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1. Recent Advances in the Temple University Digital Pathology Corpus

   https://doi.org/10.1109/SPMB47826.2019.9037859  

   Hunt, I. ; Husain, S. ; Simon, J. ; Obeid, I. ; Picone, J. ( December 2019 , IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, Iyad ; Picone, Joseph ; Selesnick, Ivan (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing a large open source database of high-resolution digital pathology images known as the Temple University Digital Pathology Corpus (TUDP) [1]. Our long-term goal is to release one million images. We expect to release the first 100,000 image corpus by December 2020. The data is being acquired at the Department of Pathology at Temple University Hospital (TUH) using a Leica Biosystems Aperio AT2 scanner [2] and consists entirely of clinical pathology images. More information about the data and the project can be found in Shawki et al. [3]. We currently have a National Science Foundation (NSF) planning grant [4] to explore how best the community can leverage this resource. One goal of this poster presentation is to stimulate community-wide discussions about this project and determine how this valuable resource can best meet the needs of the public. The computing infrastructure required to support this database is extensive [5] and includes two HIPAA-secure computer networks, dual petabyte file servers, and Aperio’s eSlide Manager (eSM) software [6]. We currently have digitized over 50,000 slides from 2,846 patients and 2,942 clinical cases. There is an average of 12.4 slides per patient and 10.5 slides per casemore »with one report per case. The data is organized by tissue type as shown below: Filenames: tudp/v1.0.0/svs/gastro/000001/00123456/2015_03_05/0s15_12345/0s15_12345_0a001_00123456_lvl0001_s000.svs tudp/v1.0.0/svs/gastro/000001/00123456/2015_03_05/0s15_12345/0s15_12345_00123456.docx Explanation: tudp: root directory of the corpus v1.0.0: version number of the release svs: the image data type gastro: the type of tissue 000001: six-digit sequence number used to control directory complexity 00123456: 8-digit patient MRN 2015_03_05: the date the specimen was captured 0s15_12345: the clinical case name 0s15_12345_0a001_00123456_lvl0001_s000.svs: the actual image filename consisting of a repeat of the case name, a site code (e.g., 0a001), the type and depth of the cut (e.g., lvl0001) and a token number (e.g., s000) 0s15_12345_00123456.docx: the filename for the corresponding case report We currently recognize fifteen tissue types in the first installment of the corpus. The raw image data is stored in Aperio’s “.svs” format, which is a multi-layered compressed JPEG format [3,7]. Pathology reports containing a summary of how a pathologist interpreted the slide are also provided in a flat text file format. A more complete summary of the demographics of this pilot corpus will be presented at the conference. Another goal of this poster presentation is to share our experiences with the larger community since many of these details have not been adequately documented in scientific publications. There are quite a few obstacles in collecting this data that have slowed down the process and need to be discussed publicly. Our backlog of slides dates back to 1997, meaning there are a lot that need to be sifted through and discarded for peeling or cracking. Additionally, during scanning a slide can get stuck, stalling a scan session for hours, resulting in a significant loss of productivity. Over the past two years, we have accumulated significant experience with how to scan a diverse inventory of slides using the Aperio AT2 high-volume scanner. We have been working closely with the vendor to resolve many problems associated with the use of this scanner for research purposes. This scanning project began in January of 2018 when the scanner was first installed. The scanning process was slow at first since there was a learning curve with how the scanner worked and how to obtain samples from the hospital. From its start date until May of 2019 ~20,000 slides we scanned. In the past 6 months from May to November we have tripled that number and how hold ~60,000 slides in our database. This dramatic increase in productivity was due to additional undergraduate staff members and an emphasis on efficient workflow. The Aperio AT2 scans 400 slides a day, requiring at least eight hours of scan time. The efficiency of these scans can vary greatly. When our team first started, approximately 5% of slides failed the scanning process due to focal point errors. We have been able to reduce that to 1% through a variety of means: (1) best practices regarding daily and monthly recalibrations, (2) tweaking the software such as the tissue finder parameter settings, and (3) experience with how to clean and prep slides so they scan properly. Nevertheless, this is not a completely automated process, making it very difficult to reach our production targets. With a staff of three undergraduate workers spending a total of 30 hours per week, we find it difficult to scan more than 2,000 slides per week using a single scanner (400 slides per night x 5 nights per week). The main limitation in achieving this level of production is the lack of a completely automated scanning process, it takes a couple of hours to sort, clean and load slides. We have streamlined all other aspects of the workflow required to database the scanned slides so that there are no additional bottlenecks. To bridge the gap between hospital operations and research, we are using Aperio’s eSM software. Our goal is to provide pathologists access to high quality digital images of their patients’ slides. eSM is a secure website that holds the images with their metadata labels, patient report, and path to where the image is located on our file server. Although eSM includes significant infrastructure to import slides into the database using barcodes, TUH does not currently support barcode use. Therefore, we manage the data using a mixture of Python scripts and manual import functions available in eSM. The database and associated tools are based on proprietary formats developed by Aperio, making this another important point of community-wide discussion on how best to disseminate such information. Our near-term goal for the TUDP Corpus is to release 100,000 slides by December 2020. We hope to continue data collection over the next decade until we reach one million slides. We are creating two pilot corpora using the first 50,000 slides we have collected. The first corpus consists of 500 slides with a marker stain and another 500 without it. This set was designed to let people debug their basic deep learning processing flow on these high-resolution images. We discuss our preliminary experiments on this corpus and the challenges in processing these high-resolution images using deep learning in [3]. We are able to achieve a mean sensitivity of 99.0% for slides with pen marks, and 98.9% for slides without marks, using a multistage deep learning algorithm. While this dataset was very useful in initial debugging, we are in the midst of creating a new, more challenging pilot corpus using actual tissue samples annotated by experts. The task will be to detect ductal carcinoma (DCIS) or invasive breast cancer tissue. There will be approximately 1,000 images per class in this corpus. Based on the number of features annotated, we can train on a two class problem of DCIS or benign, or increase the difficulty by increasing the classes to include DCIS, benign, stroma, pink tissue, non-neoplastic etc. Those interested in the corpus or in participating in community-wide discussions should join our listserv, nedc_tuh_dpath@googlegroups.com, to be kept informed of the latest developments in this project. You can learn more from our project website: https://www.isip.piconepress.com/projects/nsf_dpath.« less
2. On the Hardness and Inapproximability of Recognizing Wheeler Graphs

