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1. Unsupervised vessel trajectory reconstruction

   https://doi.org/10.3389/fams.2023.1124091  

   Chen, Chih-Wei ; Huang, Hsin-Hsiung ( March 2023 , Frontiers in Applied Mathematics and Statistics)

   A trajectory is a sequence of observations in time and space, for examples, the path formed by maritime vessels, orbital debris, or aircraft. It is important to track and reconstruct vessel trajectories using the Automated Identification System (AIS) data in real-world applications for maritime navigation safety. In this project, we use the National Science Foundation (NSF)'s Algorithms for Threat Detection program (ATD) 2019 Challenge AIS data to develop novel trajectory reconstruction method. Given a sequence ofNunlabeled timestamped observations, the goal is to track trajectories by clustering the AIS points with predicted positions using the information from the true trajectoriesΧ. It is a natural way to connect the observed pointx_îwith the closest point that is estimated by using the location, time, speed, and angle information from a set of the points under considerationx_i∀i∈ {1, 2, …,N}. The introduced method is an unsupervised clustering-based method that does not train a supervised model which may incur a significant computational cost, so it leads to a real-time, reliable, and accurate trajectory reconstruction method. Our experimental results show that the proposed method successfully clusters vessel trajectories. 

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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 Method for Granular Traffic Data Imputation Based on PARATUCK2

   https://doi.org/10.1177/03611981221089298  

   Nouri, Mina ; Reisi-Gahrooei, Mostafa ; Ilbeigi, Mohammad ( April 2022 , Transportation Research Record: Journal of the Transportation Research Board)

   Imputing missing data is a critical task in data-driven intelligent transportation systems. During recent decades there has been a considerable investment in developing various types of sensors and smart systems, including stationary devices (e.g., loop detectors) and floating vehicles equipped with global positioning system (GPS) trackers to collect large-scale traffic data. However, collected data may not include observations from all road segments in a traffic network for different reasons, including sensor failure, transmission error, and because GPS-equipped vehicles may not always travel through all road segments. The first step toward developing real-time traffic monitoring and disruption prediction models is to estimate missing values through a systematic data imputation process. Many of the existing data imputation methods are based on matrix completion techniques that utilize the inherent spatiotemporal characteristics of traffic data. However, these methods may not fully capture the clustered structure of the data. This paper addresses this issue by developing a novel data imputation method using PARATUCK2 decomposition. The proposed method captures both spatial and temporal information of traffic data and constructs a low-dimensional and clustered representation of traffic patterns. The identified spatiotemporal clusters are used to recover network traffic profiles and estimate missing values. The proposed method is implemented using traffic data in the road network of Manhattan in New York City. The performance of the proposed method is evaluated in comparison with two state-of-the-art benchmark methods. The outcomes indicate that the proposed method outperforms the existing state-of-the-art imputation methods in complex and large-scale traffic networks.

    

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4. MetaTP: Traffic Prediction with Unevenly-Distributed Road Sensing Data via Fast Adaptation

   https://doi.org/10.1145/3478083  

   Zhong, Weida ; Suo, Qiuling ; Gupta, Abhishek ; Jia, Xiaowei ; Qiao, Chunming ; Su, Lu ( September 2021 , Proceedings of the ACM on Interactive, Mobile, Wearable and Ubiquitous Technologies)

   With the popularity of smartphones, large-scale road sensing data is being collected to perform traffic prediction, which is an important task in modern society. Due to the nature of the roving sensors on smartphones, the collected traffic data which is in the form of multivariate time series, is often temporally sparse and unevenly distributed across regions. Moreover, different regions can have different traffic patterns, which makes it challenging to adapt models learned from regions with sufficient training data to target regions. Given that many regions may have very sparse data, it is also impossible to build individual models for each region separately. In this paper, we propose a meta-learning based framework named MetaTP to overcome these challenges. MetaTP has two key parts, i.e., basic traffic prediction network (base model) and meta-knowledge transfer. In base model, a two-layer interpolation network is employed to map original time series onto uniformly-spaced reference time points, so that temporal prediction can be effectively performed in the reference space. The meta-learning framework is employed to transfer knowledge from source regions with a large amount of data to target regions with a few data examples via fast adaptation, in order to improve model generalizability on target regions. Moreover, we use two memory networks to capture the global patterns of spatial and temporal information across regions. We evaluate the proposed framework on two real-world datasets, and experimental results show the effectiveness of the proposed framework. 

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5. Traffic Anomaly Detection Via Conditional Normalizing Flow

   https://doi.org/10.1109/ITSC55140.2022.9922061  

   Kang, Zhuangwei ; Mukhopadhyay, Ayan ; Gokhale, Aniruddha ; Wen, Shijie ; Dubey, Abhishek ( October 2022 , 2022 IEEE 25th International Conference on Intelligent Transportation Systems (ITSC))

   Traffic congestion anomaly detection is of paramount importance in intelligent traffic systems. The goals of transportation agencies are two-fold: to monitor the general traffic conditions in the area of interest and to locate road segments under abnormal congestion states. Modeling congestion patterns can achieve these goals for citywide roadways, which amounts to learning the distribution of multivariate time series (MTS). However, existing works are either not scalable or unable to capture the spatial-temporal information in MTS simultaneously. To this end, we propose a principled and comprehensive framework consisting of a data-driven generative approach that can perform tractable density estimation for detecting traffic anomalies. Our approach first clusters segments in the feature space and then uses conditional normalizing flow to identify anomalous temporal snapshots at the cluster level in an unsupervised setting. Then, we identify anomalies at the segment level by using a kernel density estimator on the anomalous cluster. Extensive experiments on synthetic datasets show that our approach significantly outperforms several state-of-the-art congestion anomaly detection and diagnosis methods in terms of Recall and F1-Score. We also use the generative model to sample labeled data, which can train classifiers in a supervised setting, alleviating the lack of labeled data for anomaly detection in sparse settings. 

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