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1. Recursive Rules With Aggregation: A Simple Unified Semantics

   https://doi.org/10.1007/978-3-030-93100-1_11  

   Liu, Yanhong A. ; Stoller, Scott D. ( January 2022 , Logical Foundations of Computer Science (LFCS 2022))

   Artemov, Sergei ; Nerode, Anil (Ed.)

   Complex reasoning problems are most clearly and easily specified using logical rules, but require recursive rules with aggregation such as counts and sums for practical applications. Unfortunately, the meaning of such rules has been a significant challenge, leading to many disagreeing semantics. This paper describes a unified semantics for recursive rules with aggregation, extending the unified founded semantics and constraint semantics for recursive rules with negation. The key idea is to support simple expression of the different assumptions underlying different semantics, and orthogonally interpret aggregation operations using their simple usual meaning. We present formal definition of the semantics, prove important properties of the semantics, and compare with prior semantics. In particular, we present an efficient inference over aggregation that gives precise answers to all examples we have studied from the literature. We also applied our semantics to a wide range of challenging examples, and performed experiments on the most challenging ones, all confirming our analyzed results. 

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2. Automatic Amortized Resource Analysis with Regular Recursive Types

   Jessie Grosen ; David M. Kahn ; Jan Hoffmann ( July 2023 , LICS '23: Proceedings of the 38th Annual ACM/IEEE Symposium on Logic in Computer Science)

   The goal of automatic resource bound analysis is to statically infer symbolic bounds on the resource consumption of the evaluation of a program. A longstanding challenge for automatic resource analysis is the inference of bounds that are functions of complex custom data structures. This article builds on type-based automatic amortized resource analysis (AARA) to address this challenge. AARA is based on the potential method of amortized analysis and reduces bound inference to standard type inference with additional linear constraint solving, even when deriving non-linear bounds. A key component of AARA is resource functions that generate the space of possible bounds for values of a given type while enjoying necessary closure properties. Existing work on AARA defined such functions for many data structures such as lists of lists but the question of whether such functions exist for arbitrary data structures remained open. This work answers this questions positively by uniformly constructing resource polynomials for algebraic data structures defined by regular recursive types. These functions are a generalization of all previously proposed polynomial resource functions and can be seen as a general notion of polynomials for values of a given recursive type. A resource type system for FPC, a core language with recursive types, demonstrates how resource polynomials can be integrated with AARA while preserving all benefits of past techniques. The article also proposes the use of new techniques useful for stating the rules of this type system and proving it sound. First, multivariate potential annotations are stated in terms of free semimodules, substantially abstracting details of the presentation of annotations and the proofs of their properties. Second, a logical relation giving semantic meaning to resource types enables a proof of soundness by a single induction on typing derivations. 

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3. Sia: Optimizing Queries using Learned Predicates

   Qi Zhou, Joy Arulraj ( January 2021 , SIGMOD record)

   Predicate-centric rules for rewriting queries is a key technique in optimizing queries. These include pushing down the predicate below the join and aggregation operators, or optimizing the order of evaluating predicates. However, many of these rules are only applicable when the predicate uses a certain set of columns. For example, to move the predicate below the join operator, the predicate must only use columns from one of the joined tables. By generating a predicate that satisfies these column constraints and preserves the semantics of the original query, the optimizer may leverage additional predicate-centric rules that were not applicable before. Researchers have proposed syntax-driven rewrite rules and machine learning algorithms for inferring such predicates. However, these techniques suffer from two limitations. First, they do not let the optimizer constrain the set of columns that may be used in the learned predicate. Second, machine learning algorithms do not guarantee that the learned predicate preserves semantics. In this paper, we present SIA, a system for learning predicates while being guided by counter-examples and a verification technique, that addresses these limitations. The key idea is to leverage satisfiability modulo theories to generate counter-examples and use them to iteratively learn a valid, optimal predicate. We formalize this problem by proving the key properties of synthesized predicates. We implement our approach in SIA and evaluate its efficacy and efficiency. We demonstrate that it synthesizes a larger set of valid predicates compared to prior approaches. On a collection of 200 queries derived from the TPC-H benchmark, SIA successfully rewrites 114 queries with learned predicates. 66 of these rewritten queries exhibit more than 2X speed up. 

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4. 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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5. A deep semantic matching approach for identifying relevant messages for social media analysis

   https://doi.org/10.1038/s41598-023-38761-y  

   Biggers, Frederick Brown ; Mohanty, Somya D. ; Manda, Prashanti ( July 2023 , Scientific Reports)

   There is a growing interest in using social media content for Natural Language Processing applications. However, it is not easy to computationally identify the most relevant set of tweets related to any specific event. Challenging semantics coupled with different ways for using natural language in social media make it difficult for retrieving the most relevant set of data from any social media outlet. This paper seeks to demonstrate a way to present the changing semantics of Twitter within the context of a crisis event, specifically tweets during Hurricane Irma. These methods can be used to identify the most relevant corpus of text for analysis in relevance to a specific incident such as a hurricane. Using an implementation of the Word2Vec method of Neural Network training mechanisms to create Word Embeddings, this paper will: discuss how the relative meaning of words changes as events unfold; present a mechanism for scoring tweets based upon dynamic, relative context relatedness; and show that similarity between words is not necessarily static. We present different methods for training the vector model in Word2Vec for identification of the most relevant tweets for any search query. The impact of tuning parameters such as Word Window Size, Minimum Word Frequency, Hidden Layer Dimensionality, and Negative Sampling on model performance was explored. The window containing the local maximum for AU_ROC for each parameter serves as a guide for other studies using the methods presented here for social media data analysis.

    

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