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1. Discriminative Self-Paced Group-Metric Adaptation for Online Visual Identification

   https://doi.org/10.1109/TPAMI.2022.3200036  

   Zhou, Jiahuan ; Su, Bing ; Wu, Ying ( August 2022 , IEEE Transactions on Pattern Analysis and Machine Intelligence)

   Existing solutions to instance-level visual identification usually aim to learn faithful and discriminative feature extractors from offline training data and directly use them for the unseen online testing data. However, their performance is largely limited due to the severe distribution shifting issue between training and testing samples. Therefore, we propose a novel online group-metric adaptation model to adapt the offline learned identification models for the online data by learning a series of metrics for all sharing-subsets. Each sharing-subset is obtained from the proposed novel frequent sharing-subset mining module and contains a group of testing samples that share strong visual similarity relationships to each other. Furthermore, to handle potentially large-scale testing samples, we introduce self-paced learning (SPL) to gradually include samples into adaptation from easy to difficult which elaborately simulates the learning principle of humans. Unlike existing online visual identification methods, our model simultaneously takes both the sample-specific discriminant and the set-based visual similarity among testing samples into consideration. Our method is generally suitable to any off-the-shelf offline learned visual identification baselines for online performance improvement which can be verified by extensive experiments on several widely-used visual identification benchmarks. 

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2. Learning Visual Instance Retrieval from Failure: Efficient Online Local Metric Adaptation from Negative Samples

   https://doi.org/10.1109/TPAMI.2019.2918208  

   Zhou, Jiahuan ; Wu, Ying ( May 2019 , IEEE Transactions on Pattern Analysis and Machine Intelligence)

   Existing visual instance retrieval (VIR) approaches attempt to learn a faithful global matching metric or discriminative feature embedding offline to cover enormous visual appearance variations, so as to directly use it online on various unseen probes for retrieval. However, their requirement for a huge set of positive training pairs is very demanding in practice and the performance is largely constrained for the unseen testing samples due to the severe data shifting issue. In contrast, this paper advocates a different paradigm: part of the learning can be performed online but with nominal costs, so as to achieve online metric adaptation for different query probes. By exploiting easily-available negative samples, we propose a novel solution to achieve the optimal local metric adaptation effectively and efficiently. The insight of our method is the local hard negative samples can actually provide tight constraints to fine tune the metric locally. Our local metric adaptation method is generally applicable to be used on top of any offline-learned baselines. In addition, this paper gives in-depth theoretical analyses of the proposed method to guarantee the reduction of the classification error both asymptotically and practically. Extensive experiments on various VIR tasks have confirmed our effectiveness and superiority. 

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3. Towards Automated Ethogramming: Cognitively-Inspired Event Segmentation for Streaming Wildlife Video Monitoring

   https://doi.org/10.1007/s11263-023-01781-2  

   Mounir, Ramy ; Shahabaz, Ahmed ; Gula, Roman ; Theuerkauf, Jörn ; Sarkar, Sudeep ( April 2023 , International Journal of Computer Vision)

   Advances in visual perceptual tasks have been mainly driven by the amount, and types, of annotations of large-scale datasets. Researchers have focused on fully-supervised settings to train models using offline epoch-based schemes. Despite the evident advancements, limitations and cost of manually annotated datasets have hindered further development for event perceptual tasks, such as detection and localization of objects and events in videos. The problem is more apparent in zoological applications due to the scarcity of annotations and length of videos-most videos are at most ten minutes long. Inspired by cognitive theories, we present a self-supervised perceptual prediction framework to tackle the problem of temporal event segmentation by building a stable representation of event-related objects. The approach is simple but effective. We rely on LSTM predictions of high-level features computed by a standard deep learning backbone. For spatial segmentation, the stable representation of the object is used by an attention mechanism to filter the input features before the prediction step. The self-learned attention maps effectively localize the object as a side effect of perceptual prediction. We demonstrate our approach on long videos from continuous wildlife video monitoring, spanning multiple days at 25 FPS. We aim to facilitate automated ethogramming by detecting and localizing events without the need for labels. Our approach is trained in an online manner on streaming input and requires only a single pass through the video, with no separate training set. Given the lack of long and realistic (includes real-world challenges) datasets, we introduce a new wildlife video dataset–nest monitoring of the Kagu (a flightless bird from New Caledonia)–to benchmark our approach. Our dataset features a video from 10 days (over 23 million frames) of continuous monitoring of the Kagu in its natural habitat. We annotate every frame with bounding boxes and event labels. Additionally, each frame is annotated with time-of-day and illumination conditions. We will make the dataset, which is the first of its kind, and the code available to the research community. We find that the approach significantly outperforms other self-supervised, traditional (e.g., Optical Flow, Background Subtraction) and NN-based (e.g., PA-DPC, DINO, iBOT), baselines and performs on par with supervised boundary detection approaches (i.e., PC). At a recall rate of 80%, our best performing model detects one false positive activity every 50 min of training. On average, we at least double the performance of self-supervised approaches for spatial segmentation. Additionally, we show that our approach is robust to various environmental conditions (e.g., moving shadows). We also benchmark the framework on other datasets (i.e., Kinetics-GEBD, TAPOS) from different domains to demonstrate its generalizability. The data and code are available on our project page:https://aix.eng.usf.edu/research_automated_ethogramming.html

    

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4. Online Resource Allocation with Matching Constraints

   Dickerson, John ; Sankararaman, Karthik ; Sarpatwar, Kanthi ; Srinivasan, Aravind ; Wu, Kung-Lu ; Xu, Pan ( January 2019 , International Conference on Autonomous Agents and Multiagent Systems (AAMAS))

   Matching markets with historical data are abundant in many applications, e.g., matching candidates to jobs in hiring, workers to tasks in crowdsourcing markets, and jobs to servers in cloud services. In all these applications, a match consumes one or more shared and limited resources and the goal is to best utilize these to maximize a global objective. Additionally, one often has historical data and hence some statistics (usually first-order moments) of the arriving agents (e.g., candidates, workers, and jobs) can be learnt. To model these scenarios, we propose a unifying framework, called Multi- Budgeted Online Assignment with Known Adversarial Distributions. In this model,we have a set of offline servers with different deadlines and a set of online job types. At each time, a job of type j arrives. Assigning this job to a server i yields a profit w(i, j) while consuming a(i,j) -- a vector lying in [0, 1]^K -- quantities of distinct resources. The goal is to design an (online) assignment policy that maximizes the total expected profit without violating the (hard) budget constraint. We propose and theoretically analyze two linear programming (LP) based algorithms which are almost optimal among all LP-based approaches. We also propose several heuristics adapted from our algorithms and compare them to other LP-agnostic algorithms using both synthetic as well as real-time cloud scheduling and public safety datasets. Experimental results show that our proposed algorithms are effective and significantly out-perform the baselines. Moreover, we show empirically the trade-off between fairness and efficiency of our algorithms which does well even on fairness metrics without explicitly optimizing for it. 

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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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