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1. Physics guided RNNs for modeling dynamical systems: A case study in simulating lake temperature profiles

   Jia, X. ; Willard, J. ; Karpatne, A. ; Read, J. ; Zwart, J. ; Steinbach, M. ; Kumar, V. ( May 2019 , Proceedings of the 2019 SIAM International Conference on Data Mining)

   This paper proposes a physics-guided recurrent neural network model (PGRNN) that combines RNNs and physics-based models to leverage their complementary strengths and improve the modeling of physical processes. Specifically, we show that a PGRNN can improve prediction accuracy over that of physical models, while generating outputs consistent with physical laws, and achieving good generalizability. Standard RNNs, even when producing superior prediction accuracy, often produce physically inconsistent results and lack generalizability. We further enhance this approach by using a pre-training method that leverages the simulated data from a physics-based model to address the scarcity of observed data. Although we present and evaluate this methodology in the context of modeling the dynamics of temperature in lakes, it is applicable more widely to a range of scientific and engineering disciplines where mechanistic (also known as process-based) models are used, e.g., power engineering, climate science, materials science, computational chemistry, and biomedicine. 

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2. Learning Controllable Adaptive Simulation for Multi-resolution Physics

   Wu, Tailin ; Maruyama, Takashi ; Zhao, Qingqing ; Wetzstein, Gordon ; Leskovec, Jure ( May 2023 , International Conference on Learning Representations (ICLR))

   Simulating the time evolution of physical systems is pivotal in many scientific and engineering problems. An open challenge in simulating such systems is their multi-resolution dynamics: a small fraction of the system is extremely dynamic, and requires very fine-grained resolution, while a majority of the system is changing slowly and can be modeled by coarser spatial scales. Typical learning-based surrogate models use a uniform spatial scale, which needs to resolve to the finest required scale and can waste a huge compute to achieve required accuracy. We introduced Learning controllable Adaptive simulation for Multiresolution Physics (LAMP) as the first full deep learning-based surrogate model that jointly learns the evolution model and optimizes appropriate spatial resolutions that devote more compute to the highly dynamic regions. LAMP consists of a Graph Neural Network (GNN) for learning the forward evolution, and a GNNbased actor-critic for learning the policy of spatial refinement and coarsening. We introduced learning techniques that optimize LAMP with weighted sum of error and computational cost as objective, allowing LAMP to adapt to varying relative importance of error vs. computation tradeoff at inference time. We evaluated our method in a 1D benchmark of nonlinear PDEs and a challenging 2D mesh-based simulation. We demonstrated that our LAMP outperforms state-of-the-art deep learning surrogate models, and can adaptively trade-off computation to improve long-term prediction error: it achieves an average of 33.7% error reduction for 1D nonlinear PDEs, and outperforms MeshGraphNets + classical Adaptive Mesh Refinement (AMR) in 2D mesh-based simulations. 

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3. Strain-Actuated Solar Arrays for Spacecraft Attitude Control Assisted by Viscoelastic Damping

   Yong Hoon Lee, Vedant ( May 2019 , 13th World Congress of Structural and Multidisciplinary Optimization)

   This article presents a utilization of viscoelastic damping to reduce control system complexity for strain-actuated solar array (SASA) based spacecraft attitude control systems (ACSs). SASA utilizes intelligent structures for attitude control, and is a promising next-generation spacecraft ACS technology with the potential to achieve unprecedented levels of pointing accuracy and jitter reduction during key scientific observation periods. The current state-of-the-art SASA implementation utilizes piecewise modeling of distributed piezoelectric (PZT) actuators, resulting in a monolithic structure with the potential for enhanced ACS reliability. PZT actuators can operate at high frequencies, which enables active vibration damping to achieve ultra-quiet operation for sensitive instruments. Relying on active damping alone, however, requires significant control system complexity, which has so far limited adoption of intelligent structures in spacecraft control systems. Here we seek to understand how to modify passive system design in strategic ways to reduce control system complexity while maintaining high performance. An integrated physical and control system design (codesign) optimization strategy is employed to ensure system-optimal performance, and to help understand design coupling between passive physical aspects of design and active control system design. In this study, we present the possibility of utilizing viscoelastic material distributed throughout the SASA substructure to provide tailored passive damping, intending to reduce control system complexity. At this early phase of study, the effect of temperature variation on material behavior is not considered; the study focuses instead on the design coupling between distributed material and control systems. The spatially-distributed design of both elastic and viscoelastic material in the SASA substructure is considered in an integrated manner. An approximate model is used that balances predictive accuracy and computational efficiency. This model approximates the distributed compliant SASA structure using a series of rigid links connected by generalized torsional springs and dampers. This multi-link pseudo-rigid-body dynamic model (PRBDM) with lumped viscoelastic damping models is derived, and is used in numerical co-design studies to quantify the tradeoffs and benefits of using distributed passive damping to reduce the complexity of SASA control systems. 

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4. 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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5. Accelerating Thermal Simulations in Additive Manufacturing by Training Physics-Informed Neural Networks With Randomly Synthesized Data

   https://doi.org/10.1115/1.4062852  

   Chen, Jiangce ; Pierce, Justin ; Williams, Glen ; Simpson, Timothy W. ; Meisel, Nicholas ; Prabha Narra, Sneha ; McComb, Christopher ( January 2024 , Journal of Computing and Information Science in Engineering)

   Abstract The temperature history of an additively manufactured part plays a critical role in determining process–structure–property relationships in fusion-based additive manufacturing (AM) processes. Therefore, fast thermal simulation methods are needed for a variety of AM tasks, from temperature history prediction for part design and process planning to in situ temperature monitoring and control during manufacturing. However, conventional numerical simulation methods fall short in satisfying the strict requirements of time efficiency in these applications due to the large space and time scales of the required multiscale simulation. While data-driven surrogate models are of interest for their rapid computation capabilities, the performance of these models relies on the size and quality of the training data, which is often prohibitively expensive to create. Physics-informed neural networks (PINNs) mitigate the need for large datasets by imposing physical principles during the training process. This work investigates the use of a PINN to predict the time-varying temperature distribution in a part during manufacturing with laser powder bed fusion (L-PBF). Notably, the use of the PINN in this study enables the model to be trained solely on randomly synthesized data. These training data are both inexpensive to obtain, and the presence of stochasticity in the dataset improves the generalizability of the trained model. Results show that the PINN model achieves higher accuracy than a comparable artificial neural network trained on labeled data. Further, the PINN model trained in this work maintains high accuracy in predicting temperature for laser path scanning strategies unseen in the training data. 

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