   https://doi.org/10.4230/LIPIcs.ESA.2019.51  

   Gibney, Daniel ;  Thankachan, Sharma V. ( January 2019 , 27th Annual European Symposium on Algorithms (ESA) 2019)

   In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced. Some of these are used to index structures far more complex than a single string, as was originally done with the FM-index [Ferragina and Manzini, J. ACM 2005]. As such, there has been an increasing effort to better understand under which conditions such an indexing scheme is possible. This has led to the introduction of Wheeler graphs [Gagie et al., Theor. Comput. Sci., 2017]. Gagie et al. showed that de Bruijn graphs, generalized compressed suffix arrays, and several other BWT related structures can be represented as Wheeler graphs and that Wheeler graphs can be indexed in a way which is space-efficient. Hence, being able to recognize whether a given graph is a Wheeler graph, or being able to approximate a given graph by a Wheeler graph, could have numerous applications in indexing. Here we resolve the open question of whether there exists an efficient algorithm for recognizing if a given graph is a Wheeler graph. We present - The problem of recognizing whether a given graph G=(V,E) is a Wheeler graph is NP-complete for any edge label alphabet of size sigma >= 2, evenmore »when G is a DAG. This holds even on a restricted, subset of graphs called d-NFA's for d >= 5. This is in contrast to recent results demonstrating the problem can be solved in polynomial time for d-NFA's where d <= 2. We also show the recognition problem can be solved in linear time for sigma =1; - There exists an 2^{e log sigma + O(n + e)} time exact algorithm where n = |V| and e = |E|. This algorithm relies on graph isomorphism being computable in strictly sub-exponential time; - We define an optimization variant of the problem called Wheeler Graph Violation, abbreviated WGV, where the aim is to remove the minimum number of edges in order to obtain a Wheeler graph. We show WGV is APX-hard, even when G is a DAG, implying there exists a constant C >= 1 for which there is no C-approximation algorithm (unless P = NP). Also, conditioned on the Unique Games Conjecture, for all C >= 1, it is NP-hard to find a C-approximation; - We define the Wheeler Subgraph problem, abbreviated WS, where the aim is to find the largest subgraph which is a Wheeler Graph (the dual of the WGV). In contrast to WGV, we prove that the WS problem is in APX for sigma=O(1); The above findings suggest that most problems under this theme are computationally difficult. However, we identify a class of graphs for which the recognition problem is polynomial-time solvable, raising the open question of which parameters determine this problem's difficulty.« less
3. Energy-Efficient Deep Neural Networks with Mixed-Signal Neurons and Dense-Local and Sparse-Global Connectivity

   https://doi.org/10.1145/3394885.3431614  

   Chatterjee, Baibhab ; Sen, Shreyas ( January 2021 , Asia and South Pacific Design Automation Conference)

