skip to main content
Explore Scholarly Publications and Datasets in the NSF-PAR

Title: LANCET: labeling complex data at scale
Cutting-edge machine learning techniques often require millions of labeled data objects to train a robust model. Because relying on humans to supply such a huge number of labels is rarely practical, automated methods for label generation are needed. Unfortunately, critical challenges in auto-labeling remain unsolved, including the following research questions: (1) which objects to ask humans to label, (2) how to automatically propagate labels to other objects, and (3) when to stop labeling. These three questions are not only each challenging in their own right, but they also correspond to tightly interdependent problems. Yet existing techniques provide at best isolated solutions to a subset of these challenges. In this work, we propose the first approach, called LANCET, that successfully addresses all three challenges in an integrated framework. LANCET is based on a theoretical foundation characterizing the properties that the labeled dataset must satisfy to train an effective prediction model, namely the Covariate-shift and the Continuity conditions. First, guided by the Covariate-shift condition, LANCET maps raw input data into a semantic feature space, where an unlabeled object is expected to share the same label with its near-by labeled neighbor. Next, guided by the Continuity condition, LANCET selects objects for labeling, aiming more » to ensure that unlabeled objects always have some sufficiently close labeled neighbors. These two strategies jointly maximize the accuracy of the automatically produced labels and the prediction accuracy of the machine learning models trained on these labels. Lastly, LANCET uses a distribution matching network to verify whether both the Covariate-shift and Continuity conditions hold, in which case it would be safe to terminate the labeling process. Our experiments on diverse public data sets demonstrate that LANCET consistently outperforms the state-of-the-art methods from Snuba to GOGGLES and other baselines by a large margin - up to 30 percentage points increase in accuracy. « less
Authors:
; ; ;
Award ID(s):
2021871 2103799 2103832
Publication Date:
NSF-PAR ID:
10323735
Journal Name:
Proceedings of the VLDB Endowment
Volume:
14
Issue:
11
Page Range or eLocation-ID:
2154 to 2166
ISSN:
2150-8097
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ( , 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 notmore »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.« less
  2. ; ; ; ( , In Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing: Findings)
    Knowing whether a published research result can be replicated is important. Carrying out direct replication of published research incurs a high cost. There are efforts tried to use machine learning aided methods to predict scientific claims’ replicability. However, existing machine learning aided approaches use only hand-extracted statistics features such as p-value, sample size, etc. without utilizing research papers’ text information and train only on a very small size of annotated data without making the most use of a large number of unlabeled articles. Therefore, it is desirable to develop effective machine learning aided automatic methods which can automatically extract text information as features so that we can benefit from Natural Language Processing techniques. Besides, we aim for an approach that benefits from both labeled and the large number of unlabeled data. In this paper, we propose two weakly supervised learning approaches that use automatically extracted text information of research papers to improve the prediction accuracy of research replication using both labeled and unlabeled datasets. Our experiments over real-world datasets show that our approaches obtain much better prediction performance compared to the supervised models utilizing only statistic features and a small size of labeled dataset. Further, we are able to achievemore »an accuracy of 75.76% for predicting the replicability of research.« less
  3. ; ; ( , Technologies)
    Weakly labeled data are inevitable in various research areas in artificial intelligence (AI) where one has a modicum of knowledge about the complete dataset. One of the reasons for weakly labeled data in AI is insufficient accurately labeled data. Strict privacy control or accidental loss may also cause missing-data problems. However, supervised machine learning (ML) requires accurately labeled data in order to successfully solve a problem. Data labeling is difficult and time-consuming as it requires manual work, perfect results, and sometimes human experts to be involved (e.g., medical labeled data). In contrast, unlabeled data are inexpensive and easily available. Due to there not being enough labeled training data, researchers sometimes only obtain one or few data points per category or label. Training a supervised ML model from the small set of labeled data is a challenging task. The objective of this research is to recover missing labels from the dataset using state-of-the-art ML techniques using a semisupervised ML approach. In this work, a novel convolutional neural network-based framework is trained with a few instances of a class to perform metric learning. The dataset is then converted into a graph signal, which is recovered using a recover algorithm (RA) in graphmore »Fourier transform. The proposed approach was evaluated on a Fashion dataset for accuracy and precision and performed significantly better than graph neural networks and other state-of-the-art methods« less
  4. ; ; ; ( , Proceedings of the AAAI Conference on Artificial Intelligence)
    Making predictions that are fair with regard to protected attributes (race, gender, age, etc.) has become an important requirement for classification algorithms. Existing techniques derive a fair model from sampled labeled data relying on the assumption that training and testing data are identically and independently drawn (iid) from the same distribution. In practice, distribution shift can and does occur between training and testing datasets as the characteristics of individuals interacting with the machine learning system change. We investigate fairness under covariate shift, a relaxation of the iid assumption in which the inputs or covariates change while the conditional label distribution remains the same. We seek fair decisions under these assumptions on target data with unknown labels. We propose an approach that obtains the predictor that is robust to the worst-case testing performance while satisfying target fairness requirements and matching statistical properties of the source data. We demonstrate the benefits of our approach on benchmark prediction tasks.
  5. ; ; ( , Proc. Of the 20th IEEE International Conference on Data Mining, November 17-20, 2020, Sorrento, Italy)
    In traditional graph learning tasks, such as node classification, learning is carried out in a closed-world setting where the number of classes and their training samples are provided to help train models, and the learning goal is to correctly classify unlabeled nodes into classes already known. In reality, due to limited labeling capability and dynamic evolving of networks, some nodes in the networks may not belong to any existing/seen classes, and therefore cannot be correctly classified by closed-world learning algorithms. In this paper, we propose a new open-world graph learning paradigm, where the learning goal is to not only classify nodes belonging to seen classes into correct groups, but also classify nodes not belonging to existing classes to an unseen class. The essential challenge of the openworld graph learning is that (1) unseen class has no labeled samples, and may exist in an arbitrary form different from existing seen classes; and (2) both graph feature learning and prediction should differentiate whether a node may belong to an existing/seen class or an unseen class. To tackle the challenges, we propose an uncertain node representation learning approach, using constrained variational graph autoencoder networks, where the label loss and class uncertainty loss constraintsmore »are used to ensure that the node representation learning are sensitive to unseen class. As a result, node embedding features are denoted by distributions, instead of deterministic feature vectors. By using a sampling process to generate multiple versions of feature vectors, we are able to test the certainty of a node belonging to seen classes, and automatically determine a threshold to reject nodes not belonging to seen classes as unseen class nodes. Experiments on real-world networks demonstrate the algorithm performance, comparing to baselines. Case studies and ablation analysis also show the rationale of our design for open-world graph learning.« less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email