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1. Spike-train level backpropagation for training deep recurrent spiking neural networks

   Zhang, Wenrui ; Li, Peng ( December 2019 , Advances in neural information processing systems)

   Spiking neural networks (SNNs) well support spatio-temporal learning and energy-efficient event-driven hardware neuromorphic processors. As an important class of SNNs, recurrent spiking neural networks (RSNNs) possess great computational power. However, the practical application of RSNNs is severely limited by challenges in training. Biologically-inspired unsupervised learning has limited capability in boosting the performance of RSNNs. On the other hand, existing backpropagation (BP) methods suffer from high complexity of unfolding in time, vanishing and exploding gradients, and approximate differentiation of discontinuous spiking activities when applied to RSNNs. To enable supervised training of RSNNs under a well-defined loss function, we present a novel Spike-Train level RSNNs Backpropagation (ST-RSBP) algorithm for training deep RSNNs. The proposed ST-RSBP directly computes the gradient of a rate-coded loss function defined at the output layer of the network w.r.t tunable parameters. The scalability of ST-RSBP is achieved by the proposed spike-train level computation during which temporal effects of the SNN is captured in both the forward and backward pass of BP. Our ST-RSBP algorithm can be broadly applied to RSNNs with a single recurrent layer or deep RSNNs with multiple feedforward and recurrent layers. Based upon challenging speech and image datasets including TI46, N-TIDIGITS, Fashion-MNIST and MNIST, ST-RSBP is able to train SNNs with an accuracy surpassing that of the current state-of-the-art SNN BP algorithms and conventional non-spiking deep learning models. 

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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. AutoTransfer: AutoML with Knowledge Transfer - An Application to Graph Neural Networks

   Cao, Kaidi ; You, Jiaxuan ; Liu, Jiaju ; Leskovec, Jure ( May 2023 , International Conference on Learning Representations (ICLR))

   AutoML has demonstrated remarkable success in finding an effective neural architecture for a given machine learning task defined by a specific dataset and an evaluation metric. However, most present AutoML techniques consider each task independently from scratch, which requires exploring many architectures, leading to high computational costs. We proposed AutoTransfer, an AutoML solution that improves search efficiency by transferring the prior architectural design knowledge to the novel task of interest. Our key innovation includes a task-model bank that captures the model performance over a diverse set of GNN architectures and tasks, and a computationally efficient task embedding that can accurately measure the similarity among different tasks. Based on the task-model bank and the task embeddings, our method estimates the design priors of desirable models of the novel task, by aggregating a similarity-weighted sum of the top-K design distributions on tasks that are similar to the task of interest. The computed design priors can be used with any AutoML search algorithm. We evaluated AutoTransfer on six datasets in the graph machine learning domain. Experiments demonstrate that (i) our proposed task embedding can be computed efficiently, and that tasks with similar embeddings have similar best-performing architectures; (ii) AutoTransfer significantly improves search efficiency with the transferred design priors, reducing the number of explored architectures by an order of magnitude. Finally, we released GNN-BANK-101, a large-scale dataset of detailed GNN training information of 120,000 task-model combinations to facilitate and inspire future research. 

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4. Deep-Dup: An Adversarial Weight Duplication Attack Framework to Crush Deep Neural Network in Multi-Tenant FPGA

   Rakin, Adnan Siraj ; Luo, Yukui ; Xu, Xiaolin ; Fan, Deliang ( August 2021 , 30th USENIX Security Symposium)

   The wide deployment of Deep Neural Networks (DNN) in high-performance cloud computing platforms brought to light multi-tenant cloud field-programmable gate arrays (FPGA) as a popular choice of accelerator to boost performance due to its hardware reprogramming flexibility. Such a multi-tenant FPGA setup for DNN acceleration potentially exposes DNN interference tasks under severe threat from malicious users. This work, to the best of our knowledge, is the first to explore DNN model vulnerabilities in multi-tenant FPGAs. We propose a novel adversarial attack framework: Deep-Dup, in which the adversarial tenant can inject adversarial faults to the DNN model in the victim tenant of FPGA. Specifically, she can aggressively overload the shared power distribution system of FPGA with malicious power-plundering circuits, achieving adversarial weight duplication (AWD) hardware attack that duplicates certain DNN weight packages during data transmission between off-chip memory and on-chip buffer, to hijack the DNN function of the victim tenant. Further, to identify the most vulnerable DNN weight packages for a given malicious objective, we propose a generic vulnerable weight package searching algorithm, called Progressive Differential Evolution Search (P-DES), which is, for the first time, adaptive to both deep learning white-box and black-box attack models. The proposed Deep-Dup is experimentally validated in a developed multi-tenant FPGA prototype, for two popular deep learning applications, i.e., Object Detection and Image Classification. Successful attacks are demonstrated in six popular DNN architectures (e.g., YOLOv2, ResNet-50, MobileNet, etc.) on three datasets (COCO, CIFAR-10, and ImageNet). 

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5. Deep learning versus kernel learning: an empirical study of loss landscape geometry and the time evolution of the Neural Tangent Kernel

   Fort, S ; Dziugaite, G.K. ; Paul, M. ; Kharaghani, S. ; Roy, D.M. ; Ganguli, S. ( December 2020 , Advances in neural information processing systems)

   null (Ed.)

   In suitably initialized wide networks, small learning rates transform deep neural networks (DNNs) into neural tangent kernel (NTK) machines, whose training dynamics is well-approximated by a linear weight expansion of the network at initialization. Standard training, however, diverges from its linearization in ways that are poorly understood. We study the relationship between the training dynamics of nonlinear deep networks, the geometry of the loss landscape, and the time evolution of a data-dependent NTK. We do so through a large-scale phenomenological analysis of training, synthesizing diverse measures characterizing loss landscape geometry and NTK dynamics. In multiple neural architectures and datasets, we find these diverse measures evolve in a highly correlated manner, revealing a universal picture of the deep learning process. In this picture, deep network training exhibits a highly chaotic rapid initial transient that within 2 to 3 epochs determines the final linearly connected basin of low loss containing the end point of training. During this chaotic transient, the NTK changes rapidly, learning useful features from the training data that enables it to outperform the standard initial NTK by a factor of 3 in less than 3 to 4 epochs. After this rapid chaotic transient, the NTK changes at constant velocity, and its performance matches that of full network training in 15\% to 45\% of training time. Overall, our analysis reveals a striking correlation between a diverse set of metrics over training time, governed by a rapid chaotic to stable transition in the first few epochs, that together poses challenges and opportunities for the development of more accurate theories of deep learning. 

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