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1. Guiding supervised topic modeling for content based tag recommendation

   https://doi.org/10.1016/j.neucom.2018.07.011  

   Yu, Yong ; Xi, Shengqu ; Yao, Yuan ; Xu, Feng ; Tong, Hanghang ; Lu, Jian ( January 2018 , Neurocomputing)

   Automatically recommending suitable tags for online content is a necessary task for better information organization and retrieval. In this article, we propose a generative model SimWord for the tag recommendation problem on textual content. The key observation of our model is that the tags and their relevant/similar words may have appeared in the corresponding content. In particular, we first empirically verify this observation in real data sets, and then design a supervised topic model which is guided by the above observation for tag recommendation. Experimental evaluations demonstrate that the proposed method outperforms several existing methods in terms of recommendation accuracy. 

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2. 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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3. Hashtag Recommendation for Photo Sharing Services

   https://doi.org/10.1609/aaai.v33i01.33015805  

   Zhang, Suwei ; Yao, Yuan ; Xu, Feng ; Tong, Hanghang ; Yan, Xiaohui ; Lu, Jian ( July 2019 , Proceedings of the AAAI Conference on Artificial Intelligence)

   Hashtags can greatly facilitate content navigation and improve user engagement in social media. Meaningful as it might be, recommending hashtags for photo sharing services such as Instagram and Pinterest remains a daunting task due to the following two reasons. On the endogenous side, posts in photo sharing services often contain both images and text, which are likely to be correlated with each other. Therefore, it is crucial to coherently model both image and text as well as the interaction between them. On the exogenous side, hashtags are generated by users and different users might come up with different tags for similar posts, due to their different preference and/or community effect. Therefore, it is highly desirable to characterize the users’ tagging habits. In this paper, we propose an integral and effective hashtag recommendation approach for photo sharing services. In particular, the proposed approach considers both the endogenous and exogenous effects by a content modeling module and a habit modeling module, respectively. For the content modeling module, we adopt the parallel co-attention mechanism to coherently model both image and text as well as the interaction between them; for the habit modeling module, we introduce an external memory unit to characterize the historical tagging habit of each user. The overall hashtag recommendations are generated on the basis of both the post features from the content modeling module and the habit influences from the habit modeling module. We evaluate the proposed approach on real Instagram data. The experimental results demonstrate that the proposed approach significantly outperforms the state-of-theart methods in terms of recommendation accuracy, and that both content modeling and habit modeling contribute significantly to the overall recommendation accuracy. 

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4. Contrastive Trajectory Learning for Tour Recommendation

   https://doi.org/10.1145/3462331  

   Zhou, Fan ; Wang, Pengyu ; Xu, Xovee ; Tai, Wenxin ; Trajcevski, Goce ( February 2022 , ACM Transactions on Intelligent Systems and Technology)

   The main objective of Personalized Tour Recommendation (PTR) is to generate a sequence of point-of-interest (POIs) for a particular tourist, according to the user-specific constraints such as duration time, start and end points, the number of attractions planned to visit, and so on. Previous PTR solutions are based on either heuristics for solving the orienteering problem to maximize a global reward with a specified budget or approaches attempting to learn user visiting preferences and transition patterns with the stochastic process or recurrent neural networks. However, existing learning methodologies rely on historical trips to train the model and use the next visited POI as the supervised signal, which may not fully capture the coherence of preferences and thus recommend similar trips to different users, primarily due to the data sparsity problem and long-tailed distribution of POI popularity. This work presents a novel tour recommendation model by distilling knowledge and supervision signals from the trips in a self-supervised manner. We propose Contrastive Trajectory Learning for Tour Recommendation (CTLTR), which utilizes the intrinsic POI dependencies and traveling intent to discover extra knowledge and augments the sparse data via pre-training auxiliary self-supervised objectives. CTLTR provides a principled way to characterize the inherent data correlations while tackling the implicit feedback and weak supervision problems by learning robust representations applicable for tour planning. We introduce a hierarchical recurrent encoder-decoder to identify tourists’ intentions and use the contrastive loss to discover subsequence semantics and their sequential patterns through maximizing the mutual information. Additionally, we observe that a data augmentation step as the preliminary of contrastive learning can solve the overfitting issue resulting from data sparsity. We conduct extensive experiments on a range of real-world datasets and demonstrate that our model can significantly improve the recommendation performance over the state-of-the-art baselines in terms of both recommendation accuracy and visiting orders. 

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5. TaxoClass: Hierarchical Multi-Label Text Classification Using Only Class Names

   https://doi.org/10.18653/v1/2021.naacl-main.335  

   Shen, Jiaming ; Qiu, Wenda ; Meng, Yu ; Shang, Jingbo ; Ren, Xiang ; Han, Jiawei ( June 2021 , NAAC'21: Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, {NAACL-HLT} 2021)

   null (Ed.)

   Hierarchical multi-label text classification (HMTC) aims to tag each document with a set of classes from a class hierarchy. Most existing HMTC methods train classifiers using massive human-labeled documents, which are often too costly to obtain in real-world applications. In this paper, we explore to conduct HMTC based on only class surface names as supervision signals. We observe that to perform HMTC, human experts typically first pinpoint a few most essential classes for the document as its “core classes”, and then check core classes’ ancestor classes to ensure the coverage. To mimic human experts, we propose a novel HMTC framework, named TaxoClass. Specifically, TaxoClass (1) calculates document-class similarities using a textual entailment model, (2) identifies a document’s core classes and utilizes confident core classes to train a taxonomyenhanced classifier, and (3) generalizes the classifier via multi-label self-training. Our experiments on two challenging datasets show TaxoClass can achieve around 0.71 Example- F1 using only class names, outperforming the best previous method by 25%. 

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