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  1. Article ; Online: Machine learning-based prediction of surgical benefit in borderline resectable and locally advanced pancreatic cancer.

    Zhang, Leiming / Yu, Zehao / Jin, Rong / Yang, Xuanang / Ying, Dongjian

    Journal of cancer research and clinical oncology

    2023  Volume 149, Issue 13, Page(s) 11857–11871

    Abstract: Introduction: Surgery represents a primary therapeutic approach for borderline resectable and locally advanced pancreatic cancer (BR/LAPC). However, BR/LAPC lesions exhibit high heterogeneity and not all BR/LAPC patients who undergo surgery can derive ... ...

    Abstract Introduction: Surgery represents a primary therapeutic approach for borderline resectable and locally advanced pancreatic cancer (BR/LAPC). However, BR/LAPC lesions exhibit high heterogeneity and not all BR/LAPC patients who undergo surgery can derive beneficial outcomes. The present study aims to employ machine learning (ML) algorithms to identify those who would obtain benefits from the primary tumor surgery.
    Methods: We retrieved clinical data of patients with BR/LAPC from the Surveillance, Epidemiology, and End Results (SEER) database and classified them into surgery and non-surgery groups based on primary tumor surgery status. To eliminate confounding factors, propensity score matching (PSM) was employed. We hypothesized that patients who underwent surgery and had a longer median cancer-specific survival (CSS) than those who did not undergo surgery would certainly benefit from surgical intervention. Clinical and pathological features were utilized to construct six ML models, and model effectiveness was compared through measures such as the area under curve (AUC), calibration plots, and decision curve analysis (DCA). We selected the best-performing algorithm (i.e., XGBoost) to predict postoperative benefits. The SHapley Additive exPlanations (SHAP) approach was used to interpret the XGBoost model. Additionally, data from 53 Chinese patients prospectively collected was used for external validation of the model.
    Results: According to the results of the tenfold cross-validation in the training cohort, the XGBoost model yielded the best performance (AUC = 0.823, 95%CI 0.707-0.938). The internal (74.3% accuracy) and external (84.3% accuracy) validation demonstrated the generalizability of the model. The SHAP analysis provided explanations independent of the model, highlighting important factors related to postoperative survival benefits in BR/LAPC, with age, chemotherapy, and radiation therapy being the top three important factors.
    Conclusion: By integrating of ML algorithms and clinical data, we have established a highly efficient model to facilitate clinical decision-making and assist clinicians in selecting the population that would benefit from surgery.
    MeSH term(s) Humans ; Pancreatic Neoplasms/pathology ; Machine Learning ; Pancreatic Neoplasms
    Language English
    Publishing date 2023-07-06
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 134792-5
    ISSN 1432-1335 ; 0171-5216 ; 0084-5353 ; 0943-9382
    ISSN (online) 1432-1335
    ISSN 0171-5216 ; 0084-5353 ; 0943-9382
    DOI 10.1007/s00432-023-05071-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Extracting Thyroid Nodules Characteristics from Ultrasound Reports Using Transformer-based Natural Language Processing Methods.

    Pathak, Aman / Yu, Zehao / Paredes, Daniel / Monsour, Elio Paul / Rocha, Andrea Ortiz / Brito, Juan P / Ospina, Naykky Singh / Wu, Yonghui

    AMIA ... Annual Symposium proceedings. AMIA Symposium

    2024  Volume 2023, Page(s) 1193–1200

    Abstract: The ultrasound characteristics of thyroid nodules guide the evaluation of thyroid cancer in patients with thyroid nodules. However, the characteristics of thyroid nodules are often documented in clinical narratives such as ultrasound reports. Previous ... ...

    Abstract The ultrasound characteristics of thyroid nodules guide the evaluation of thyroid cancer in patients with thyroid nodules. However, the characteristics of thyroid nodules are often documented in clinical narratives such as ultrasound reports. Previous studies have examined natural language processing (NLP) methods in extracting a limited number of characteristics (<9) using rule-based NLP systems. In this study, a multidisciplinary team of NLP experts and thyroid specialists, identified thyroid nodule characteristics that are important for clinical care, composed annotation guidelines, developed a corpus, and compared 5 state-of-the-art transformer-based NLP methods, including BERT, RoBERTa, LongFormer, DeBERTa, and GatorTron, for extraction of thyroid nodule characteristics from ultrasound reports. Our GatorTron model, a transformer-based large language model trained using over 90 billion words of text, achieved the best strict and lenient F1-score of 0.8851 and 0.9495 for the extraction of a total number of 16 thyroid nodule characteristics, and 0.9321 for linking characteristics to nodules, outperforming other clinical transformer models. To the best of our knowledge, this is the first study to systematically categorize and apply transformer-based NLP models to extract a large number of clinical relevant thyroid nodule characteristics from ultrasound reports. This study lays ground for assessing the documentation quality of thyroid ultrasound reports and examining outcomes of patients with thyroid nodules using electronic health records.
    MeSH term(s) Humans ; Thyroid Nodule/diagnostic imaging ; Natural Language Processing ; Electronic Health Records ; Ultrasonography ; Narration
    Language English
    Publishing date 2024-01-11
    Publishing country United States
    Document type Journal Article
    ISSN 1942-597X
    ISSN (online) 1942-597X
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Assessing the Documentation of Social Determinants of Health for Lung Cancer Patients in Clinical Narratives.

