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1. Learning Generative Models of 3D Structures

   https://doi.org/10.1111/cgf.14020  

   Chaudhuri, Siddhartha ; Ritchie, Daniel ; Wu, Jiajun ; Xu, Kai ; Zhang, Hao ( July 2020 , Computer graphics forum)

   3D models of objects and scenes are critical to many academic disciplines and industrial applications. Of particular interest is the emerging opportunity for 3D graphics to serve artificial intelligence: computer vision systems can benefit from synthetically-generated training data rendered from virtual 3D scenes, and robots can be trained to navigate in and interact with real-world environments by first acquiring skills in simulated ones. One of the most promising ways to achieve this is by learning and applying generative models of 3D content: computer programs that can synthesize new 3D shapes and scenes. To allow users to edit and manipulate the synthesized 3D content to achieve their goals, the generative model should also be structure-aware: it should express 3D shapes and scenes using abstractions that allow manipulation of their high-level structure. This state-of-the- art report surveys historical work and recent progress on learning structure-aware generative models of 3D shapes and scenes. We present fundamental representations of 3D shape and scene geometry and structures, describe prominent methodologies including probabilistic models, deep generative models, program synthesis, and neural networks for structured data, and cover many recent methods for structure-aware synthesis of 3D shapes and indoor scenes. 

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2. ThreeDWorld: A platform for interactive multi-modal physical simulation

   Gan, C. ; Schwartz, J. ; Alter, S. ; Schrimpf, M. ; Traer, J. ; De Freitas, J. ; Kubilius, J. ; Bhandwaldar, A. ; Haber, N. ; Sano, M. ; et al ( October 2021 , Advances in Neural Information Processing Systems (NeurIPS))

   We introduce ThreeDWorld (TDW), a platform for interactive multi-modal physical simulation. TDW enables the simulation of high-fidelity sensory data and physical interactions between mobile agents and objects in rich 3D environments. Unique properties include: real-time near-photo-realistic image rendering; a library of objects and environments, and routines for their customization; generative procedures for efficiently building classes of new environments; high-fidelity audio rendering; realistic physical interactions for a variety of material types, including cloths, liquid, and deformable objects; customizable avatars that embody AI agents; and support for human interactions with VR devices. TDW's API enables multiple agents to interact within a simulation and returns a range of sensor and physics data representing the state of the world. We present initial experiments enabled by TDW in emerging research directions in computer vision, machine learning, and cognitive science, including multi-modal physical scene understanding, physical dynamics predictions, multi-agent interactions, models that 'learn like a child', and attention studies in humans and neural networks. 

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3. ThreeDWorld: A Platform for Interactive Multi-Modal Physical Simulation

   https://doi.org/https://doi.org/10.48550/arXiv.2007.04954  

   o Gan C, Schartz S ( July 2020 , ArXivorg)

   We introduce ThreeDWorld (TDW), a platform for interactive multi-modal physical simulation. TDW enables simulation of high-fidelity sensory data and physical interactions between mobile agents and objects in rich 3D environments. Unique properties include: real-time near-photo-realistic image rendering; a library of objects and environments, and routines for their customization; generative procedures for efficiently building classes of new environments; high-fidelity audio rendering; realistic physical interactions for a variety of material types, including cloths, liquid, and deformable objects; customizable agents that embody AI agents; and support for human interactions with VR devices. TDW's API enables multiple agents to interact within a simulation and returns a range of sensor and physics data representing the state of the world. We present initial experiments enabled by TDW in emerging research directions in computer vision, machine learning, and cognitive science, including multi-modal physical scene understanding, physical dynamics predictions, multi-agent interactions, models that learn like a child, and attention studies in humans and neural networks. 

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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. ∇-Prox: Differentiable Proximal Algorithm Modeling for Large-Scale Optimization

   https://doi.org/10.1145/3592144  

   Lai, Zeqiang ; Wei, Kaixuan ; Fu, Ying ; Härtel, Philipp ; Heide, Felix ( August 2023 , ACM Transactions on Graphics)

   Tasks across diverse application domains can be posed as large-scale optimization problems, these include graphics, vision, machine learning, imaging, health, scheduling, planning, and energy system forecasting. Independently of the application domain, proximal algorithms have emerged as a formal optimization method that successfully solves a wide array of existing problems, often exploiting problem-specific structures in the optimization. Although model-based formal optimization provides a principled approach to problem modeling with convergence guarantees, at first glance, this seems to be at odds with black-box deep learning methods. A recent line of work shows that, when combined with learning-based ingredients, model-based optimization methods are effective, interpretable, and allow for generalization to a wide spectrum of applications with little or no extra training data. However, experimenting with such hybrid approaches for different tasks by hand requires domain expertise in both proximal optimization and deep learning, which is often error-prone and time-consuming. Moreover, naively unrolling these iterative methods produces lengthy compute graphs, which when differentiated via autograd techniques results in exploding memory consumption, making batch-based training challenging. In this work, we introduce ∇-Prox, a domain-specific modeling language and compiler for large-scale optimization problems using differentiable proximal algorithms. ∇-Prox allows users to specify optimization objective functions of unknowns concisely at a high level, and intelligently compiles the problem into compute and memory-efficient differentiable solvers. One of the core features of ∇-Prox is its full differentiability, which supports hybrid model- and learning-based solvers integrating proximal optimization with neural network pipelines. Example applications of this methodology include learning-based priors and/or sample-dependent inner-loop optimization schedulers, learned with deep equilibrium learning or deep reinforcement learning. With a few lines of code, we show ∇-Prox can generate performant solvers for a range of image optimization problems, including end-to-end computational optics, image deraining, and compressive magnetic resonance imaging. We also demonstrate ∇-Prox can be used in a completely orthogonal application domain of energy system planning, an essential task in the energy crisis and the clean energy transition, where it outperforms state-of-the-art CVXPY and commercial Gurobi solvers. 

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