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1. Towards a Better Understanding of Public Transportation Traffic: A Case Study of the Washington, DC Metro

   https://doi.org/10.3390/urbansci2030065  

   Truong, Robert ; Gkountouna, Olga ; Pfoser, Dieter ; Züfle, Andreas ( September 2018 , Urban Science)

   The problem of traffic prediction is paramount in a plethora of applications, ranging from individual trip planning to urban planning. Existing work mainly focuses on traffic prediction on road networks. Yet, public transportation contributes a significant portion to overall human mobility and passenger volume. For example, the Washington, DC metro has on average 600,000 passengers on a weekday. In this work, we address the problem of modeling, classifying and predicting such passenger volume in public transportation systems. We study the case of the Washington, DC metro exploring fare card data, and specifically passenger in- and outflow at stations. To reduce dimensionality of the data, we apply principal component analysis to extract latent features for different stations and for different calendar days. Our unsupervised clustering results demonstrate that these latent features are highly discriminative. They allow us to derive different station types (residential, commercial, and mixed) and to effectively classify and identify the passenger flow of “unknown” stations. Finally, we also show that this classification can be applied to predict the passenger volume at stations. By learning latent features of stations for some time, we are able to predict the flow for the following hours. Extensive experimentation using a baseline neural network and two naïve periodicity approaches shows the considerable accuracy improvement when using the latent feature based approach. 

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2. Operations Design of Modular Vehicles on an Oversaturated Corridor with First-in, First-out Passenger Queueing

   https://doi.org/10.1287/trsc.2021.1074  

   Shi, Xiaowei ; Li, Xiaopeng ( August 2021 , Transportation Science)

   null (Ed.)

   Although urban transit systems (UTS) often have fixed vehicle capacity and relatively constant departure headways, they may need to accommodate dramatically fluctuating passenger demands over space and time, resulting in either excessive passenger waiting or vehicle capacity and energy waste. Therefore, on the one hand, optimal operations of UTS rely on accurate modeling of passenger queuing dynamics, which is particularly complex on a multistop transit corridor. On the other hand, capacities of transit vehicles can be made variable and adaptive to time-variant passenger demand so as to minimize energy waste, especially with the emergence of modular vehicle technologies. This paper investigates operations of a multistop transit corridor in which vehicles may have different capacities across dispatches. We specify skewed time coordinates to simplify the problem structure while incorporating traffic congestion. Then, we propose a mixed integer linear programming model that determines the optimal dynamic headways and vehicle capacities over the study time horizon to minimize the overall system cost for the transit corridor. In particular, the proposed model considers a realistic multistop first-in, first-out (MSFIFO) rule that gives the same boarding priority to passengers arriving at a station in the same time interval yet with different destinations. A customized dynamic programming (DP) algorithm is proposed to solve this model efficiently. To circumvent the rapid increase of the state space of a typical DP algorithm, we analyze the theoretical properties of the investigated problem and identify upper and lower bounds to a feasible solution. The bounds largely reduce the state space during the DP iterations and greatly improve the efficiency of the proposed DP algorithm. The state dimensions are also reduced with the MSFIFO rule such that all queues with different destinations at the same origin can be tracked with a single boarding position state variable at each stage. A hypothetical example and a real-world case study show that the proposed DP algorithm greatly outperforms a state-of-the-art commercial solver (Gurobi) in both solution quality and time. 

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3. Dynamic Integration of Heterogeneous Transportation Modes Under Disruptive Events

   Yuan, Y. ; Zhang, D. ; Miao, F. ; Stankovic, J. ; He, T. ; Pappas, G. ; Lin, S. ( January 2018 , ACM/IEEE International Conference on Cyber-Physical Systems)

   An integrated urban transportation system usually consists of multiple transport modes that have complementary characteristics of capacities, speeds, and costs, facilitating smooth passenger transfers according to planned schedules. However, such an integration is not designed to operate under disruptive events, e.g., a signal failure at a subway station or a breakdown of a bus, which have rippling effects on passenger demand and significantly increase delays. To address these disruptive events, current solutions mainly rely on a substitute service to transport passengers from and to affected areas using adhoc schedules. To fully utilize heterogeneous transportation systems under disruptive events, we design a service called eRoute based on a hierarchical receding horizon control framework to automatically reroute, reschedule, and reallocate multi-mode transportation systems based on real-time and predicted demand and supply. Focusing on an integration of subway and bus, we implement and evaluate eRoute with large datasets including (i) a bus system with 13,000 buses, (ii) a subway system with 127 subway stations, (iii) an automatic fare collection system with a total of 16,840 readers and 8 million card users from a metropolitan city. The data-driven evaluation results show that our solution improves the ratio of served passengers (RSP) by up to 11.5 times and reduces the average traveling time by up to 82.1% compared with existing solutions. 

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4. Individualized passenger travel pattern multi-clustering based on graph regularized tensor latent dirichlet allocation

   https://doi.org/10.1007/s10618-022-00842-3  

   Li, Ziyue ; Yan, Hao ; Zhang, Chen ; Tsung, Fugee ( July 2022 , Data Mining and Knowledge Discovery)

   Abstract Individual passenger travel patterns have significant value in understanding passenger’s behavior, such as learning the hidden clusters of locations, time, and passengers. The learned clusters further enable commercially beneficial actions such as customized services, promotions, data-driven urban-use planning, peak hour discovery, and so on. However, the individualized passenger modeling is very challenging for the following reasons: 1) The individual passenger travel data are multi-dimensional spatiotemporal big data, including at least the origin, destination, and time dimensions; 2) Moreover, individualized passenger travel patterns usually depend on the external environment, such as the distances and functions of locations, which are ignored in most current works. This work proposes a multi-clustering model to learn the latent clusters along the multiple dimensions of Origin, Destination, Time, and eventually, Passenger (ODT-P). We develop a graph-regularized tensor Latent Dirichlet Allocation (LDA) model by first extending the traditional LDA model into a tensor version and then applies to individual travel data. Then, the external information of stations is formulated as semantic graphs and incorporated as the Laplacian regularizations; Furthermore, to improve the model scalability when dealing with massive data, an online stochastic learning method based on tensorized variational Expectation-Maximization algorithm is developed. Finally, a case study based on passengers in the Hong Kong metro system is conducted and demonstrates that a better clustering performance is achieved compared to state-of-the-arts with the improvement in point-wise mutual information index and algorithm convergence speed by a factor of two. 

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5. 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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