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1. DETECTION OF CLOUDS IN MEDIUM-RESOLUTION SATELLITE IMAGERY USING DEEP CONVOLUTIONAL NEURAL NETS

   https://doi.org/10.5194/isprs-archives-XLVI-M-2-2022-103-2022  

   Hasan, A. ; Witharana, C. ; Udawalpola, M. R. ; Liljedahl, A. K. ( July 2022 , The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences)

   Cloud detection is an inextricable pre-processing step in remote sensing image analysis workflows. Most of the traditional rule-based and machine-learning-based algorithms utilize low-level features of the clouds and classify individual cloud pixels based on their spectral signatures. Cloud detection using such approaches can be challenging due to a multitude of factors including harsh lighting conditions, the presence of thin clouds, the context of surrounding pixels, and complex spatial patterns. In recent studies, deep convolutional neural networks (CNNs) have shown outstanding results in the computer vision domain. These methods are practiced for better capturing the texture, shape as well as context of images. In this study, we propose a deep learning CNN approach to detect cloud pixels from medium-resolution satellite imagery. The proposed CNN accounts for both the low-level features, such as color and texture information as well as high-level features extracted from successive convolutions of the input image. We prepared a cloud-pixel dataset of approximately 7273 randomly sampled 320 by 320 pixels image patches taken from a total of 121 Landsat-8 (30m) and Sentinel-2 (20m) image scenes. These satellite images come with cloud masks. From the available data channels, only blue, green, red, and NIR bands are fed into the model. The CNN model was trained on 5300 image patches and validated on 1973 independent image patches. As the final output from our model, we extract a binary mask of cloud pixels and non-cloud pixels. The results are benchmarked against established cloud detection methods using standard accuracy metrics.

    

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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. Multi-scale Hierarchical Vision Transformer with Cascaded Attention Decoding for Medical Image Segmentation

   M. M. Rahman, R. Marculescu ( July 2023 , Medical Imaging with Deep Learning (MIDL) conference)

   Transformers have shown great success in medical image segmentation. However, transformers may exhibit a limited generalization ability due to the underlying single-scale selfattention (SA) mechanism. In this paper, we address this issue by introducing a Multiscale hiERarchical vIsion Transformer (MERIT) backbone network, which improves the generalizability of the model by computing SA at multiple scales. We also incorporate an attention-based decoder, namely Cascaded Attention Decoding (CASCADE), for further refinement of the multi-stage features generated by MERIT. Finally, we introduce an effective multi-stage feature mixing loss aggregation (MUTATION) method for better model training via implicit ensembling. Our experiments on two widely used medical image segmentation benchmarks (i.e., Synapse Multi-organ and ACDC) demonstrate the superior performance of MERIT over state-of-the-art methods. Our MERIT architecture and MUTATION loss aggregation can be used with other downstream medical image and semantic segmentation tasks. 

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4. Deep Learning Methods for Sign Language Translation

   https://doi.org/10.1145/3477498  

   Ananthanarayana, Tejaswini ; Srivastava, Priyanshu ; Chintha, Akash ; Santha, Akhil ; Landy, Brian ; Panaro, Joseph ; Webster, Andre ; Kotecha, Nikunj ; Sah, Shagan ; Sarchet, Thomastine ; et al ( December 2021 , ACM Transactions on Accessible Computing)

   Many sign languages are bona fide natural languages with grammatical rules and lexicons hence can benefit from machine translation methods. Similarly, since sign language is a visual-spatial language, it can also benefit from computer vision methods for encoding it. With the advent of deep learning methods in recent years, significant advances have been made in natural language processing (specifically neural machine translation) and in computer vision methods (specifically image and video captioning). Researchers have therefore begun expanding these learning methods to sign language understanding. Sign language interpretation is especially challenging, because it involves a continuous visual-spatial modality where meaning is often derived based on context. The focus of this article, therefore, is to examine various deep learning–based methods for encoding sign language as inputs, and to analyze the efficacy of several machine translation methods, over three different sign language datasets. The goal is to determine which combinations are sufficiently robust for sign language translation without any gloss-based information. To understand the role of the different input features, we perform ablation studies over the model architectures (input features + neural translation models) for improved continuous sign language translation. These input features include body and finger joints, facial points, as well as vector representations/embeddings from convolutional neural networks. The machine translation models explored include several baseline sequence-to-sequence approaches, more complex and challenging networks using attention, reinforcement learning, and the transformer model. We implement the translation methods over multiple sign languages—German (GSL), American (ASL), and Chinese sign languages (CSL). From our analysis, the transformer model combined with input embeddings from ResNet50 or pose-based landmark features outperformed all the other sequence-to-sequence models by achieving higher BLEU2-BLEU4 scores when applied to the controlled and constrained GSL benchmark dataset. These combinations also showed significant promise on the other less controlled ASL and CSL datasets. 

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5. Concept Detection and Caption Prediction in ImageCLEFmedical Caption 2023 with Convolutional Neural Networks; Vision and Text-to-Text Transfer Transformers

   Hasan M ; Layode O ; Rahman M. ( October 2023 , Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2023))

   Aliannejadi, M ; Faggioli, G ; Ferro, N ; Vlachos, M. (Ed.)

   This work discusses the participation of CS_Morgan in the Concept Detection and Caption Prediction tasks of the ImageCLEFmedical 2023 Caption benchmark evaluation campaign. The goal of this task is to automatically identify relevant concepts and their locations in images, as well as generate coherent captions for the images. The dataset used for this task is a subset of the extended Radiology Objects in Context (ROCO) dataset. The implementation approach employed by us involved the use of pre-trained Convolutional Neural Networks (CNNs), Vision Transformer (ViT), and Text-to-Text Transfer Transformer (T5) architectures. These models were leveraged to handle the different aspects of the tasks, such as concept detection and caption generation. In the Concept Detection task, the objective was to classify multiple concepts associated with each image. We utilized several deep learning architectures with ‘sigmoid’ activation to enable multilabel classification using the Keras framework. We submitted a total of five (5) runs for this task, and the best run achieved an F1 score of 0.4834, indicating its effectiveness in detecting relevant concepts in the images. For the Caption Prediction task, we successfully submitted eight (8) runs. Our approach involved combining the ViT and T5 models to generate captions for the images. For the caption prediction task, the ranking is based on the BERTScore, and our best run achieved a score of 0.5819 based on generating captions using the fine-tuned T5 model from keywords generated using the pretrained ViT as the encoder. 

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