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1. Understanding and Mitigating Bias in Online Health Search

   https://doi.org/10.1145/3404835.3462930  

   Hashavit, Anat ; Wang, Hongning ; Lin, Raz ; Stern, Tamar ; Kraus, Sarit ( July 2021 , Proceedings of the 44th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR '21))

   null (Ed.)

   Search engines are perceived as a reliable source for general information needs. However, finding the answer to medical questions using search engines can be challenging for an ordinary user. Content can be biased and results may present different opinions. In addition, interpreting medically related content can be difficult for users with no medical background. All of these can lead users to incorrect conclusions regarding health related questions. In this work we address this problem from two perspectives. First, to gain insight on users' ability to correctly answer medical questions using search engines, we conduct a comprehensive user study. We show that for questions regarding medical treatment effectiveness, participants struggle to find the correct answer and are prone to overestimating treatment effectiveness. We analyze participants' demographic traits according to age and education level and show that this problem persists in all demographic groups. We then propose a semi-automatic machine learning approach to find the correct answer to queries on medical treatment effectiveness as it is viewed by the medical community. The model relies on the opinions presented in medical papers related to the queries, as well as features representing their impact. We show that, compared to human behaviour, our method is less prone to bias. We compare various configurations of our inference model and a baseline method that determines treatment effectiveness based solely on the opinion of medical papers. The results bolster our confidence that our approach can pave the way to developing automatic bias-free tools that can help mediate complex health related content to users. 

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2. WeaQA: Weak Supervision via Captions for Visual Question Answering

   https://doi.org/10.18653/v1/2021.findings-acl.302  

   Banerjee, Pratyay ; Gokhale, Tejas ; Yang, Yezhou ; Baral, Chitta ( January 2021 , Findings of the Association for Computational Linguistics: ACL-IJCNLP 2021)

   Zong, Chengqing ; Xia, Fei ; Li, Wenjie ; Navigli, Roberto (Ed.)

   Methodologies for training visual question answering (VQA) models assume the availability of datasets with human-annotated ImageQuestion-Answer (I-Q-A) triplets. This has led to heavy reliance on datasets and a lack of generalization to new types of questions and scenes. Linguistic priors along with biases and errors due to annotator subjectivity have been shown to percolate into VQA models trained on such samples. We study whether models can be trained without any human-annotated Q-A pairs, but only with images and their associated textual descriptions or captions. We present a method to train models with synthetic Q-A pairs generated procedurally from captions. Additionally, we demonstrate the efficacy of spatial-pyramid image patches as a simple but effective alternative to dense and costly object bounding box annotations used in existing VQA models. Our experiments on three VQA benchmarks demonstrate the efficacy of this weakly-supervised approach, especially on the VQA-CP challenge, which tests performance under changing linguistic priors. 

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3. Visual Query Answering by Entity-Attribute Graph Matching and Reasoning

   Xiong, Peixi ; Zhan, Huayi ; Wang, Xin ; Shinha, Baivab ; Wu, Ying ( June 2019 , Proc. IEEE/CVF Conf. on Computer Vision and Pattern Recognition)

   Visual Query Answering (VQA) is of great significance in offering people convenience: one can raise a question for details of objects, or high-level understanding about the scene, over an image. This paper proposes a novel method to address the VQA problem. In contrast to prior works, our method that targets single scene VQA, replies on graph-based techniques and involves reasoning. In a nutshell, our approach is centered on three graphs. The first graph, referred to as inference graph GI , is constructed via learning over labeled data. The other two graphs, referred to as query graph Q and entity-attribute graph GEA, are generated from natural language query Qnl and image Img, that are issued from users, respectively. As GEA often does not take sufficient information to answer Q, we develop techniques to infer missing information of GEA with GI . Based on GEA and Q, we provide techniques to find matches of Q in GEA, as the answer of Qnl in Img. Unlike commonly used VQA methods that are based on end-to-end neural networks, our graph-based method shows well-designed reasoning capability, and thus is highly interpretable. We also create a dataset on soccer match (Soccer-VQA) with rich annotations. The experimental results show that our approach outperforms the state-of-the-art method and has high potential for future investigation. 

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4. VQA-LOL: Visual Question Answering Under the Lens of Logic

   https://doi.org/10.1007/978-3-030-58589-1  

   Gokhale, T. ; Banerjee, P. ; Baral, C ; Yang, Y. ( November 2020 , ECCV 2020: Computer Vision – ECCV 2020)

   null (Ed.)

   Logical connectives and their implications on the meaning of a natural language sentence are a fundamental aspect of understanding. In this paper, we investigate whether visual question answering (VQA) systems trained to answer a question about an image, are able to answer the logical composition of multiple such questions. When put under this Lens of Logic, state-of-the-art VQA models have difficulty in correctly answering these logically composed questions. We construct an augmentation of the VQA dataset as a benchmark, with questions containing logical compositions and linguistic transformations (negation, disjunction, conjunction, and antonyms). We propose our Lens of Logic (LOL) model which uses question-attention and logic-attention to understand logical connectives in the question, and a novel Fréchet-Compatibility Loss, which ensures that the answers of the component questions and the composed question are consistent with the inferred logical operation. Our model shows substantial improvement in learning logical compositions while retaining performance on VQA. We suggest this work as a move towards robustness by embedding logical connectives in visual understanding. 

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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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