skip to main content

Explore Research Products in the NSF-PAR

Title: Deep Active Learning via Open-Set Recognition
In many applications, data is easy to acquire but expensive and time-consuming to label, prominent examples include medical imaging and NLP. This disparity has only grown in recent years as our ability to collect data improves. Under these constraints, it makes sense to select only the most informative instances from the unlabeled pool and request an oracle (e.g., a human expert) to provide labels for those samples. The goal of active learning is to infer the informativeness of unlabeled samples so as to minimize the number of requests to the oracle. Here, we formulate active learning as an open-set recognition problem. In this paradigm, only some of the inputs belong to known classes; the classifier must identify the rest as unknown . More specifically, we leverage variational neural networks (VNNs), which produce high-confidence (i.e., low-entropy) predictions only for inputs that closely resemble the training data. We use the inverse of this confidence measure to select the samples that the oracle should label. Intuitively, unlabeled samples that the VNN is uncertain about contain features that the network has not been exposed to; thus they are more informative for future training. We carried out an extensive evaluation of our novel, probabilistic formulation of active learning, achieving state-of-the-art results on MNIST, CIFAR-10, CIFAR-100, and FashionMNIST. Additionally, unlike current active learning methods, our algorithm can learn even in the presence of out-of-distribution outliers. As our experiments show, when the unlabeled pool consists of a mixture of samples from multiple datasets, our approach can automatically distinguish between samples from seen vs. unseen datasets. Overall, our results show that high-quality uncertainty measures are key for pool-based active learning.  more » « less
Award ID(s):
1849946
NSF-PAR ID:
10340601
Author(s) / Creator(s):
; ;
Date Published:
Journal Name:
Frontiers in Artificial Intelligence
Volume:
5
ISSN:
2624-8212
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ( , Advances in neural information processing systems)
    Active learning has proven to be useful for minimizing labeling costs by selecting the most informative samples. However, existing active learning methods do not work well in realistic scenarios such as imbalance or rare classes, out-of-distribution data in the unlabeled set, and redundancy. In this work, we propose SIMILAR (Submodular Information Measures based actIve LeARning), a unified active learning framework using recently proposed submodular information measures (SIM) as acquisition functions. We argue that SIMILAR not only works in standard active learning, but also easily extends to the realistic settings considered above and acts as a one-stop solution for active learning that is scalable to large real-world datasets. Empirically, we show that SIMILAR significantly outperforms existing active learning algorithms by as much as ~5% - 18% in the case of rare classes and ~5% - 10% in the case of out-of-distribution data on several image classification tasks like CIFAR-10, MNIST, and ImageNet. SIMILAR is available as a part of the DISTIL toolkit: "this https URL". 
    more » « less
  2. ; ; ; ; ; ( , 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. 
    more » « less
  3. ; ; ; ; ; ; ; ( , Bioinformatics)
    Xu, Jinbo (Ed.)
    Abstract Motivation Cryo-Electron Tomography (cryo-ET) is a 3D bioimaging tool that visualizes the structural and spatial organization of macromolecules at a near-native state in single cells, which has broad applications in life science. However, the systematic structural recognition and recovery of macromolecules captured by cryo-ET are difficult due to high structural complexity and imaging limits. Deep learning-based subtomogram classification has played critical roles for such tasks. As supervised approaches, however, their performance relies on sufficient and laborious annotation on a large training dataset. Results To alleviate this major labeling burden, we proposed a Hybrid Active Learning (HAL) framework for querying subtomograms for labeling from a large unlabeled subtomogram pool. Firstly, HAL adopts uncertainty sampling to select the subtomograms that have the most uncertain predictions. This strategy enforces the model to be aware of the inductive bias during classification and subtomogram selection, which satisfies the discriminativeness principle in AL literature. Moreover, to mitigate the sampling bias caused by such strategy, a discriminator is introduced to judge if a certain subtomogram is labeled or unlabeled and subsequently the model queries the subtomogram that have higher probabilities to be unlabeled. Such query strategy encourages to match the data distribution between the labeled and unlabeled subtomogram samples, which essentially encodes the representativeness criterion into the subtomogram selection process. Additionally, HAL introduces a subset sampling strategy to improve the diversity of the query set, so that the information overlap is decreased between the queried batches and the algorithmic efficiency is improved. Our experiments on subtomogram classification tasks using both simulated and real data demonstrate that we can achieve comparable testing performance (on average only 3% accuracy drop) by using less than 30% of the labeled subtomograms, which shows a very promising result for subtomogram classification task with limited labeling resources. Availability and implementation https://github.com/xulabs/aitom. Supplementary information Supplementary data are available at Bioinformatics online. 
    more » « less
  4. ; ; ( , Proceedings of the Thirty-Ninth Conference on Uncertainty in Artificial Intelligence)
    Active learning is commonly used to train label-efficient models by adaptively selecting the most informative queries. However, most active learning strategies are designed to either learn a representation of the data (e.g., embedding or metric learning) or perform well on a task (e.g., classification) on the data. However, many machine learning tasks involve a combination of both representation learning and a task-specific goal. Motivated by this, we propose a novel unified query framework that can be applied to any problem in which a key component is learning a representation of the data that reflects similarity. Our approach builds on similarity or nearest neighbor (NN) queries which seek to select samples that result in improved embeddings. The queries consist of a reference and a set of objects, with an oracle selecting the object most similar (i.e., nearest) to the reference. In order to reduce the number of solicited queries, they are chosen adaptively according to an information theoretic criterion. We demonstrate the effectiveness of the proposed strategy on two tasks - active metric learning and active classification - using a variety of synthetic and real world datasets. In particular, we demonstrate that actively selected NN queries outperform recently developed active triplet selection methods in a deep metric learning setting. Further, we show that in classification, actively selecting class labels can be reformulated as a process of selecting the most informative NN query, allowing direct application of our method. 
    more » « less
  5. ; ( , Proceedings of the 31st Conference On Learning Theory)
    In this work, we show that for a nontrivial hypothesis class C, we can estimate the distance of a target function f to C (estimate the error rate of the best h∈C) using substantially fewer labeled examples than would be needed to actually {\em learn} a good h∈C. Specifically, we show that for the class C of unions of d intervals on the line, in the active learning setting in which we have access to a pool of unlabeled examples drawn from an arbitrary underlying distribution D, we can estimate the error rate of the best h∈C to an additive error ϵ with a number of label requests that is {\em independent of d} and depends only on ϵ. In particular, we make O((1/ϵ^6)log(1/ϵ)) label queries to an unlabeled pool of size O((d/ϵ^2)log(1/ϵ)). This task of estimating the distance of an unknown f to a given class C is called {\em tolerant testing} or {\em distance estimation} in the testing literature, usually studied in a membership query model and with respect to the uniform distribution. Our work extends that of Balcan et al. (2012) who solved the {\em non}-tolerant testing problem for this class (distinguishing the zero-error case from the case that the best hypothesis in the class has error greater than ϵ). We also consider the related problem of estimating the performance of a given learning algorithm A in this setting. That is, given a large pool of unlabeled examples drawn from distribution D, can we, from only a few label queries, estimate how well A would perform if the entire dataset were labeled and given as training data to A? We focus on k-Nearest Neighbor style algorithms, and also show how our results can be applied to the problem of hyperparameter tuning (selecting the best value of k for the given learning problem). 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email