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1. Real-Time Camera Localization during Robot-Assisted Telecystoscopy for Bladder Cancer Surveillance

   https://doi.org/10.1142/S2424905X22410021  

   Gong, Chen ; Zhou, Yaxuan ; Lewis, Andrew ; Chen, Pengcheng ; Speich, Jason R. ; Porter, Michael P. ; Hannaford, Blake ; Seibel, Eric J. ( May 2022 , Journal of Medical Robotics Research)

   Telecystoscopy can lower the barrier to access critical urologic diagnostics for patients around the world. A major challenge for robotic control of flexible cystoscopes and intuitive teleoperation is the pose estimation of the scope tip. We propose a novel real-time camera localization method using video recordings from a prior cystoscopy and 3D bladder reconstruction to estimate cystoscope pose within the bladder during follow-up telecystoscopy. We map prior video frames into a low-dimensional space as a dictionary so that a new image can be likewise mapped to efficiently retrieve its nearest neighbor among the dictionary images. The cystoscope pose is then estimated by the correspondence among the new image, its nearest dictionary image, and the prior model from 3D reconstruction. We demonstrate performance of our methods using bladder phantoms with varying fidelity and a servo-controlled cystoscope to simulate the use case of bladder surveillance through telecystoscopy. The servo-controlled cystoscope with 3 degrees of freedom (angulation, roll, and insertion axes) was developed for collecting cystoscope videos from bladder phantoms. Cystoscope videos were acquired in a 2.5D bladder phantom (bladder-shape cross-section plus height) with a panorama of a urothelium attached to the inner surface. Scans of the 2.5D phantom were performed in separate arc trajectories each of which is generated by actuation on the angulation with a fixed roll and insertion length. We further included variance in moving speed, imaging distance and existence of bladder tumors. Cystoscope videos were also acquired in a water-filled 3D silicone bladder phantom with hand-painted vasculature. Scans of the 3D phantom were performed in separate circle trajectories each of which is generated by actuation on the roll axis under a fixed angulation and insertion length. These videos were used to create 3D reconstructions, dictionary sets, and test data sets for evaluating the computational efficiency and accuracy of our proposed method in comparison with a method based on global Scale-Invariant Feature Transform (SIFT) features, named SIFT-only. Our method can retrieve the nearest dictionary image for 94–100% of test frames in under 55[Formula: see text]ms per image, whereas the SIFT-only method can only find the image match for 56–100% of test frames in 6000–40000[Formula: see text]ms per image depending on size of the dictionary set and richness of SIFT features in the images. Our method, with a speed of around 20 Hz for the retrieval stage, is a promising tool for real-time image-based scope localization in robotic cystoscopy when prior cystoscopy images are available. 

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2. Equation Attention Relationship Network (EARN) : A Geometric Deep Metric Framework for Learning Similar Math Expression Embedding

   https://doi.org/10.1109/ICPR48806.2021.9412619  

   Ahmed, Saleem ; Davila, Kenny ; Setlur, Srirangaraj ; Govindaraju, Venu ( May 2021 , 2020 25th International Conference on Pattern Recognition (ICPR))

   null (Ed.)

   Representational Learning in the form of high dimensional embeddings have been used for multiple pattern recognition applications. There has been a significant interest in building embedding based systems for learning representations in the mathematical domain. At the same time, retrieval of structured information such as mathematical expressions is an important need for modern IR systems. In this work, our motivation is to introduce a robust framework for learning representations for similarity based retrieval of mathematical expressions. Given a query by example, the embedding can find the closest matching expression as a function of euclidean distance between them. We leverage recent advancements in image-based and graph-based deep learning algorithms to learn our similarity embeddings. We do this first, by using unimodal encoders in graph space and image space and then, a multi-modal combination of the same. To overcome the lack of training data, we force the networks to learn a deep metric using triplets generated with a heuristic scoring function. We also adopt a custom strategy for mining hard samples to train our neural networks. Our system produces rankings similar to those generated by the original scoring function, but using only a fraction of the time. Our results establish the viability of using such a multi-modal embedding for this task. 

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3. 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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4. Generalized Loss-Sensitive Adversarial Learning with Manifold Margins

   Edraki, Marzieh ; Qi, Guo-Jun ( September 2018 , Proceedings of European Conference on Computer Vision (ECCV 2018))

   The classic Generative Adversarial Net (GAN) and its variants can be roughly categorized into two large families: the unregularized versus regularized GANs. By relaxing the non-parametric assumption on the discriminator in the classic GAN, the regularized GANs have better generalization ability to produce new samples drawn from the real distribution. Although the regularized GANs have shown compelling performances, there still exist some unaddressed problems. It is well known that the real data like natural images are not uniformly distributed over the whole data space. Instead, they are often restricted to a low-dimensional manifold of the ambient space. Such a manifold assumption suggests the distance over the manifold should be a better measure to characterize the distinct between real and fake samples. Thus, we define a pullback operator to map samples back to their data manifold, and a manifold margin is defined as the distance between the pullback representations to distinguish between real and fake samples and learn the optimal generators. We justify the proposed model from both theoretical and empirical perspectives, demonstrating it can produce high quality images as compared with the other state-of-the-art GAN models. 

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5. ARKGraph: All-Range Approximate K-Nearest-Neighbor Graph

   https://doi.org/10.14778/3603581.3603601  

   Zuo, Chaoji ; Deng, Dong ( June 2023 , Proceedings of the VLDB Endowment)

   Given a collection of vectors, the approximate K-nearest-neighbor graph (KGraph for short) connects every vector to its approximate K-nearest-neighbors (KNN for short). KGraph plays an important role in high dimensional data visualization, semantic search, manifold learning, and machine learning. The vectors are typically vector representations of real-world objects (e.g., images and documents), which often come with a few structured attributes, such as times-tamps and locations. In this paper, we study the all-range approximate K-nearest-neighbor graph (ARKGraph) problem. Specifically, given a collection of vectors, each associated with a numerical search key (e.g., a timestamp), we aim to build an index that takes a search key range as the query and returns the KGraph of vectors whose search keys are within the query range. ARKGraph can facilitate interactive high dimensional data visualization, data mining, etc. A key challenge of this problem is the huge index size. This is because, given n vectors, a brute-force index stores a KGraph for every search key range, which results in O (K n 3 ) index size as there are O ( n 2 ) search key ranges and each KGraph takes O (K n ) space. We observe that the KNN of a vector in nearby ranges are often the same, which can be grouped together to save space. Based on this observation, we propose a series of novel techniques that reduce the index size significantly to just O (K n log n ) in the average case. Furthermore, we develop an efficient indexing algorithm that constructs the optimized ARKGraph index directly without exhaustively calculating the distance between every pair of vectors. To process a query, for each vector in the query range, we only need O (log log n + K log K) to restore its KNN in the query range from the optimized ARKGraph index. We conducted extensive experiments on real-world datasets. Experimental results show that our optimized ARKGraph index achieved a small index size, low query latency, and good scalability. Specifically, our approach was 1000x faster than the baseline method that builds a KGraph for all the vectors in the query range on-the-fly. 

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