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  1. Book ; Online: Reinforcement Learning for Topic Models

    Costello, Jeremy / Reformat, Marek Z.

    2023  

    Abstract: We apply reinforcement learning techniques to topic modeling by replacing the variational autoencoder in ProdLDA with a continuous action space reinforcement learning policy. We train the system with a policy gradient algorithm REINFORCE. Additionally, ... ...

    Abstract We apply reinforcement learning techniques to topic modeling by replacing the variational autoencoder in ProdLDA with a continuous action space reinforcement learning policy. We train the system with a policy gradient algorithm REINFORCE. Additionally, we introduced several modifications: modernize the neural network architecture, weight the ELBO loss, use contextual embeddings, and monitor the learning process via computing topic diversity and coherence for each training step. Experiments are performed on 11 data sets. Our unsupervised model outperforms all other unsupervised models and performs on par with or better than most models using supervised labeling. Our model is outperformed on certain data sets by a model using supervised labeling and contrastive learning. We have also conducted an ablation study to provide empirical evidence of performance improvements from changes we made to ProdLDA and found that the reinforcement learning formulation boosts performance.

    Comment: 18 pages, 6 figures, Findings of ACL2023, code available at https://github.com/jeremy-costello/rl-for-topic-models
    Keywords Computer Science - Computation and Language ; Computer Science - Machine Learning
    Subject code 006
    Publishing date 2023-05-08
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Negated Complementary Commonsense using Large Language Models

    Rezaei, Navid / Reformat, Marek Z.

    2023  

    Abstract: Larger language models, such as GPT-3, have shown to be excellent in many tasks. However, we demonstrate that out-of-ordinary questions can throw the model off guard. This work focuses on finding answers to negated complementary questions in commonsense ... ...

    Abstract Larger language models, such as GPT-3, have shown to be excellent in many tasks. However, we demonstrate that out-of-ordinary questions can throw the model off guard. This work focuses on finding answers to negated complementary questions in commonsense scenarios. We illustrate how such questions adversely affect the model responses. We propose a model-agnostic methodology to improve the performance in negated complementary scenarios. Our method outperforms few-shot generation from GPT-3 (by more than 11 points) and, more importantly, highlights the significance of studying the response of large language models in negated complementary questions. The code, data, and experiments are available under: https://github.com/navidre/negated_complementary_commonsense.

    Comment: Appeared in Natural Language Reasoning and Structured Explanations Workshop (NLRSE) - ACL 2023
    Keywords Computer Science - Computation and Language ; Computer Science - Artificial Intelligence
    Subject code 401
    Publishing date 2023-07-13
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Applying Machine Learning and Point-Set Registration to Automatically Measure the Severity of Spinal Curvature on Radiographs.

    Wong, Jason / Reformat, Marek / Lou, Edmond

    IEEE journal of translational engineering in health and medicine

    2023  Volume 12, Page(s) 151–161

    Abstract: Objective: Measuring the severity of the lateral spinal curvature, or Cobb angle, is critical for monitoring and making treatment decisions for children with adolescent idiopathic scoliosis (AIS). However, manual measurement is time-consuming and ... ...

