More Like this

1. A Manifold Laplacian Regularized Semi-supervised Sparse Image Classification Method with a Variant Trace Lasso Norm

   https://doi.org/DOI: 10.1109/ACCESS.2020.2997413  

   Zhang, Wenjuan ; Feng, Xiangchu ; Chen, Yunmei ( May 2020 , IEEE access)

   Since the cost of labeling data is getting higher and higher, we hope to make full use of the large amount of unlabeled data and improve image classification effect through adding some unlabeled samples for training. In addition, we expect to uniformly realize two tasks, namely the clustering of the unlabeled data and the recognition of the query image. We achieve the goal by designing a novel sparse model based on manifold assumption, which has been proved to work well in many tasks. Based on the assumption that images of the same class lie on a sub-manifold and an image can be approximately represented as the linear combination of its neighboring data due to the local linear property of manifold, we proposed a sparse representation model on manifold. Specifically, there are two regularizations, i.e., a variant Trace lasso norm and the manifold Laplacian regularization. The first regularization term enables the representation coefficients satisfying sparsity between groups and density within a group. And the second term is manifold Laplacian regularization by which label can be accurately propagated from labeled data to unlabeled data. Augmented Lagrange Multiplier (ALM) scheme and Gauss Seidel Alternating Direction Method of Multiplier (GS-ADMM) are given to solve the problem numerically. We conduct some experiments on three human face databases and compare the proposed work with several state-of-the-art methods. For each subject, some labeled face images are randomly chosen for training for those supervised methods, and a small amount of unlabeled images are added to form the training set of the proposed approach. All experiments show our method can get better classification results due to the addition of unlabeled samples. 

   more » « less
2. Deep Convolutional Neural Network for Flood Extent Mapping Using Unmanned Aerial Vehicles Data

   https://doi.org/10.3390/s19071486  

   Gebrehiwot, Asmamaw ; Hashemi-Beni, Leila ; Thompson, Gary ; Kordjamshidi, Parisa ; Langan, Thomas ( April 2019 , Sensors)

   Flooding is one of the leading threats of natural disasters to human life and property, especially in densely populated urban areas. Rapid and precise extraction of the flooded areas is key to supporting emergency-response planning and providing damage assessment in both spatial and temporal measurements. Unmanned Aerial Vehicles (UAV) technology has recently been recognized as an efficient photogrammetry data acquisition platform to quickly deliver high-resolution imagery because of its cost-effectiveness, ability to fly at lower altitudes, and ability to enter a hazardous area. Different image classification methods including SVM (Support Vector Machine) have been used for flood extent mapping. In recent years, there has been a significant improvement in remote sensing image classification using Convolutional Neural Networks (CNNs). CNNs have demonstrated excellent performance on various tasks including image classification, feature extraction, and segmentation. CNNs can learn features automatically from large datasets through the organization of multi-layers of neurons and have the ability to implement nonlinear decision functions. This study investigates the potential of CNN approaches to extract flooded areas from UAV imagery. A VGG-based fully convolutional network (FCN-16s) was used in this research. The model was fine-tuned and a k-fold cross-validation was applied to estimate the performance of the model on the new UAV imagery dataset. This approach allowed FCN-16s to be trained on the datasets that contained only one hundred training samples, and resulted in a highly accurate classification. Confusion matrix was calculated to estimate the accuracy of the proposed method. The image segmentation results obtained from FCN-16s were compared from the results obtained from FCN-8s, FCN-32s and SVMs. Experimental results showed that the FCNs could extract flooded areas precisely from UAV images compared to the traditional classifiers such as SVMs. The classification accuracy achieved by FCN-16s, FCN-8s, FCN-32s, and SVM for the water class was 97.52%, 97.8%, 94.20% and 89%, respectively. 

   more » « less
3. Tag N’ Train: a technique to train improved classifiers on unlabeled data

   https://doi.org/10.1007/JHEP01(2021)153  

   Amram, Oz ; Suarez, Cristina Mantilla ( January 2021 , Journal of High Energy Physics)

   A bstract There has been substantial progress in applying machine learning techniques to classification problems in collider and jet physics. But as these techniques grow in sophistication, they are becoming more sensitive to subtle features of jets that may not be well modeled in simulation. Therefore, relying on simulations for training will lead to sub-optimal performance in data, but the lack of true class labels makes it difficult to train on real data. To address this challenge we introduce a new approach, called Tag N’ Train (TNT), that can be applied to unlabeled data that has two distinct sub-objects. The technique uses a weak classifier for one of the objects to tag signal-rich and background-rich samples. These samples are then used to train a stronger classifier for the other object. We demonstrate the power of this method by applying it to a dijet resonance search. By starting with autoencoders trained directly on data as the weak classifiers, we use TNT to train substantially improved classifiers. We show that Tag N’ Train can be a powerful tool in model-agnostic searches and discuss other potential applications. 

   more » « less
4. 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. 

   more » « less
5. Active learning to classify macromolecular structures in situ for less supervision in cryo-electron tomography

   https://doi.org/10.1093/bioinformatics/btab123  

   Du, Xuefeng ; Wang, Haohan ; Zhu, Zhenxi ; Zeng, Xiangrui ; Chang, Yi-Wei ; Zhang, Jing ; Xing, Eric ; Xu, Min ( February 2021 , Bioinformatics)

   Xu, Jinbo (Ed.)

   Abstract Motivation Cryo-Electron Tomography (cryo-ET) is a 3D bioimaging tool that visualizes the structural and spatial organization of macromolecules at a near-native state in single cells, which has broad applications in life science. However, the systematic structural recognition and recovery of macromolecules captured by cryo-ET are difficult due to high structural complexity and imaging limits. Deep learning-based subtomogram classification has played critical roles for such tasks. As supervised approaches, however, their performance relies on sufficient and laborious annotation on a large training dataset. Results To alleviate this major labeling burden, we proposed a Hybrid Active Learning (HAL) framework for querying subtomograms for labeling from a large unlabeled subtomogram pool. Firstly, HAL adopts uncertainty sampling to select the subtomograms that have the most uncertain predictions. This strategy enforces the model to be aware of the inductive bias during classification and subtomogram selection, which satisfies the discriminativeness principle in AL literature. Moreover, to mitigate the sampling bias caused by such strategy, a discriminator is introduced to judge if a certain subtomogram is labeled or unlabeled and subsequently the model queries the subtomogram that have higher probabilities to be unlabeled. Such query strategy encourages to match the data distribution between the labeled and unlabeled subtomogram samples, which essentially encodes the representativeness criterion into the subtomogram selection process. Additionally, HAL introduces a subset sampling strategy to improve the diversity of the query set, so that the information overlap is decreased between the queried batches and the algorithmic efficiency is improved. Our experiments on subtomogram classification tasks using both simulated and real data demonstrate that we can achieve comparable testing performance (on average only 3% accuracy drop) by using less than 30% of the labeled subtomograms, which shows a very promising result for subtomogram classification task with limited labeling resources. Availability and implementation https://github.com/xulabs/aitom. Supplementary information Supplementary data are available at Bioinformatics online. 

   more » « less