More Like this

1. 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. 

   more » « less
2. Postural mechanisms in moderate-to-severe cerebral palsy

   https://doi.org/10.1152/jn.00549.2020  

   Goodworth, Adam ; Saavedra, Sandra ( May 2021 , Journal of Neurophysiology)

   null (Ed.)

   People with moderate-to-severe cerebral palsy (CP) have the greatest need for postural control research yet are usually excluded from research due to deficits in sitting ability. We use a support system that allows us to quantify and model postural mechanisms in nonambulatory children with CP. A continuous external bench tilt stimulus was used to evoke trunk postural responses in seven sitting children with CP (ages 2.5 to 13 yr) in several test sessions. Eight healthy adults were also included. Postural sway was analyzed with root mean square (RMS) sway and RMS sway velocity, along with frequency response functions (FRF, gain and phase) and coherence functions across two different stimulus amplitudes. A feedback model (including sensorimotor noise, passive, reflexive, and sensory integration mechanisms) was developed to hypothesize how postural control mechanisms are organized and function. Experimental results showed large RMS sway, FRF gains, and variability compared with adults. Modeling suggested that many subjects with CP adopted “simple” control with major contributions from a passive and reflexive mechanism and only a small contribution from active sensory integration. In contrast, mature trunk postural control includes major contributions from sensory integration and sensory reweighting. Relative to their body size, subjects with CP showed significantly lower damping, three to five times larger corrective torque, and much higher sensorimotor noise compared with the healthy mature system. Results are the first characterization of trunk postural responses and the first attempt at system identification in moderate-to-severe CP, an important step toward developing and evaluating more targeted interventions. NEW & NOTEWORTHY Cerebral palsy (CP) is the most common cause of motor disability in children. People with moderate-to-severe CP are typically nonambulatory and have major impairments in trunk postural control. We present the first systems identification study to investigate postural responses to external stimulus in this population and hypothesize at how the atypical postural control system functions with use of a feedback model. People with moderate-to-severe CP may use a simple control system with significant sensorimotor noise. 

   more » « less
3. Surrogate modeling of structural seismic response using probabilistic learning on manifolds

   https://doi.org/10.1002/eqe.3839  

   Zhong, Kuanshi ; Navarro, Javier G. ; Govindjee, Sanjay ; Deierlein, Gregory G. ( February 2023 , Earthquake Engineering & Structural Dynamics)

   Nonlinear response history analysis (NLRHA) is generally considered to be a reliable and robust method to assess the seismic performance of buildings under strong ground motions. While NLRHA is fairly straightforward to evaluate individual structures for a select set of ground motions at a specific building site, it becomes less practical for performing large numbers of analyses to evaluate either (1) multiple models of alternative design realizations with a site‐specific set of ground motions, or (2) individual archetype building models at multiple sites with multiple sets of ground motions. In this regard, surrogate models offer an alternative to running repeated NLRHAs for variable design realizations or ground motions. In this paper, a recently developed surrogate modeling technique, called probabilistic learning on manifolds (PLoM), is presented to estimate structural seismic response. Essentially, the PLoM method provides an efficient stochastic model to develop mappings between random variables, which can then be used to efficiently estimate the structural responses for systems with variations in design/modeling parameters or ground motion characteristics. The PLoM algorithm is introduced and then used in two case studies of 12‐story buildings for estimating probability distributions of structural responses. The first example focuses on the mapping between variable design parameters of a multidegree‐of‐freedom analysis model and its peak story drift and acceleration responses. The second example applies the PLoM technique to estimate structural responses for variations in site‐specific ground motion characteristics. In both examples, training data sets are generated for orthogonal input parameter grids, and test data sets are developed for input parameters with prescribed statistical distributions. Validation studies are performed to examine the accuracy and efficiency of the PLoM models. Overall, both examples show good agreement between the PLoM model estimates and verification data sets. Moreover, in contrast to other common surrogate modeling techniques, the PLoM model is able to preserve correlation structure between peak responses. Parametric studies are conducted to understand the influence of different PLoM tuning parameters on its prediction accuracy.

