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1. Explaining patterns of fusion in morphological paradigms using the memory-surprisal tradeoff

   Rathi, N. ( January 2022 , Proceedings of the 44th Annual Conference of the Cognitive Science Society)

   J. Culbertson, A. Perfors (Ed.)

   Languages often express grammatical information through inflectional morphology, in which grammatical features are grouped into strings of morphemes. In this work, we propose that cross-linguistic generalizations about morphological fusion, in which multiple features are expressed through one morpheme, can be explained in part by optimization of processing efficiency, as formalized using the memory--surprisal tradeoff of Hahn et al. (2021). We show in a toy setting that fusion of highly informative neighboring morphemes can lead to greater processing efficiency under our processing model. Next, based on paradigm and frequency data from four languages, we consider both total fusion and gradable fusion using empirical measures developed by Rathi et al. (2021), and find that the degree of fusion is predicted by closeness of optimal morpheme ordering as determined by optimization of processing efficiency. Finally, we show that optimization of processing efficiency can successfully predict typological patterns involving suppletion. 

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2. Surface Statistics of an Unknown Language Indicate How to Parse It

   https://doi.org/10.1162/tacl_a_00248  

   Wang, Dingquan ; Eisner, Jason ( December 2018 , Transactions of the Association for Computational Linguistics)

   We introduce a novel framework for delexicalized dependency parsing in a new language. We show that useful features of the target language can be extracted automatically from an unparsed corpus, which consists only of gold part-of-speech (POS) sequences. Providing these features to our neural parser enables it to parse sequences like those in the corpus. Strikingly, our system has no supervision in the target language. Rather, it is a multilingual system that is trained end-to-end on a variety of other languages, so it learns a feature extractor that works well. We show experimentally across multiple languages: (1) Features computed from the unparsed corpus improve parsing accuracy. (2) Including thousands of synthetic languages in the training yields further improvement. (3) Despite being computed from unparsed corpora, our learned task-specific features beat previous work’s interpretable typological features that require parsed corpora or expert categorization of the language. Our best method improved attachment scores on held-out test languages by an average of 5.6 percentage points over past work that does not inspect the unparsed data (McDonald et al., 2011), and by 20.7 points over past “grammar induction” work that does not use training languages (Naseem et al., 2010). 

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3. Neural Polysynthetic Language Modelling

   Schwartz, Lane ; Tyers, Francis ; Levin, Lori ; Kirov, Christo ; Littell, Patrick ; Lo, Chi-kiu ; Prud'hommeaux, Emily ; Park, Hyunji Hayley ; Steimel, Kenneth ; Knowles, Rebecca ; et al ( May 2020 , Final Report of the Frederick Jelinek Memorial Summer Workshop)

   null (Ed.)

   Many techniques in modern computational linguistics and natural language processing (NLP) make the assumption that approaches that work well on English and other widely used European (and sometimes Asian) languages are “language agnostic” – that is that they will also work across the typologically diverse languages of the world. In high-resource languages, especially those that are analytic rather than synthetic, a common approach is to treat morphologically-distinct variants of a common root (such as dog and dogs) as completely independent word types. Doing so relies on two main assumptions: that there exist a limited number of morphological inflections for any given root, and that most or all of those variants will appear in a large enough corpus (conditioned on assumptions about domain, etc.) so that the model can adequately learn statistics about each variant. Approaches like stemming, lemmatization, morphological analysis, subword segmentation, or other normalization techniques are frequently used when either of those assumptions are likely to be violated, particularly in the case of synthetic languages like Czech and Russian that have more inflectional morphology than English. Within the NLP literature, agglutinative languages like Finnish and Turkish are commonly held up as extreme examples of morphological complexity that challenge common modelling assumptions. Yet, when considering all of the world’s languages, Finnish and Turkish are closer to the average case in terms of synthesis. When we consider polysynthetic languages (those at the extreme of morphological complexity), even approaches like stemming, lemmatization, or subword modelling may not suffice. These languages have very high numbers of hapax legomena (words appearing only once in a corpus), underscoring the need for appropriate morphological handling of words, without which there is no hope for a model to capture enough statistical information about those words. Moreover, many of these languages have only very small text corpora, substantially magnifying these challenges. To this end, we examine the current state-of-the-art in language modelling, machine translation, and predictive text completion in the context of four polysynthetic languages: Guaraní, St. Lawrence Island Yupik, Central Alaskan Yup’ik, and Inuktitut. We have a particular focus on Inuit-Yupik, a highly challenging family of endangered polysynthetic languages that ranges geographically from Greenland through northern Canada and Alaska to far eastern Russia. The languages in this family are extraordinarily challenging from a computational perspective, with pervasive use of derivational morphemes in addition to rich sets of inflectional suffixes and phonological challenges at morpheme boundaries. Finally, we propose a novel framework for language modelling that combines knowledge representations from finite-state morphological analyzers with Tensor Product Representations (Smolensky, 1990) in order to enable successful neural language models capable of handling the full linguistic variety of typologically variant languages. 

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4. Neural Polysynthetic Language Modelling

   Schwartz, Lane ; Tyers, Francis ; Levin, Lori ; Kirov, Christo ; Littell, Patrick ; Lo, Chi-kiu ; Prud'hommeaux, Emily ; Park, Hyunji Hayley ; Steimel, Kenneth ; Knowles, Rebecca ; et al ( May 2020 , ArXivorg)

   Many techniques in modern computational linguistics and natural language processing (NLP) make the assumption that approaches that work well on English and other widely used European (and sometimes Asian) languages are “language agnostic” – that is that they will also work across the typologically diverse languages of the world. In high-resource languages, especially those that are analytic rather than synthetic, a common approach is to treat morphologically-distinct variants of a common root (such as dog and dogs) as completely independent word types. Doing so relies on two main assumptions: that there exist a limited number of morphological inflections for any given root, and that most or all of those variants will appear in a large enough corpus (conditioned on assumptions about domain, etc.) so that the model can adequately learn statistics about each variant. Approaches like stemming, lemmatization, morphological analysis, subword segmentation, or other normalization techniques are frequently used when either of those assumptions are likely to be violated, particularly in the case of synthetic languages like Czech and Russian that have more inflectional morphology than English. Within the NLP literature, agglutinative languages like Finnish and Turkish are commonly held up as extreme examples of morphological complexity that challenge common modelling assumptions. Yet, when considering all of the world’s languages, Finnish and Turkish are closer to the average case in terms of synthesis. When we consider polysynthetic languages (those at the extreme of morphological complexity), even approaches like stemming, lemmatization, or subword modelling may not suffice. These languages have very high numbers of hapax legomena (words appearing only once in a corpus), underscoring the need for appropriate morphological handling of words, without which there is no hope for a model to capture enough statistical information about those words. Moreover, many of these languages have only very small text corpora, substantially magnifying these challenges. To this end, we examine the current state-of-the-art in language modelling, machine translation, and predictive text completion in the context of four polysynthetic languages: Guaraní, St. Lawrence Island Yupik, Central Alaskan Yup’ik, and Inuktitut. We have a particular focus on Inuit-Yupik, a highly challenging family of endangered polysynthetic languages that ranges geographically from Greenland through northern Canada and Alaska to far eastern Russia. The languages in this family are extraordinarily challenging from a computational perspective, with pervasive use of derivational morphemes in addition to rich sets of inflectional suffixes and phonological challenges at morpheme boundaries. Finally, we propose a novel framework for language modelling that combines knowledge representations from finite-state morphological analyzers with Tensor Product Representations (Smolensky, 1990) in order to enable successful neural language models capable of handling the full linguistic variety of typologically variant languages. 

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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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