A major bottleneck of the current Machine Learning (ML) workflow is the time consuming, error prone engineering required to get data from a datastore or a database (DB) to the point an ML algorithm can be applied to it. This is further exacerbated since ML algorithms are now trained on large volumes of data, yet we need predictions in real-time, especially in a variety of time-series applications such as finance and real-time control systems. Hence, we explore the feasibility of directly integrating prediction functionality on top of a data store or DB. Such a system ideally: (i) provides an intuitive prediction query interface which alleviates the unwieldy data engineering; (ii) provides state-of-the-art statistical accuracy while ensuring incremental model update, low model training time and low latency for making predictions. As the main contribution we explicitly instantiate a proof-of-concept, tspDB which directly integrates with PostgreSQL. We rigorously test tspDB’s statistical and computational performance against the state-of-the-art time series algorithms, including a Long-Short-Term-Memory (LSTM) neural network and DeepAR (industry standard deep learning library by Amazon). Statistically, on standard time series benchmarks, tspDB outperforms LSTM and DeepAR with 1.1-1.3x higher relative accuracy. Computationally, tspDB is 59-62x and 94-95x faster compared to LSTM and DeepAR in terms of median ML model training time and prediction query latency, respectively. Further, compared to PostgreSQL’s bulk insert time and its SELECT query latency, tspDB is slower only by 1.3x and 2.6x respectively. That is, tspDB is a real-time prediction system in that its model training / prediction query time is similar to just inserting, reading data from a DB. As an algorithmic contribution, we introduce an incremental multivariate matrix factorization based time series method, which tspDB is built off. We show this method also allows one to produce reliable prediction intervals by accurately estimating the time-varying variance of a time series, thereby addressing an important problem in time series analysis. more »« less
Deep learning now offers state-of-the-art accuracy for many prediction tasks. A form of deep learning called deep convolutional neural networks (CNNs) are especially popular on image, video, and time series data. Due to its high computational cost, CNN inference is often a bottleneck in analytics tasks on such data. Thus, a lot of work in the computer architecture, systems, and compilers communities study how to make CNN inference faster. In this work, we show that by elevating the abstraction level and re-imagining CNN inference as queries , we can bring to bear database-style query optimization techniques to improve CNN inference efficiency. We focus on tasks that perform CNN inference repeatedly on inputs that are only slightly different . We identify two popular CNN tasks with this behavior: occlusion-based explanations (OBE) and object recognition in videos (ORV). OBE is a popular method for “explaining” CNN predictions. It outputs a heatmap over the input to show which regions (e.g., image pixels) mattered most for a given prediction. It leads to many re-inference requests on locally modified inputs. ORV uses CNNs to identify and track objects across video frames. It also leads to many re-inference requests. We cast such tasks in a unified manner as a novel instance of the incremental view maintenance problem and create a comprehensive algebraic framework for incremental CNN inference that reduces computational costs. We produce materialized views of features produced inside a CNN and connect them with a novel multi-query optimization scheme for CNN re-inference. Finally, we also devise novel OBE-specific and ORV-specific approximate inference optimizations exploiting their semantics. We prototype our ideas in Python to create a tool called Krypton that supports both CPUs and GPUs. Experiments with real data and CNNs show that Krypton reduces runtimes by up to 5× (respectively, 35×) to produce exact (respectively, high-quality approximate) results without raising resource requirements.
Wireless x-haul networks rely on microwave and millimeter-wave links between 4G and/or 5G
base-stations to support ultra-high data rate and ultra-low latency. A major challenge associated with
these high frequency links is their susceptibility to weather conditions. In particular, precipitation may
cause severe signal attenuation, which significantly degrades the network performance. In this paper, we
develop a Predictive Network Reconfiguration (PNR) framework that uses historical data to predict the
future condition of each link and then prepares the network ahead of time for imminent disturbances.
The PNR framework has two components: (i) an Attenuation Prediction (AP) mechanism; and (ii)
a Multi-Step Network Reconfiguration (MSNR) algorithm. The AP mechanism employs an encoderdecoder Long Short-Term Memory (LSTM) model to predict the sequence of future attenuation levels
of each link. The MSNR algorithm leverages these predictions to dynamically optimize routing and
admission control decisions aiming to maximize network utilization, while preserving max-min fairness
among the base-stations sharing the network and preventing transient congestion that may be caused
by re-routing. We train, validate, and evaluate the PNR framework using a dataset containing over 2
million measurements collected from a real-world city-scale backhaul network. The results show that
the framework: (i) predicts attenuation with high accuracy, with an RMSE of less than 0.4 dB for a
prediction horizon of 50 seconds; and (ii) can improve the instantaneous network utilization by more than
200% when compared to reactive network reconfiguration algorithms that cannot leverage information
about future disturbances
Neural architecture search (NAS) is a promising technique to design efficient and high-performance deep neural networks (DNNs). As the performance requirements of ML applications grow continuously, the hardware accelerators start playing a central role in DNN design. This trend makes NAS even more complicated and time-consuming for most real applications. This paper proposes FLASH, a very fast NAS methodology that co-optimizes the DNN accuracy and performance on a real hardware platform. As the main theoretical contribution, we first propose the NN-Degree, an analytical metric to quantify the topological characteristics of DNNs with skip connections (e.g., DenseNets, ResNets, Wide-ResNets, and MobileNets). The newly proposed NN-Degree allows us to do training-free NAS within one second and build an accuracy predictor by training as few as 25 samples out of a vast search space with more than 63 billion configurations. Second, by performing inference on the target hardware, we fine-tune and validate our analytical models to estimate the latency, area, and energy consumption of various DNN architectures while executing standard ML datasets. Third, we construct a hierarchical algorithm based on simplicial homology global optimization (SHGO) to optimize the model-architecture co-design process, while considering the area, latency, and energy consumption of the target hardware. We demonstrate that, compared to the state-of-the-art NAS approaches, our proposed hierarchical SHGO-based algorithm enables more than four orders of magnitude speedup (specifically, the execution time of the proposed algorithm is about 0.1 seconds). Finally, our experimental evaluations show that FLASH is easily transferable to different hardware architectures, thus enabling us to do NAS on a Raspberry Pi-3B processor in less than 3 seconds.
