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1. Concept Detection and Caption Prediction in ImageCLEFmedical Caption 2023 with Convolutional Neural Networks; Vision and Text-to-Text Transfer Transformers

   Hasan M ; Layode O ; Rahman M. ( October 2023 , Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2023))

   Aliannejadi, M ; Faggioli, G ; Ferro, N ; Vlachos, M. (Ed.)

   This work discusses the participation of CS_Morgan in the Concept Detection and Caption Prediction tasks of the ImageCLEFmedical 2023 Caption benchmark evaluation campaign. The goal of this task is to automatically identify relevant concepts and their locations in images, as well as generate coherent captions for the images. The dataset used for this task is a subset of the extended Radiology Objects in Context (ROCO) dataset. The implementation approach employed by us involved the use of pre-trained Convolutional Neural Networks (CNNs), Vision Transformer (ViT), and Text-to-Text Transfer Transformer (T5) architectures. These models were leveraged to handle the different aspects of the tasks, such as concept detection and caption generation. In the Concept Detection task, the objective was to classify multiple concepts associated with each image. We utilized several deep learning architectures with ‘sigmoid’ activation to enable multilabel classification using the Keras framework. We submitted a total of five (5) runs for this task, and the best run achieved an F1 score of 0.4834, indicating its effectiveness in detecting relevant concepts in the images. For the Caption Prediction task, we successfully submitted eight (8) runs. Our approach involved combining the ViT and T5 models to generate captions for the images. For the caption prediction task, the ranking is based on the BERTScore, and our best run achieved a score of 0.5819 based on generating captions using the fine-tuned T5 model from keywords generated using the pretrained ViT as the encoder. 

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2. Identify diabetic retinopathy-related clinical concepts and their attributes using transformer-based natural language processing methods

   https://doi.org/10.1186/s12911-022-01996-2  

   Yu, Zehao ; Yang, Xi ; Sweeting, Gianna L. ; Ma, Yinghan ; Stolte, Skylar E. ; Fang, Ruogu ; Wu, Yonghui ( September 2022 , BMC Medical Informatics and Decision Making)

   Abstract Background Diabetic retinopathy (DR) is a leading cause of blindness in American adults. If detected, DR can be treated to prevent further damage causing blindness. There is an increasing interest in developing artificial intelligence (AI) technologies to help detect DR using electronic health records. The lesion-related information documented in fundus image reports is a valuable resource that could help diagnoses of DR in clinical decision support systems. However, most studies for AI-based DR diagnoses are mainly based on medical images; there is limited studies to explore the lesion-related information captured in the free text image reports. Methods In this study, we examined two state-of-the-art transformer-based natural language processing (NLP) models, including BERT and RoBERTa, compared them with a recurrent neural network implemented using Long short-term memory (LSTM) to extract DR-related concepts from clinical narratives. We identified four different categories of DR-related clinical concepts including lesions, eye parts, laterality, and severity, developed annotation guidelines, annotated a DR-corpus of 536 image reports, and developed transformer-based NLP models for clinical concept extraction and relation extraction. We also examined the relation extraction under two settings including ‘gold-standard’ setting—where gold-standard concepts were used–and end-to-end setting. Results For concept extraction, the BERT model pretrained with the MIMIC III dataset achieve the best performance (0.9503 and 0.9645 for strict/lenient evaluation). For relation extraction, BERT model pretrained using general English text achieved the best strict/lenient F1-score of 0.9316. The end-to-end system, BERT_general_e2e, achieved the best strict/lenient F1-score of 0.8578 and 0.8881, respectively. Another end-to-end system based on the RoBERTa architecture, RoBERTa_general_e2e, also achieved the same performance as BERT_general_e2e in strict scores. Conclusions This study demonstrated the efficiency of transformer-based NLP models for clinical concept extraction and relation extraction. Our results show that it’s necessary to pretrain transformer models using clinical text to optimize the performance for clinical concept extraction. Whereas, for relation extraction, transformers pretrained using general English text perform better. 

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3. fNIRS-based classification of mind-wandering with personalized window selection for multimodal learning interfaces

   https://doi.org/10.1007/s12193-020-00325-z  

   Liu, Ruixue ; Walker, Erin ; Friedman, Leah ; Arrington, Catherine M. ; Solovey, Erin T. ( June 2020 , Journal on Multimodal User Interfaces)