    Abstract Objective: Measuring the severity of the lateral spinal curvature, or Cobb angle, is critical for monitoring and making treatment decisions for children with adolescent idiopathic scoliosis (AIS). However, manual measurement is time-consuming and subject to human error. Therefore, clinicians seek an automated measurement method to streamline workflow and improve accuracy. This paper reports on a novel machine learning algorithm of cascaded convolutional neural networks (CNN) to measure the Cobb angle on spinal radiographs automatically.
    Methods: The developed method consisted of spinal column segmentation using a CNN, vertebra localization and segmentation using iterative vertebra body location coupled with another CNN, point-set registration to correct vertebra segmentations, and Cobb angle measurement using the final segmentations. Measurement performance was evaluated with the circular mean absolute error (CMAE) and percentage within clinical acceptance ([Formula: see text]) between automatic and manual measurements. Analysis was separated by curve severity to identify any potential systematic biases using independent samples Student's t-tests.
    Results: The method detected 346 of the 352 manually measured Cobb angles (98%), with a CMAE of 2.8° and 91% of measurements within the 5° clinical acceptance. No statistically significant differences were found between the CMAEs of mild ([Formula: see text]), moderate (25°-45°), and severe ([Formula: see text]) groups. The average measurement time per radiograph was 17.7±10.2s, improving upon the estimated average of 30s it takes an experienced rater to measure. Additionally, the algorithm outputs segmentations with the measurement, allowing clinicians to interpret measurement results.
    Discussion/conclusion: The developed method measured Cobb angles on radiographs automatically with high accuracy, quick measurement time, and interpretability, suggesting clinical feasibility.
    MeSH term(s) Adolescent ; Child ; Humans ; Spine/diagnostic imaging ; Scoliosis/diagnosis ; Radiography ; Kyphosis ; Algorithms
    Language English
    Publishing date 2023-11-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2696555-0
    ISSN 2168-2372 ; 2168-2372
    ISSN (online) 2168-2372
    ISSN 2168-2372
    DOI 10.1109/JTEHM.2023.3332618
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Super-Prompting

    Rezaei, Navid / Reformat, Marek Z.

    Utilizing Model-Independent Contextual Data to Reduce Data Annotation Required in Visual Commonsense Tasks

    2022  

    Abstract: Pre-trained language models have shown excellent results in few-shot learning scenarios using in-context learning. Although it is impressive, the size of language models can be prohibitive to make them usable in on-device applications, such as sensors or ...

    Abstract Pre-trained language models have shown excellent results in few-shot learning scenarios using in-context learning. Although it is impressive, the size of language models can be prohibitive to make them usable in on-device applications, such as sensors or smartphones. With smaller language models, task-specific data annotation is needed to fine-tune the language model for a specific purpose. However, data annotation can have a substantial financial and time burden for small research groups, startups, and even companies. In this paper, we analyze different prompt-based fine-tuning techniques to improve results on both language and multimodal causal transformer models. To evaluate our results, we use a dataset focusing on visual commonsense reasoning in time. Our results show that by simple model-agnostic prompt-based fine-tuning, comparable results can be reached by only using 35%-40% of the fine-tuning training dataset. The proposed approaches result in significant time and financial savings. As the proposed methods make minimal architectural assumptions, other researchers can use the results in their transformer models with minimal adaptations. We plan to release the source code freely to make it easier for the community to use and contribute to our work.
    Keywords Computer Science - Computation and Language ; Computer Science - Artificial Intelligence
    Subject code 004
    Publishing date 2022-04-25
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Leveraging Knowledge Graphs and Natural Language Processing for Automated Web Resource Labeling and Knowledge Mobilization in Neurodevelopmental Disorders: Development and Usability Study.

    Costello, Jeremy / Kaur, Manpreet / Reformat, Marek Z / Bolduc, Francois V

    Journal of medical Internet research

    2023  Volume 25, Page(s) e45268

    Abstract: Background: Patients and families need to be provided with trusted information more than ever with the abundance of online information. Several organizations aim to build databases that can be searched based on the needs of target groups. One such group ...

