-Inclusive Smartphone Application

   https://doi.org/10.3390/sym11060790  

   Kalwa, Upender ; Legner, Christopher ; Kong, Taejoon ; Pandey, Santosh ( June 2019 , Symmetry)

   Among the different types of skin cancer, melanoma is considered to be the deadliest and is difficult to treat at advanced stages. Detection of melanoma at earlier stages can lead to reduced mortality rates. Desktop-based computer-aided systems have been developed to assist dermatologists with early diagnosis. However, there is significant interest in developing portable, at-home melanoma diagnostic systems which can assess the risk of cancerous skin lesions. Here, we present a smartphone application that combines image capture capabilities with preprocessing and segmentation to extract the Asymmetry, Border irregularity, Color variegation, and Diameter (ABCD) features of a skin lesion. Using the feature sets, classification of malignancy is achieved through support vector machine classifiers. By using adaptive algorithms in the individual data-processing stages, our approach is made computationally light, user friendly, and reliable in discriminating melanoma cases from benign ones. Images of skin lesions are either captured with the smartphone camera or imported from public datasets. The entire process from image capture to classification runs on an Android smartphone equipped with a detachable 10x lens, and processes an image in less than a second. The overall performance metrics are evaluated on a public database of 200 images with Synthetic Minority Over-sampling Technique (SMOTE) (80% sensitivity, 90% specificity, 88% accuracy, and 0.85 area under curve (AUC)) and without SMOTE (55% sensitivity, 95% specificity, 90% accuracy, and 0.75 AUC). The evaluated performance metrics and computation times are comparable or better than previous methods. This all-inclusive smartphone application is designed to be easy-to-download and easy-to-navigate for the end user, which is imperative for the eventual democratization of such medical diagnostic systems. 

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