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1. FIgLib & SmokeyNet: Dataset and Deep Learning Model for Real-Time Wildland Fire Smoke Detection

   https://doi.org/10.3390/rs14041007  

   Dewangan, Anshuman ; Pande, Yash ; Braun, Hans-Werner ; Vernon, Frank ; Perez, Ismael ; Altintas, Ilkay ; Cottrell, Garrison W. ; Nguyen, Mai H. ( February 2022 , Remote Sensing)

   The size and frequency of wildland fires in the western United States have dramatically increased in recent years. On high-fire-risk days, a small fire ignition can rapidly grow and become out of control. Early detection of fire ignitions from initial smoke can assist the response to such fires before they become difficult to manage. Past deep learning approaches for wildfire smoke detection have suffered from small or unreliable datasets that make it difficult to extrapolate performance to real-world scenarios. In this work, we present the Fire Ignition Library (FIgLib), a publicly available dataset of nearly 25,000 labeled wildfire smoke images as seen from fixed-view cameras deployed in Southern California. We also introduce SmokeyNet, a novel deep learning architecture using spatiotemporal information from camera imagery for real-time wildfire smoke detection. When trained on the FIgLib dataset, SmokeyNet outperforms comparable baselines and rivals human performance. We hope that the availability of the FIgLib dataset and the SmokeyNet architecture will inspire further research into deep learning methods for wildfire smoke detection, leading to automated notification systems that reduce the time to wildfire response. 

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2. Wildland Fire Detection and Monitoring Using a Drone-Collected RGB/IR Image Dataset

   Chen, Xiwen and ( January 2022 , IEEE Access)

   Current forest monitoring technologies including satellite remote sensing, manned/piloted aircraft, and observation towers leave uncertainties about a wildfire’s extent, behavior, and conditions in the fire’s near environment, particularly during its early growth. Rapid mapping and real-time fire monitoring can inform in-time intervention or management solutions to maximize beneficial fire outcomes. Drone systems’ unique features of 3D mobility, low flight altitude, and fast and easy deployment make them a valuable tool for early detection and assessment of wildland fires, especially in remote forests that are not easily accessible by ground vehicles. In addition, the lack of abundant, well-annotated aerial datasets – in part due to unmanned aerial vehicles’ (UAVs’) flight restrictions during prescribed burns and wildfires – has limited research advances in reliable data-driven fire detection and modeling techniques. While existing wildland fire datasets often include either color or thermal fire images, here we present (1) a multi-modal UAV-collected dataset of dual-feed side-by-side videos including both RGB and thermal images of a prescribed fire in an open canopy pine forest in Northern Arizona and (2) a deep learning-based methodology for detecting fire and smoke pixels at accuracy much higher than the usual single-channel video feeds. The collected images are labeled to “fire” or “no-fire” frames by two human experts using side-by-side RGB and thermal images to determine the label. To provide context to the main dataset’s aerial imagery, the included supplementary dataset provides a georeferenced pre-burn point cloud, an RGB orthomosaic, weather information, a burn plan, and other burn information. By using and expanding on this guide dataset, research can develop new data-driven fire detection, fire segmentation, and fire modeling techniques. 

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3. Adaptive Privacy Preserving Deep Learning Algorithms for Medical Data

   Zhang, Xinyue ; Ding, Jiahao ; Wu, Maoqiang ; Wong, Stephen TC. ; Nguyen, Hien V. ; Pan, Miao ( January 2021 , IEEE Winter Conference on Applications of Computer Vision)

   null (Ed.)

   Deep learning holds a great promise of revolutionizing healthcare and medicine. Unfortunately, various inference attack models demonstrated that deep learning puts sensitive patient information at risk. The high capacity of deep neural networks is the main reason behind the privacy loss. In particular, patient information in the training data can be unintentionally memorized by a deep network. Adversarial parties can extract that information given the ability to access or query the network. In this paper, we propose a novel privacy-preserving mechanism for training deep neural networks. Our approach adds decaying Gaussian noise to the gradients at every training iteration. This is in contrast to the mainstream approach adopted by Google's TensorFlow Privacy, which employs the same noise scale in each step of the whole training process. Compared to existing methods, our proposed approach provides an explicit closed-form mathematical expression to approximately estimate the privacy loss. It is easy to compute and can be useful when the users would like to decide proper training time, noise scale, and sampling ratio during the planning phase. We provide extensive experimental results using one real-world medical dataset (chest radiographs from the CheXpert dataset) to validate the effectiveness of the proposed approach. The proposed differential privacy based deep learning model achieves significantly higher classification accuracy over the existing methods with the same privacy budget. 

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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. 

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5. Modeling wildland fire burn severity in California using a spatial Super Learner approach

   https://doi.org/10.1007/s10651-024-00601-1  

   Simafranca, Nicholas ; Willoughby, Bryant ; O’Neil, Erin ; Farr, Sophie ; Reich, Brian J. ; Giertych, Naomi ; Johnson, Margaret C. ; Pascolini-Campbell, Madeleine A. ( March 2024 , Environmental and Ecological Statistics)

   Given the increasing prevalence of wildland fires in the Western US, there is a crit- ical need to develop tools to understand and accurately predict burn severity. We develop a novel machine learning model to predict post-fire burn severity using pre- fire remotely sensed data. Hydrological, ecological, and topographical variables col- lected from four regions of California — the site of the Kincade fire (2019), the CZU Lightning Complex fire (2020), the Windy fire (2021), and the KNP Fire (2021) — are used as predictors of the differenced normalized burn ratio. We hypothesize that a Super Learner (SL) algorithm that accounts for spatial autocorrelation using Vec- chia’s Gaussian approximation will accurately model burn severity. We use a cross- validation study to show that the spatial SL model can predict burn severity with reasonable classification accuracy, including high burn severity events. After fitting and verifying the performance of the SL model, we use interpretable machine learn- ing tools to determine the main drivers of severe burn damage, including greenness, elevation, and fire weather variables. These findings provide actionable insights that enable communities to strategize interventions, such as early fire detection systems, pre-fire season vegetation clearing activities, and resource allocation during emer- gency responses. When implemented, this model has the potential to minimize the loss of human life, property, resources, and ecosystems in California. 

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