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1. Learning with Free Object Segments for Long-Tailed Instance Segmentation

   Zhang, Cheng ; Pan, Tai-Yu ; Chen, Tianle ; Zhong, Jike ; Fu, Wenjin ; and Chao, Wei-Lun ( January 2022 , L3D-IVU: Workshop on Learning with Limited Labeled Data for Image and Video Understanding, in conjunction with the IEEE / CVF Computer Vision and Pattern Recognition Conference)

   In this paper, we explore the possibility to increase the training examples without laborious data collection and annotation for long-tailed instance segmentation. We find that an abundance of instance segments can potentially be obtained freely from object-centric images, according to two insights: (i) an object-centric image usually contains one salient object in a simple background; (ii) objects from the same class often share similar appearances or similar contrasts to the background. Motivated by these insights, we propose a simple and scalable framework FREESEG for extracting and leveraging these “free” object segments to facilitate model training. Concretely, we investigate the similarity among object-centric images of the same class to propose candidate segments of foreground instances, followed by a novel ranking of segment quality. The resulting high quality object segments can then be used to augment the existing long-tailed datasets, e.g., by copying and pasting the segments onto the original training images. Extensive experiments show that FREESEG yields substantial improvements on top of strong baselines and achieves state-of-the-art accuracy for segmenting rare object categories. 

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2. On Model Calibration for Long-Tailed Object Detection and Instance Segmentation

   Pan, Tai-Yu ; Zhang, Cheng ; Li, Yandong ; Hu, Hexiang ; Xuan, Dong ; Changpinyo, Soravit ; Gong, Boqing ; Chao, Wei-Lun ( January 2021 , Advances in neural information processing systems)

   Vanilla models for object detection and instance segmentation suffer from the heavy bias toward detecting frequent objects in the long-tailed setting. Existing methods address this issue mostly during training, e.g., by re-sampling or re- weighting. In this paper, we investigate a largely overlooked approach — post- processing calibration of confidence scores. We propose NORCAL, Normalized Calibration for long-tailed object detection and instance segmentation, a simple and straightforward recipe that reweighs the predicted scores of each class by its training sample size. We show that separately handling the background class and normalizing the scores over classes for each proposal are keys to achieving superior performance. On the LVIS dataset, NORCAL can effectively improve nearly all the baseline models not only on rare classes but also on common and frequent classes. Finally, we conduct extensive analysis and ablation studies to offer insights into various modeling choices and mechanisms of our approach. Our code is publicly available at https://github.com/tydpan/NorCal. 

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3. Collaging Class-specific GANs for Semantic Image Synthesis

   https://doi.org/10.1109/iccv48922.2021.01415  

   Li, Yuheng ; Li, Yijun ; Lu, Jingwan ; Shechtman, Eli ; Lee, Yong Jae ; Singh, Krishna Kumar ( October 2021 , International Conference on Computer Vision (ICCV))

   We propose a new approach for high resolution semantic image synthesis. It consists of one base image generator and multiple class-specific generators. The base generator generates high quality images based on a segmentation map. To further improve the quality of different objects, we create a bank of Generative Adversarial Networks (GANs) by separately training class-specific models. This has several benefits including – dedicated weights for each class; centrally aligned data for each model; additional training data from other sources, potential of higher resolution and quality; and easy manipulation of a specific object in the scene. Experiments show that our approach can generate high quality images in high resolution while having flexibility of object-level control by using class-specific generators. Project page: https://yuheng-li.github.io/CollageGAN/ 

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4. Image-to-Image Translation for Autonomous Driving from Coarsely-Aligned Image Pairs

   Xia, Youya ; Monica, Josephine ; Chao, Wei-Lun ; Hariharan, Bharath ; Weinberger, Kilian ; Campbell, Mark ( May 2023 , Proceedings IEEE International Conference on Robotics and Automation)

   A self-driving car must be able to reliably handle adverse weather conditions (e.g., snowy) to operate safely. In this paper, we investigate the idea of turning sensor inputs (i.e., images) captured in an adverse condition into a benign one (i.e., sunny), upon which the downstream tasks (e.g., semantic segmentation) can attain high accuracy. Prior work primarily formulates this as an unpaired image-to-image translation problem due to the lack of paired images captured under the exact same camera poses and semantic layouts. While perfectly- aligned images are not available, one can easily obtain coarsely- paired images. For instance, many people drive the same routes daily in both good and adverse weather; thus, images captured at close-by GPS locations can form a pair. Though data from repeated traversals are unlikely to capture the same foreground objects, we posit that they provide rich contextual information to supervise the image translation model. To this end, we propose a novel training objective leveraging coarsely- aligned image pairs. We show that our coarsely-aligned training scheme leads to a better image translation quality and improved downstream tasks, such as semantic segmentation, monocular depth estimation, and visual localization. 

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5. 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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