   Neuromorphic Computing has become tremendously popular due to its ability to solve certain classes of learning tasks better than traditional von-Neumann computers. Data-intensive classification and pattern recognition problems have been of special interest to Neuromorphic Engineers, as these problems present complex use-cases for Deep Neural Networks (DNNs) which are motivated from the architecture of the human brain, and employ densely connected neurons and synapses organized in a hierarchical manner. However, as these systems become larger in order to handle an increasing amount of data and higher dimensionality of features, the designs often become connectivity constrained. To solve this, the computation is divided into multiple cores/islands, called processing engines (PEs). Today, the communication among these PEs are carried out through a power-hungry network-on-chip (NoC), and hence the optimal distribution of these islands along with energy-efficient compute and communication strategies become extremely important in reducing the overall energy of the neuromorphic computer, which is currently orders of magnitude higher than the biological human brain. In this paper, we extensively analyze the choice of the size of the islands based on mixed-signal neurons/synapses for 3-8 bit-resolution within allowable ranges for system-level classification error, determined by the analog non-idealities (noise and mismatch) in themore »neurons, and propose strategies involving local and global communication for reduction of the system-level energy consumption. AC-coupled mixed-signal neurons are shown to have 10X lower non-idealities than DC-coupled ones, while the choice of number of islands are shown to be a function of the network, constrained by the analog to digital conversion (or viceversa) power at the interface of the islands. The maximum number of layers in an island is analyzed and a global bus-based sparse connectivity is proposed, which consumes orders of magnitude lower power than the competing powerline communication techniques.« less
4. Approximating Back-propagation for a Biologically Plausible Local Learning Rule in Spiking Neural Networks

   https://doi.org/10.1145/3354265.3354275  

   Shrestha, Amar ; Fang, Haowen ; Wu, Qing ; Qiu, Qinru ( July 2019 , International Conference on Neuromorphic Systems)

   Asynchronous event-driven computation and communication using spikes facilitate the realization of spiking neural networks (SNN) to be massively parallel, extremely energy efficient and highly robust on specialized neuromorphic hardware. However, the lack of a unified robust learning algorithm limits the SNN to shallow networks with low accuracies. Artificial neural networks (ANN), however, have the backpropagation algorithm which can utilize gradient descent to train networks which are locally robust universal function approximators. But backpropagation algorithm is neither biologically plausible nor neuromorphic implementation friendly because it requires: 1) separate backward and forward passes, 2) differentiable neurons, 3) high-precision propagated errors, 4) coherent copy of weight matrices at feedforward weights and the backward pass, and 5) non-local weight update. Thus, we propose an approximation of the backpropagation algorithm completely with spiking neurons and extend it to a local weight update rule which resembles a biologically plausible learning rule spike-timing-dependent plasticity (STDP). This will enable error propagation through spiking neurons for a more biologically plausible and neuromorphic implementation friendly backpropagation algorithm for SNNs. We test the proposed algorithm on various traditional and non-traditional benchmarks with competitive results.
5. Self-supervised 4D Spatio-temporal Feature Learning via Order Prediction of Sequential Point Cloud Clips

   Wang, H ; Yang, L ; Rong, X ; Feng, J ; Tian, Y. ( June 2021 , Winter Conference on Applications of Computer Vision (WACV), 2021.)

   Recently 3D scene understanding attracts attention for many applications, however, annotating a vast amount of 3D data for training is usually expensive and time consuming. To alleviate the needs of ground truth, we propose a self-supervised schema to learn 4D spatio-temporal features (i.e. 3 spatial dimensions plus 1 temporal dimension) from dynamic point cloud data by predicting the temporal order of sampled and shuffled point cloud clips. 3D sequential point cloud contains precious geometric and depth information to better recognize activities in 3D space compared to videos. To learn the 4D spatio-temporal features, we introduce 4D convolution neural networks to predict the temporal order on a self-created large scale dataset, NTU- PCLs, derived from the NTU-RGB+D dataset. The efficacy of the learned 4D spatio-temporal features is verified on two tasks: 1) Self-supervised 3D nearest neighbor retrieval; and 2) Self-supervised representation learning transferred for action recognition on smaller 3D dataset. Our extensive experiments prove the effectiveness of the proposed self-supervised learning method which achieves comparable results w.r.t. the fully-supervised methods on action recognition on MSRAction3D dataset.