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1. Do Attention Heads in BERT Track Syntactic Dependencies?

   no surname), Phu Mon ; Phang, Jason ; Bordia, Shikha ; Bowman, Samuel R. ( January 2019 , NY Academy of Sciences NLP, Dialog, and Speech Workshop)

   We investigate the extent to which individual attention heads in pretrained transformer language models, such as BERT and RoBERTa, implicitly capture syntactic dependency relations. We employ two methods---taking the maximum attention weight and computing the maximum spanning tree---to extract implicit dependency relations from the attention weights of each layer/head, and compare them to the ground-truth Universal Dependency (UD) trees. We show that, for some UD relation types, there exist heads that can recover the dependency type significantly better than baselines on parsed English text, suggesting that some self-attention heads act as a proxy for syntactic structure. We also analyze BERT fine-tuned on two datasets---the syntax-oriented CoLA and the semantics-oriented MNLI---to investigate whether fine-tuning affects the patterns of their self-attention, but we do not observe substantial differences in the overall dependency relations extracted using our methods. Our results suggest that these models have some specialist attention heads that track individual dependency types, but no generalist head that performs holistic parsing significantly better than a trivial baseline, and that analyzing attention weights directly may not reveal much of the syntactic knowledge that BERT-style models are known to learn.
2. An Empirical Study of Pre-trained Transformers for Arabic Information Extraction

   https://doi.org/10.18653/v1/2020.emnlp-main.382  

   Lan, Wuwei ; Chen, Yang ; Xu, Wei ; Ritter, Alan ( January 2020 , Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP))

   Multilingual pre-trained Transformers, such as mBERT (Devlin et al., 2019) and XLM-RoBERTa (Conneau et al., 2020a), have been shown to enable effective cross-lingual zero-shot transfer. However, their performance on Arabic information extraction (IE) tasks is not very well studied. In this paper, we pre-train a customized bilingual BERT, dubbed GigaBERT, that is designed specifically for Arabic NLP and English-to-Arabic zero-shot transfer learning. We study GigaBERT’s effectiveness on zero-short transfer across four IE tasks: named entity recognition, part-of-speech tagging, argument role labeling, and relation extraction. Our best model significantly outperforms mBERT, XLM-RoBERTa, and AraBERT (Antoun et al., 2020) in both the supervised and zero-shot transfer settings. We have made our pre-trained models publicly available at: https://github.com/lanwuwei/GigaBERT.
3. 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 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
4. Predicting Human Judgments of Relational Similarity: A Comparison of Computational Models Based on Vector Representations of Meaning

   Snefjella, B. ; Ichien, N. ; Holyoak, K. J. ; Lu, H. ( January 2022 , Proceedings of the 44th Annual Meeting of the Cognitive Science Society)

   Computational models of verbal analogy and relational similarity judgments can employ different types of vector representations of word meanings (embeddings) generated by machine-learning algorithms. An important question is whether human-like relational processing depends on explicit representations of relations (i.e., representations separable from those of the concepts being related), or whether implicit relation representations suffice. Earlier machine-learning models produced static embeddings for individual words, identical across all contexts. However, more recent Large Language Models (LLMs), which use transformer architectures applied to much larger training corpora, are able to produce contextualized embeddings that have the potential to capture implicit knowledge of semantic relations. Here we compare multiple models based on different types of embeddings to human data concerning judgments of relational similarity and solutions of verbal analogy problems. For two datasets, a model that learns explicit representations of relations, Bayesian Analogy with Relational Transformations (BART), captured human performance more successfully than either a model using static embeddings (Word2vec) or models using contextualized embeddings created by LLMs (BERT, RoBERTa, and GPT-2). These findings support the proposal that human thinking depends on representations that separate relations from the concepts they relate.
5. Towards Improving Open Student Answer Assessment using Pretrained Transformers

   https://doi.org/10.32473/flairs.v34i1.128483  

   Ait Khayi, Nisrine ; Rus, Vasile ; Tamang, Lasang ( May 2021 , The International FLAIRS Conference Proceedings)

   The transfer learning pretraining-finetuning  paradigm has revolutionized the natural language processing field yielding state-of the art results in  several subfields such as text classification and question answering. However, little work has been done investigating pretrained language models for the  open student answer assessment task. In this paper, we fine tune pretrained T5, BERT, RoBERTa, DistilBERT, ALBERT and XLNet models on the DT-Grade dataset which contains freely generated (or open) student answers together with judgment of their correctness. The experimental results demonstrated the effectiveness of these models based on the transfer learning pretraining-finetuning paradigm for open student answer assessment. An improvement of 8%-15% in accuracy was obtained over previous methods. Particularly, a T5 based method led to state-of-the-art results with an accuracy and F1 score of 0.88.