Title: Discriminative Topic Mining via Category-Name Guided Text Embedding
Mining a set of meaningful and distinctive topics automatically
from massive text corpora has broad applications. Existing topic
models, however, typically work in a purely unsupervised way,
which often generate topics that do not fit users’ particular needs
and yield suboptimal performance on downstream tasks. We propose
a new task, discriminative topic mining, which leverages a set
of user-provided category names to mine discriminative topics from
text corpora. This new task not only helps a user understand clearly
and distinctively the topics he/she is most interested in, but also
benefits directly keyword-driven classification tasks. We develop
CatE, a novel category-name guided text embedding method for discriminative
topic mining, which effectively leverages minimal user
guidance to learn a discriminative embedding space and discover
category representative terms in an iterative manner. We conduct
a comprehensive set of experiments to show that CatE mines highquality
set of topics guided by category names only, and benefits a
variety of downstream applications including weakly-supervised
classification and lexical entailment direction identification. more »« less
Meng, Yu; Huang, Jiaxin; Zhang, Yu; Han, Jiawei(
, KDD'21:The 27th {ACM} {SIGKDD} Conference on Knowledge Discovery and Data Mining, August 14-18, 2021)
null
(Ed.)
Recent years have witnessed the enormous success of text representation
learning in a wide range of text mining tasks. Earlier
word embedding learning approaches represent words as fixed
low-dimensional vectors to capture their semantics. The word embeddings
so learned are used as the input features of task-specific
models. Recently, pre-trained language models (PLMs), which learn
universal language representations via pre-training Transformer-based
neural models on large-scale text corpora, have revolutionized
the natural language processing (NLP) field. Such pre-trained
representations encode generic linguistic features that can be transferred
to almost any text-related applications. PLMs outperform
previous task-specific models in many applications as they only
need to be fine-tuned on the target corpus instead of being trained
from scratch.
In this tutorial, we introduce recent advances in pre-trained text
embeddings and language models, as well as their applications to a
wide range of text mining tasks. Specifically, we first overview a
set of recently developed self-supervised and weakly-supervised
text embedding methods and pre-trained language models that
serve as the fundamentals for downstream tasks. We then present
several new methods based on pre-trained text embeddings and
language models for various text mining applications such as topic
discovery and text classification. We focus on methods that are
weakly-supervised, domain-independent, language-agnostic, effective
and scalable for mining and discovering structured knowledge
from large-scale text corpora. Finally, we demonstrate with real world
datasets how pre-trained text representations help mitigate
the human annotation burden and facilitate automatic, accurate
and efficient text analyses.
Balepur, Nishant; Agarwal, Shivam; Venkat Ramanan, Karthik; Yoon, Susik; Yang, Diyi; Han, Jiawei(
, Association for Computational Linguistics)
Dynamic topic models (DTMs) analyze text streams to capture the evolution of topics. Despite their popularity, existing DTMs are either fully supervised, requiring expensive human annotations, or fully unsupervised, generating topic evolutions that often do not cater to a user’s needs. Further, the topic evolutions produced by DTMs tend to contain generic terms that are not indicative of their designated time steps. To address these issues, we propose the task of discriminative dynamic topic discovery. This task aims to discover topic evolutions from temporal corpora that distinctly align with a set of user-provided category names and uniquely capture topics at each time step. We solve this task by developing DynaMiTE, a framework that ensembles semantic similarity, category indicative, and time indicative scores to produce informative topic evolutions. Through experiments on three diverse datasets, including the use of a newly-designed human evaluation experiment, we demonstrate that DynaMiTE is a practical and efficient framework for helping users discover high-quality topic evolutions suited to their interests.
Zhang, Yu; Chen, Xiusi; Meng, Yu; Han, Jiawei(
, WSDM'21, The Fourteenth ACM International Conference on Web Search and Data Mining, March 2021)
null
(Ed.)
Categorizing documents into a given label hierarchy is intuitively appealing due to the ubiquity of hierarchical topic structures in massive text corpora. Although related studies have achieved satisfying performance in fully supervised hierarchical document classification, they usually require massive human-annotated training data and only utilize text information. However, in many domains, (1) annotations are quite expensive where very few training samples can be acquired; (2) documents are accompanied by metadata information. Hence, this paper studies how to integrate the label hierarchy, metadata, and text signals for document categorization under weak supervision. We develop HiMeCat, an embedding-based generative framework for our task. Specifically, we propose a novel joint representation learning module that allows simultaneous modeling of category dependencies, metadata information and textual semantics, and we introduce a data augmentation module that hierarchically synthesizes training documents to complement
the original, small-scale training set. Our experiments demonstrate a consistent improvement of HiMeCat over competitive baselines and validate the contribution of our representation learning and data augmentation modules.
Wevodau, Z.; Doshna, B.; Jhala, N.; Akhtar, I.; Obeid, I.; Picone, J.(
, 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.
Huang, Jiaxin; Meng, Yu; Guo, Fang; Ji, Heng; Han, Jiawei(
, EMNLP'20: 2020 Conf. on Empirical Methods in Natural Language Processing, Nov. 2020)
null
(Ed.)
Aspect-based sentiment analysis of review texts is of great value for understanding user feedback in a fine-grained manner. It has in general two sub-tasks: (i) extracting aspects from each review, and (ii) classifying aspect-based reviews by sentiment polarity. In this pa-per, we propose a weakly-supervised approach for aspect-based sentiment analysis, which uses only a few keywords describing each aspect/sentiment without using any labeled examples. Existing methods are either designed only for one of the sub-tasks, neglecting the benefit of coupling both, or are based on topic models that may contain overlapping concepts. We propose to first learn sentiment, aspectjoint topic embeddings in the word embedding space by imposing regularizations to encourage topic distinctiveness, and then use neural models to generalize the word-level discriminative information by pre-training the classifiers with embedding-based predictions and self-training them on unlabeled data. Our comprehensive performance analysis shows that our method generates quality joint topics and outperforms the baselines significantly (7.4%and 5.1% F1-score gain on average for aspect and sentiment classification respectively) on benchmark datasets.
@article{osti_10160118,
place = {Country unknown/Code not available},
title = {Discriminative Topic Mining via Category-Name Guided Text Embedding},
url = {https://par.nsf.gov/biblio/10160118},
DOI = {10.1145/3366423.3380278},
abstractNote = {Mining a set of meaningful and distinctive topics automatically from massive text corpora has broad applications. Existing topic models, however, typically work in a purely unsupervised way, which often generate topics that do not fit users’ particular needs and yield suboptimal performance on downstream tasks. We propose a new task, discriminative topic mining, which leverages a set of user-provided category names to mine discriminative topics from text corpora. This new task not only helps a user understand clearly and distinctively the topics he/she is most interested in, but also benefits directly keyword-driven classification tasks. We develop CatE, a novel category-name guided text embedding method for discriminative topic mining, which effectively leverages minimal user guidance to learn a discriminative embedding space and discover category representative terms in an iterative manner. We conduct a comprehensive set of experiments to show that CatE mines highquality set of topics guided by category names only, and benefits a variety of downstream applications including weakly-supervised classification and lexical entailment direction identification.},
journal = {WWW '20: The Web Conference 2020},
volume = {1},
number = {1},
author = {Meng, Yu and Huang, Jiaxin and Wang, Guangyuan and Wang, Zihan and Zhang, Chao and Zhang, Yu and Han, Jiawei},
}
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