    

   more » « less
4. How Well Do Multisatellite Products Capture the Space–Time Dynamics of Precipitation? Part II: Building an Error Model through Spectral System Identification

   https://doi.org/10.1175/JHM-D-22-0041.1  

   Guilloteau, Clement ; Foufoula-Georgiou, Efi ; Kirstetter, Pierre ; Tan, Jackson ; Huffman, George J. ( September 2022 , Journal of Hydrometeorology)

   Satellite precipitation products, as all quantitative estimates, come with some inherent degree of uncertainty. To associate a quantitative value of the uncertainty to each individual estimate, error modeling is necessary. Most of the error models proposed so far compute the uncertainty as a function of precipitation intensity only, and only at one specific spatiotemporal scale. We propose a spectral error model that accounts for the neighboring space–time dynamics of precipitation into the uncertainty quantification. Systematic distortions of the precipitation signal and random errors are characterized distinctively in every frequency–wavenumber band in the Fourier domain, to accurately characterize error across scales. The systematic distortions are represented as a deterministic space–time linear filtering term. The random errors are represented as a nonstationary additive noise. The spectral error model is applied to the IMERG multisatellite precipitation product, and its parameters are estimated empirically through a system identification approach using the GV-MRMS gauge–radar measurements as reference (“truth”) over the eastern United States. The filtering term is found to be essentially low-pass (attenuating the fine-scale variability). While traditional error models attribute most of the error variance to random errors, it is found here that the systematic filtering term explains 48% of the error variance at the native resolution of IMERG. This fact confirms that, at high resolution, filtering effects in satellite precipitation products cannot be ignored, and that the error cannot be represented as a purely random additive or multiplicative term. An important consequence is that precipitation estimates derived from different sources shall not be expected to automatically have statistically independent errors.

   Satellite precipitation products are nowadays widely used for climate and environmental research, water management, risk analysis, and decision support at the local, regional, and global scales. For all these applications, knowledge about the accuracy of the products is critical for their usability. However, products are not systematically provided with a quantitative measure of the uncertainty associated with each individual estimate. Various parametric error models have been proposed for uncertainty quantification, mostly assuming that the uncertainty is only a function of the precipitation intensity at the pixel and time of interest. By projecting satellite precipitation fields and their retrieval errors into the Fourier frequency–wavenumber domain, we show that we can explicitly take into account the neighboring space–time multiscale dynamics of precipitation and compute a scale-dependent uncertainty.

    

   more » « less
5. Research on the stability analysis of milling of thin-walled parts based on the dynamic characteristics

   https://doi.org/10.1177/03093247221113231  

   Liu, Yang ; Zhao, Chencheng ; Cui, NingYuan ; Yan, Xinxin ; Chen, YunGao ; Liang, HaiYing ; Cai, XiaoYu ; Shan, Yue ; Bao, KuiYuan ( July 2022 , The Journal of Strain Analysis for Engineering Design)

   Chatter in thin-walled parts is easy to occur in the process of machining, so the analysis of the stability of thin-walled parts has always been a research hotspot. In this paper, considering the influence of cutter eccentricity on milling force first, the coefficients of milling force were able to be identified by combining the milling force model with genetic algorithm. The results show that this method can obtain the milling force coefficients only by one experiment, and the accuracy is higher. Then the tool point Frequency Response Function (FRF) for a given combination can be calculated by using the Receptance coupling substructure analysis (RCSA) method that uses Timoshenko beam theory. Finally, the milling system can be divided into three types by aspect ratio. That is, when aspect ratio is less than 0.03, the system is considered to be a rigid tool-flexible workpiece system, but aspect ratio is between 0.03 and 0.2, the system is considered to be a flexible tool-flexible system, then aspect ratio is greater than 0.2, the system is considered to be a flexible cutter-rigid workpiece system.

    

   more » « less