Wevodau, Z.; Doshna, B.; Jhala, N.; Akhtar, I.; Obeid, I.; Picone, J.(
, 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.
Fang, Kuai; Shen, Chaopeng(
, Journal of Hydrometeorology)
Nowcasts, or near-real-time (NRT) forecasts, of soil moisture based on the Soil Moisture Active and Passive (SMAP) mission could provide substantial value for a range of applications including hazards monitoring and agricultural planning. To provide such a NRT forecast with high fidelity, we enhanced a time series deep learning architecture, long short-term memory (LSTM), with a novel data integration (DI) kernel to assimilate the most recent SMAP observations as soon as they become available. The kernel is adaptive in that it can accommodate irregular observational schedules. Testing over the CONUS, this NRT forecast product showcases predictions with unprecedented accuracy when evaluated against subsequent SMAP retrievals. It showed smaller error than NRT forecasts reported in the literature, especially at longer forecast latency. The comparative advantage was due to LSTM’s structural improvements, as well as its ability to utilize more input variables and more training data. The DI-LSTM was compared to the original LSTM model that runs without data integration, referred to as the projection model here. We found that the DI procedure removed the autocorrelated effects of forcing errors and errors due to processes not represented in the inputs, for example, irrigation and floodplain/lake inundation, as well as mismatches due to unseen forcing conditions. The effects of this purely data-driven DI kernel are discussed for the first time in the geosciences. Furthermore, this work presents an upper-bound estimate for the random component of the SMAP retrieval error.
Agarwal, Anish and. tspDB: Time Series Predict DB. Proceedings of Machine Learning Research, 133 (). Retrieved from https://par.nsf.gov/biblio/10313410.
Agarwal, Anish and.
"tspDB: Time Series Predict DB". Proceedings of Machine Learning Research 133 (). Country unknown/Code not available. https://par.nsf.gov/biblio/10313410.
@article{osti_10313410,
place = {Country unknown/Code not available},
title = {tspDB: Time Series Predict DB},
url = {https://par.nsf.gov/biblio/10313410},
abstractNote = {A major bottleneck of the current Machine Learning (ML) workflow is the time consuming, error prone engineering required to get data from a datastore or a database (DB) to the point an ML algorithm can be applied to it. This is further exacerbated since ML algorithms are now trained on large volumes of data, yet we need predictions in real-time, especially in a variety of time-series applications such as finance and real-time control systems. Hence, we explore the feasibility of directly integrating prediction functionality on top of a data store or DB. Such a system ideally: (i) provides an intuitive prediction query interface which alleviates the unwieldy data engineering; (ii) provides state-of-the-art statistical accuracy while ensuring incremental model update, low model training time and low latency for making predictions. As the main contribution we explicitly instantiate a proof-of-concept, tspDB which directly integrates with PostgreSQL. We rigorously test tspDB’s statistical and computational performance against the state-of-the-art time series algorithms, including a Long-Short-Term-Memory (LSTM) neural network and DeepAR (industry standard deep learning library by Amazon). Statistically, on standard time series benchmarks, tspDB outperforms LSTM and DeepAR with 1.1-1.3x higher relative accuracy. Computationally, tspDB is 59-62x and 94-95x faster compared to LSTM and DeepAR in terms of median ML model training time and prediction query latency, respectively. Further, compared to PostgreSQL’s bulk insert time and its SELECT query latency, tspDB is slower only by 1.3x and 2.6x respectively. That is, tspDB is a real-time prediction system in that its model training / prediction query time is similar to just inserting, reading data from a DB. As an algorithmic contribution, we introduce an incremental multivariate matrix factorization based time series method, which tspDB is built off. We show this method also allows one to produce reliable prediction intervals by accurately estimating the time-varying variance of a time series, thereby addressing an important problem in time series analysis.},
journal = {Proceedings of Machine Learning Research},
volume = {133},
author = {Agarwal, Anish and},
}
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