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1. A Second-Order Approach to Learning with Instance-Dependent Label Noise

   Zhu, Zhaowei ; Liu, Tongliang ; Liu, Yang ( January 2021 , Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition)

   null (Ed.)

   The presence of label noise often misleads the training of deep neural networks. Departing from the recent literature which largely assumes the label noise rate is only determined by the true label class, the errors in human-annotated labels are more likely to be dependent on the difficulty levels of tasks, resulting in settings with instance-dependent label noise. We first provide evidences that the heterogeneous instance-dependent label noise is effectively down-weighting the examples with higher noise rates in a non-uniform way and thus causes imbalances, rendering the strategy of directly applying methods for class-dependent label noise questionable. Built on a recent work peer loss [24], we then propose and study the potentials of a second-order approach that leverages the estimation of several covariance terms defined between the instance-dependent noise rates and the Bayes optimal label. We show that this set of second-order statistics successfully captures the induced imbalances. We further proceed to show that with the help of the estimated second-order statistics, we identify a new loss function whose expected risk of a classifier under instance-dependent label noise is equivalent to a new problem with only class-dependent label noise. This fact allows us to apply existing solutions to handle this better-studied setting. We provide an efficient procedure to estimate these second-order statistics without accessing either ground truth labels or prior knowledge of the noise rates. Experiments on CIFAR10 and CIFAR100 with synthetic instance-dependent label noise and Clothing1M with real-world human label noise verify our approach. Our implementation is available at https://github.com/UCSC-REAL/CAL. 

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2. Automatic ML-based vestibular gait classification: examining the effects of IMU placement and gait task selection

   https://doi.org/10.1186/s12984-022-01099-z  

   Jabri, Safa ; Carender, Wendy ; Wiens, Jenna ; Sienko, Kathleen H. ( December 2022 , Journal of NeuroEngineering and Rehabilitation)

   Vestibular deficits can impair an individual’s ability to maintain postural and/or gaze stability. Characterizing gait abnormalities among individuals affected by vestibular deficits could help identify patients at high risk of falling and inform rehabilitation programs. Commonly used gait assessment tools rely on simple measures such as timing and visual observations of path deviations by clinicians. These simple measures may not capture subtle changes in gait kinematics. Therefore, we investigated the use of wearable inertial measurement units (IMUs) and machine learning (ML) approaches to automatically discriminate between gait patterns of individuals with vestibular deficits and age-matched controls. The goal of this study was to examine the effects of IMU placement and gait task selection on the performance of automatic vestibular gait classifiers.

   Thirty study participants (15 with vestibular deficits and 15 age-matched controls) participated in a single-session gait study during which they performed seven gait tasks while donning a full-body set of IMUs. Classification performance was reported in terms of area under the receiver operating characteristic curve (AUROC) scores for Random Forest models trained on data from each IMU placement for each gait task.

   Several models were able to classify vestibular gait better than random (AUROC > 0.5), but their performance varied according to IMU placement and gait task selection. Results indicated that a single IMU placed on the left arm when walking with eyes closed resulted in the highest AUROC score for a single IMU (AUROC = 0.88 [0.84, 0.89]). Feature permutation results indicated that participants with vestibular deficits reduced their arm swing compared to age-matched controls while they walked with eyes closed.

   These findings highlighted differences in upper extremity kinematics during walking with eyes closed that were characteristic of vestibular deficits and showed evidence of the discriminative ability of IMU-based automated screening for vestibular deficits. Further research should explore the mechanisms driving arm swing differences in the vestibular population.

    

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3. Detecting Corrupted Labels Without Training a Model to Predict

   Zhu, Zhaowei ; Dong, Zihao ; Liu, Yang ( January 2022 , International Conference on Machine Learning)

   Label noise in real-world datasets encodes wrong correlation patterns and impairs the generalization of deep neural networks (DNNs). It is critical to find efficient ways to detect corrupted patterns. Current methods primarily focus on designing robust training techniques to prevent DNNs from memorizing corrupted patterns. These approaches often require customized training processes and may overfit corrupted patterns, leading to a performance drop in detection. In this paper, from a more data-centric perspective, we propose a training-free solution to detect corrupted labels. Intuitively, ``closer'' instances are more likely to share the same clean label. Based on the neighborhood information, we propose two methods: the first one uses ``local voting" via checking the noisy label consensuses of nearby features. The second one is a ranking-based approach that scores each instance and filters out a guaranteed number of instances that are likely to be corrupted. We theoretically analyze how the quality of features affects the local voting and provide guidelines for tuning neighborhood size. We also prove the worst-case error bound for the ranking-based method. Experiments with both synthetic and real-world label noise demonstrate our training-free solutions consistently and significantly improve most of the training-based baselines. 

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4. Learning with Instance-Dependent Label Noise: A Sample Sieve Approach

   Cheng, Hao ; Zhu, Zhaowei ; Li, Xingyu ; Gong, Yifei ; Sun, Xing ; Liu, Yang ( May 2021 , International Conference on Learning Representations)

   null (Ed.)

   Human-annotated labels are often prone to noise, and the presence of such noise will degrade the performance of the resulting deep neural network (DNN) models. Much of the literature (with several recent exceptions) of learning with noisy labels focuses on the case when the label noise is independent of features. Practically, annotations errors tend to be instance-dependent and often depend on the difficulty levels of recognizing a certain task. Applying existing results from instance-independent settings would require a significant amount of estimation of noise rates. Therefore, providing theoretically rigorous solutions for learning with instance-dependent label noise remains a challenge. In this paper, we propose CORES (COnfidence REgularized Sample Sieve), which progressively sieves out corrupted examples. The implementation of CORES does not require specifying noise rates and yet we are able to provide theoretical guarantees of CORES in filtering out the corrupted examples. This high-quality sample sieve allows us to treat clean examples and the corrupted ones separately in training a DNN solution, and such a separation is shown to be advantageous in the instance-dependent noise setting. We demonstrate the performance of CORES^2 on CIFAR10 and CIFAR100 datasets with synthetic instance-dependent label noise and Clothing1M with real-world human noise. As of independent interests, our sample sieve provides a generic machinery for anatomizing noisy datasets and provides a flexible interface for various robust training techniques to further improve the performance. Code is available at https://github.com/UCSC-REAL/cores. 

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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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