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1. Bavarian : Betweenness Centrality Approximation with Variance-aware Rademacher Averages

   https://doi.org/10.1145/3577021  

   Cousins, Cyrus ; Wohlgemuth, Chloe ; Riondato, Matteo ( December 2023 , ACM Transactions on Knowledge Discovery from Data)

   “[A]llain Gersten, Hopfen, und Wasser” — 1516 Reinheitsgebot We present Bavarian , a collection of sampling-based algorithms for approximating the Betweenness Centrality (BC) of all vertices in a graph. Our algorithms use Monte-Carlo Empirical Rademacher Averages (MCERAs), a concept from statistical learning theory, to efficiently compute tight bounds on the maximum deviation of the estimates from the exact values. The MCERAs provide a sample-dependent approximation guarantee much stronger than the state-of-the-art, thanks to its use of variance-aware probabilistic tail bounds. The flexibility of the MCERAs allows us to introduce a unifying framework that can be instantiated with existing sampling-based estimators of BC, thus allowing a fair comparison between them, decoupled from the sample-complexity results with which they were originally introduced. Additionally, we prove novel sample-complexity results showing that, for all estimators, the sample size sufficient to achieve a desired approximation guarantee depends on the vertex-diameter of the graph, an easy-to-bound characteristic quantity. We also show progressive-sampling algorithms and extensions to other centrality measures, such as percolation centrality. Our extensive experimental evaluation of Bavarian shows the improvement over the state-of-the-art made possible by the MCERAs (2–4× reduction in the error bound), and it allows us to assess the different trade-offs between sample size and accuracy guarantees offered by the different estimators. 

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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. Local Computation Algorithms for Spanners

   Parter, Merav ; Rubinfeld, Ronitt ; Vakilian, Ali ; Yodpinyanee, Anak ( January 2019 , Innovations in Theoretical Computer Science (ITCS))

   A graph spanner is a fundamental graph structure that faithfully preserves the pairwise distances in the input graph up to a small multiplicative stretch. The common objective in the computation of spanners is to achieve the best-known existential size-stretch trade-off efficiently. Classical models and algorithmic analysis of graph spanners essentially assume that the algorithm can read the input graph, construct the desired spanner, and write the answer to the output tape. However, when considering massive graphs containing millions or even billions of nodes not only the input graph, but also the output spanner might be too large for a single processor to store. To tackle this challenge, we initiate the study of local computation algorithms (LCAs) for graph spanners in general graphs, where the algorithm should locally decide whether a given edge (u,v)∈E belongs to the output spanner. Such LCAs give the user the `illusion' that a specific sparse spanner for the graph is maintained, without ever fully computing it. We present the following results: -For general n-vertex graphs and r∈{2,3}, there exists an LCA for (2r−1)-spanners with O˜(n1+1/r) edges and sublinear probe complexity of O˜(n1−1/2r). These size/stretch tradeoffs are best possible (up to polylogarithmic factors). -For every k≥1 and n-vertex graph with maximum degree Δ, there exists an LCA for O(k2) spanners with O˜(n1+1/k) edges, probe complexity of O˜(Δ4n2/3), and random seed of size polylog(n). This improves upon, and extends the work of [Lenzen-Levi, 2018]. We also complement our results by providing a polynomial lower bound on the probe complexity of LCAs for graph spanners that holds even for the simpler task of computing a sparse connected subgraph with o(m) edges. 

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4. BC tree-based spectral sampling for big complex network visualization

   https://doi.org/10.1007/s41109-021-00405-3  

   Hu, Jingming ; Chu, Tuan Tran ; Hong, Seok-Hee ; Chen, Jialu ; Meidiana, Amyra ; Torkel, Marnijati ; Eades, Peter ; Ma, Kwan-Liu ( December 2021 , Applied Network Science)

   Abstract Graph sampling methods have been used to reduce the size and complexity of big complex networks for graph mining and visualization. However, existing graph sampling methods often fail to preserve the connectivity and important structures of the original graph. This paper introduces a new divide and conquer approach to spectral graph sampling based on graph connectivity, called the BC Tree (i.e., decomposition of a connected graph into biconnected components) and spectral sparsification. Specifically, we present two methods, spectral vertex sampling $$BC\_SV$$ B C _ S V and spectral edge sampling $$BC\_SS$$ B C _ S S by computing effective resistance values of vertices and edges for each connected component. Furthermore, we present $$DBC\_SS$$ D B C _ S S and $$DBC\_GD$$ D B C _ G D , graph connectivity-based distributed algorithms for spectral sparsification and graph drawing respectively, aiming to further improve the runtime efficiency of spectral sparsification and graph drawing by integrating connectivity-based graph decomposition and distributed computing. Experimental results demonstrate that $$BC\_SV$$ B C _ S V and $$BC\_SS$$ B C _ S S are significantly faster than previous spectral graph sampling methods while preserving the same sampling quality. $$DBC\_SS$$ D B C _ S S and $$DBC\_GD$$ D B C _ G D obtain further significant runtime improvement over sequential approaches, and $$DBC\_GD$$ D B C _ G D further achieves significant improvements in quality metrics over sequential graph drawing layouts. 

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5. G-thinker: a general distributed framework for finding qualified subgraphs in a big graph with load balancing

   https://doi.org/10.1007/s00778-021-00688-z  

   Yan, Da ; Guo, Guimu ; Khalil, Jalal ; Özsu, M. Tamer ; Ku, Wei-Shinn ; Lui, John C. ( January 2022 , The VLDB journal)

   Finding from a big graph those subgraphs that satisfy certain conditions is useful in many applications such as community detection and subgraph matching. These problems have a high time complexity, but existing systems that attempt to scale them are all IO-bound in execution. We propose the first truly CPU-bound distributed framework called G-thinker for subgraph finding algorithms, which adopts a task-based computation model, and which also provides a user-friendly subgraph-centric vertex-pulling API for writing distributed subgraph finding algorithms that can be easily adapted from existing serial algorithms. To utilize all CPU cores of a cluster, G-thinker features (1) a highly concurrent vertex cache for parallel task access and (2) a lightweight task scheduling approach that ensures high task throughput. These designs well overlap communication with computation to minimize the idle time of CPU cores. To further improve load balancing on graphs where the workloads of individual tasks can be drastically different due to biased graph density distribution, we propose to prioritize the scheduling of those tasks that tend to be long running for processing and decomposition, plus a timeout mechanism for task decomposition to prevent long-running straggler tasks. The idea has been integrated into a novelty algorithm for maximum clique finding (MCF) that adopts a hybrid task decomposition strategy, which significantly improves the running time of MCF on dense and large graphs: The algorithm finds a maximum clique of size 1,109 on a large and dense WikiLinks graph dataset in 70 minutes. Extensive experiments demonstrate that G-thinker achieves orders of magnitude speedup compared even with the fastest existing subgraph-centric system, and it scales well to much larger and denser real network data. G-thinker is open-sourced at http://bit.ly/gthinker with detailed documentation. 

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