    Abstract Background: Patients and families need to be provided with trusted information more than ever with the abundance of online information. Several organizations aim to build databases that can be searched based on the needs of target groups. One such group is individuals with neurodevelopmental disorders (NDDs) and their families. NDDs affect up to 18% of the population and have major social and economic impacts. The current limitations in communicating information for individuals with NDDs include the absence of shared terminology and the lack of efficient labeling processes for web resources. Because of these limitations, health professionals, support groups, and families are unable to share, combine, and access resources.
    Objective: We aimed to develop a natural language-based pipeline to label resources by leveraging standard and free-text vocabularies obtained through text analysis, and then represent those resources as a weighted knowledge graph.
    Methods: Using a combination of experts and service/organization databases, we created a data set of web resources for NDDs. Text from these websites was scraped and collected into a corpus of textual data on NDDs. This corpus was used to construct a knowledge graph suitable for use by both experts and nonexperts. Named entity recognition, topic modeling, document classification, and location detection were used to extract knowledge from the corpus.
    Results: We developed a resource annotation pipeline using diverse natural language processing algorithms to annotate web resources and stored them in a structured knowledge graph. The graph contained 78,181 annotations obtained from the combination of standard terminologies and a free-text vocabulary obtained using topic modeling. An application of the constructed knowledge graph is a resource search interface using the ordered weighted averaging operator to rank resources based on a user query.
    Conclusions: We developed an automated labeling pipeline for web resources on NDDs. This work showcases how artificial intelligence-based methods, such as natural language processing and knowledge graphs for information representation, can enhance knowledge extraction and mobilization, and could be used in other fields of medicine.
    MeSH term(s) Humans ; Algorithms ; Artificial Intelligence ; Natural Language Processing ; Neurodevelopmental Disorders ; Pattern Recognition, Automated ; Knowledge Bases
    Language English
    Publishing date 2023-04-17
    Publishing country Canada
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2028830-X
    ISSN 1438-8871 ; 1438-8871
    ISSN (online) 1438-8871
    ISSN 1438-8871
    DOI 10.2196/45268
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Human intelligence-based metaverse for co-learning of students and smart machines.

    Lee, Chang-Shing / Wang, Mei-Hui / Reformat, Marek / Huang, Sheng-Hui

    Journal of ambient intelligence and humanized computing

    2023  Volume 14, Issue 6, Page(s) 7695–7718

    Abstract: This paper proposes ... ...

    Abstract This paper proposes a
    Language English
    Publishing date 2023-03-09
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2543187-0
    ISSN 1868-5145 ; 1868-5137
    ISSN (online) 1868-5145
    ISSN 1868-5137
    DOI 10.1007/s12652-023-04580-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Using machine learning to automatically measure axial vertebral rotation on radiographs in adolescents with idiopathic scoliosis.

    Logithasan, Veena / Wong, Jason / Reformat, Marek / Lou, Edmond

    Medical engineering & physics

    2022  Volume 107, Page(s) 103848

    Abstract: Adolescent idiopathic scoliosis is a 3D lateral spinal curvature coupled with axial vertebral rotation (AVR). Measuring AVR during clinic is important because it affects treatment options and predicts the risk of scoliosis progression. However, manual ... ...

    Abstract Adolescent idiopathic scoliosis is a 3D lateral spinal curvature coupled with axial vertebral rotation (AVR). Measuring AVR during clinic is important because it affects treatment options and predicts the risk of scoliosis progression. However, manual measurements are time consuming and have high inter-rater and intra-rater errors. This study aimed to develop a machine learning algorithm based on convolutional neural networks (CNNs) to automatically calculate AVR on posteroanterior radiographs using three different segmentations including spinal column, individual vertebra, and pedicles. Separate labeling and training processes were performed on each of the developed segmentation algorithms. The final machine learning software was tested on 221 vertebrae from 17 spinal radiographs. An experienced rater with over 25 years of experience measured the 221 vertebral rotations manually. By comparing the manual and the fully automatic measurements, 81% (178/221) of the automatic measurements were within the clinical acceptance error (±5°). The mean absolute difference and the standard deviation between the manual and automatic measurements was 4.3° ± 5.7°. Based on the Bland-Altman plot, the manual and automatic measurements had a strong correlation and no bias. The error did not relate to the severity of the rotation. This method is fully automatic, and the result is comparable to others.
    MeSH term(s) Adolescent ; Algorithms ; Humans ; Machine Learning ; Radiography ; Scoliosis/diagnostic imaging ; Spine/diagnostic imaging ; Thoracic Vertebrae
    Language English
    Publishing date 2022-07-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1181080-4
    ISSN 1873-4030 ; 1350-4533
    ISSN (online) 1873-4030
    ISSN 1350-4533
    DOI 10.1016/j.medengphy.2022.103848
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Convolutional Neural Network to Segment Laminae on 3D Ultrasound Spinal Images to Assist Cobb Angle Measurement.