   Automatic detection of an individual’s mind-wandering state has implications for designing and evaluating engaging and effective learning interfaces. While it is difficult to differentiate whether an individual is mind-wandering or focusing on the task only based on externally observable behavior, brain-based sensing offers unique insights to internal states. To explore the feasibility, we conducted a study using functional near-infrared spectroscopy (fNIRS) and investigated machine learning classifiers to detect mind-wandering episodes based on fNIRS data, both on an individual level and a group level, specifically focusing on automated window selection to improve classification results. For individual-level classification, by using a moving window method combined with a linear discriminant classifier, we found the best windows for classification and achieved a mean F1-score of 74.8%. For group-level classification, we proposed an individual-based time window selection (ITWS) algorithm to incorporate individual differences in window selection. The algorithm first finds the best window for each individual by using embedded individual-level classifiers and then uses these windows from all participants to build the final classifier. The performance of the ITWS algorithm is evaluated when used with eXtreme gradient boosting, convolutional neural networks, and deep neural networks. Our results show that the proposed algorithm achieved significant improvement compared to the previous state of the art in terms of brain-based classification of mind-wandering, with an average F1-score of 73.2%. This builds a foundation for mind-wandering detection for both the evaluation of multimodal learning interfaces and for future attention-aware systems. 

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4. Improving Solar Energetic Particle Event Prediction through Multivariate Time Series Data Augmentation

   https://doi.org/10.3847/1538-4365/ad1de0  

   Hosseinzadeh, Pouya ; Filali Boubrahimi, Soukaina ; Hamdi, Shah Muhammad ( February 2024 , The Astrophysical Journal Supplement Series)

   Solar energetic particles (SEPs) are associated with extreme solar events that can cause major damage to space- and ground-based life and infrastructure. High-intensity SEP events, particularly ∼100 MeV SEP events, can pose severe health risks for astronauts owing to radiation exposure and affect Earth’s orbiting satellites (e.g., Landsat and the International Space Station). A major challenge in the SEP event prediction task is the lack of adequate SEP data because of the rarity of these events. In this work, we aim to improve the prediction of ∼30, ∼60, and ∼100 MeV SEP events by synthetically increasing the number of SEP samples. We explore the use of a univariate and multivariate time series of proton flux data as input to machine-learning-based prediction methods, such as time series forest (TSF). Our study covers solar cycles 22, 23, and 24. Our findings show that using data augmentation methods, such as the synthetic minority oversampling technique, remarkably increases the accuracy and F1-score of the classifiers used in this research, especially for TSF, where the average accuracy increased by 20%, reaching around 90% accuracy in the ∼100 MeV SEP prediction task. We also achieved higher prediction accuracy when using the multivariate time series data of the proton flux. Finally, we build a pipeline framework for our best-performing model, TSF, and provide a comprehensive hierarchical classification of the ∼100, ∼60, and ∼30 MeV and non-SEP prediction scenarios.

    

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5. Detection of dementia on voice recordings using deep learning: a Framingham Heart Study

   https://doi.org/10.1186/s13195-021-00888-3  

   Xue, Chonghua ; Karjadi, Cody ; Paschalidis, Ioannis Ch. ; Au, Rhoda ; Kolachalama, Vijaya B. ( December 2021 , Alzheimer's Research & Therapy)

   Abstract Background Identification of reliable, affordable, and easy-to-use strategies for detection of dementia is sorely needed. Digital technologies, such as individual voice recordings, offer an attractive modality to assess cognition but methods that could automatically analyze such data are not readily available. Methods and findings We used 1264 voice recordings of neuropsychological examinations administered to participants from the Framingham Heart Study (FHS), a community-based longitudinal observational study. The recordings were 73 min in duration, on average, and contained at least two speakers (participant and examiner). Of the total voice recordings, 483 were of participants with normal cognition (NC), 451 recordings were of participants with mild cognitive impairment (MCI), and 330 were of participants with dementia (DE). We developed two deep learning models (a two-level long short-term memory (LSTM) network and a convolutional neural network (CNN)), which used the audio recordings to classify if the recording included a participant with only NC or only DE and to differentiate between recordings corresponding to those that had DE from those who did not have DE (i.e., NDE (NC+MCI)). Based on 5-fold cross-validation, the LSTM model achieved a mean (±std) area under the receiver operating characteristic curve (AUC) of 0.740 ± 0.017, mean balanced accuracy of 0.647 ± 0.027, and mean weighted F1 score of 0.596 ± 0.047 in classifying cases with DE from those with NC. The CNN model achieved a mean AUC of 0.805 ± 0.027, mean balanced accuracy of 0.743 ± 0.015, and mean weighted F1 score of 0.742 ± 0.033 in classifying cases with DE from those with NC. For the task related to the classification of participants with DE from NDE, the LSTM model achieved a mean AUC of 0.734 ± 0.014, mean balanced accuracy of 0.675 ± 0.013, and mean weighted F1 score of 0.671 ± 0.015. The CNN model achieved a mean AUC of 0.746 ± 0.021, mean balanced accuracy of 0.652 ± 0.020, and mean weighted F1 score of 0.635 ± 0.031 in classifying cases with DE from those who were NDE. Conclusion This proof-of-concept study demonstrates that automated deep learning-driven processing of audio recordings of neuropsychological testing performed on individuals recruited within a community cohort setting can facilitate dementia screening. 

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