    Wong, Jason / Reformat, Marek / Parent, Eric / Lou, Edmond

    Annals of biomedical engineering

    2022  Volume 50, Issue 4, Page(s) 401–412

    Abstract: A recent innovation in scoliosis monitoring is the use of ultrasonography, which provides true 3D information in one scan and does not emit ionizing radiation. Measuring the severity of scoliosis on ultrasonographs requires identifying lamina pairs on ... ...

    Abstract A recent innovation in scoliosis monitoring is the use of ultrasonography, which provides true 3D information in one scan and does not emit ionizing radiation. Measuring the severity of scoliosis on ultrasonographs requires identifying lamina pairs on the most tilted vertebrae, which is difficult and time-consuming. To expedite and automate measurement steps, this paper detailed an automatic convolutional neural network-based algorithm for identifying the laminae on 3D ultrasonographs. The predicted laminae were manually paired to measure the lateral spinal curvature on the coronal view, called the Cobb angle. In total, 130 spinal ultrasonographs of adolescents with idiopathic scoliosis recruited from a scoliosis clinic were selected, with 70 for training and 60 for testing. Data augmentation increased the effective training set size to 140 ultrasonographs. Semi-automatic Cobb measurements were compared to manual measurements on the same ultrasonographs. The semi-automatic measurements demonstrated good inter-method reliability (ICC
    MeSH term(s) Adolescent ; Humans ; Neural Networks, Computer ; Reproducibility of Results ; Scoliosis/diagnostic imaging ; Spine/diagnostic imaging ; Ultrasonography/methods
    Language English
    Publishing date 2022-02-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 185984-5
    ISSN 1573-9686 ; 0191-5649 ; 0090-6964
    ISSN (online) 1573-9686
    ISSN 0191-5649 ; 0090-6964
    DOI 10.1007/s10439-022-02925-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Conference proceedings: Featured topic issue: Best papers from SEKE 2014

    Reformat, Marek

    : [26th International Conference on Software Engineering and Knowledge Engineering that took place in Vancouver, Canada, July 1 - 3, 2014]

    (International journal of software engineering and knowledge engineering ; 24.2014,10)

    2014  

    Event/congress International Conference on Software Engineering & Knowledge Engineering (26, 2014.07.01-03, VancouverCanada) ; SEKE (26, 2014.07.01-03, VancouverCanada)
    Series title International journal of software engineering and knowledge engineering ; 24.2014,10
    Language English
    Size S. 1383 - 1595, Ill., graph. Darst., Tab.
    Publisher World Scientific
    Publishing place Singapore u.a.
    Document type Book ; Conference proceedings
    Note Literaturangaben
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  10. Book ; Online: Path Based Hierarchical Clustering on Knowledge Graphs

    Pietrasik, Marcin / Reformat, Marek

    2021  

    Abstract: Knowledge graphs have emerged as a widely adopted medium for storing relational data, making methods for automatically reasoning with them highly desirable. In this paper, we present a novel approach for inducing a hierarchy of subject clusters, building ...

    Abstract Knowledge graphs have emerged as a widely adopted medium for storing relational data, making methods for automatically reasoning with them highly desirable. In this paper, we present a novel approach for inducing a hierarchy of subject clusters, building upon our earlier work done in taxonomy induction. Our method first constructs a tag hierarchy before assigning subjects to clusters on this hierarchy. We quantitatively demonstrate our method's ability to induce a coherent cluster hierarchy on three real-world datasets.

    Comment: 3 pages, 2 figures
    Keywords Computer Science - Artificial Intelligence
    Publishing date 2021-09-27
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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