    Yu, Zehao / Yang, Xi / Guo, Yi / Bian, Jiang / Wu, Yonghui

    Frontiers in public health

    2022  Volume 10, Page(s) 778463

    Abstract: Social determinants of health (SDoH) are important factors associated with cancer risk and treatment outcomes. There is an increasing interest in exploring SDoH captured in electronic health records (EHRs) to assess cancer risk and outcomes; however, ... ...

    Abstract Social determinants of health (SDoH) are important factors associated with cancer risk and treatment outcomes. There is an increasing interest in exploring SDoH captured in electronic health records (EHRs) to assess cancer risk and outcomes; however, most SDoH are only captured in free-text clinical narratives such as physicians' notes that are not readily accessible. In this study, we applied a natural language processing (NLP) system to identify 15 categories of SDoH from a total of 10,855 lung cancer patients at the University of Florida Health. We aggregated the SDoH concepts into patient-level and assessed how each of the 15 categories of SDoH were documented in cancer patient's notes. To the best of our knowledge, this is one of the first studies to examine the documentation of SDoH in clinical narratives from a real-world lung cancer patient cohort. This study could guide future studies to better utilize SDoH information documented in clinical narratives.
    MeSH term(s) Documentation ; Electronic Health Records ; Humans ; Lung Neoplasms ; Natural Language Processing ; Social Determinants of Health
    Language English
    Publishing date 2022-03-28
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2711781-9
    ISSN 2296-2565 ; 2296-2565
    ISSN (online) 2296-2565
    ISSN 2296-2565
    DOI 10.3389/fpubh.2022.778463
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: LncRNA MACC1-AS1 induces gemcitabine resistance in pancreatic cancer cells through suppressing ferroptosis.

    Zhu, Jiyun / Yu, Zehao / Wang, Xuguang / Zhang, Jinghui / Chen, Yi / Chen, Kaibo / Zhang, Bin / Sun, Jianhong / Jiang, Jianshuai / Zheng, Siming

    Cell death discovery

    2024  Volume 10, Issue 1, Page(s) 101

    Abstract: Pancreatic ductal adenocarcinoma (PDA) mortality is primarily attributed to metastasis and chemotherapy resistance. In this research, the long non-coding RNA MACC1-AS1 was studied, playing a significant role in regulating lipid oxidation processes. This ... ...

    Abstract Pancreatic ductal adenocarcinoma (PDA) mortality is primarily attributed to metastasis and chemotherapy resistance. In this research, the long non-coding RNA MACC1-AS1 was studied, playing a significant role in regulating lipid oxidation processes. This regulation could further lead to the inhibition of ferroptosis induced by chemotherapeutic drugs, making it a contributing factor to gemcitabine resistance in PDA. In both gemcitabine-resistant PDA patients and mouse models, the elevated expression level of MACC1-AS1 in the tumors was noted. Additionally, overexpression of MACC1-AS1 in pancreatic cancer cells was found to enhance tolerance to gemcitabine and suppress ferroptosis. Proteomic analysis of drug-resistant pancreatic cells revealed that overexpressed MACC1-AS1 inhibited the ubiquitination degradation of residues in the protein kinase STK33 by MDM4. Furthermore, its accumulation in the cytoplasm activated STK33, further activating the ferroptosis-suppressing proteins GPX4, thereby counteracting gemcitabine-induced cellular oxidative damage. These findings suggested that the long non-coding RNA MACC1-AS1 could play a significant role in the ability of pancreatic cancer cells to evade iron-mediated ferroptosis induced by gemcitabine. This discovery holds promise for developing clinical therapeutic strategies to combat chemotherapy resistance in pancreatic cancer.
    Language English
    Publishing date 2024-02-27
    Publishing country United States
    Document type Journal Article
    ISSN 2058-7716
    ISSN 2058-7716
    DOI 10.1038/s41420-024-01866-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Generative large language models are all-purpose text analytics engines: text-to-text learning is all your need.

    Peng, Cheng / Yang, Xi / Chen, Aokun / Yu, Zehao / Smith, Kaleb E / Costa, Anthony B / Flores, Mona G / Bian, Jiang / Wu, Yonghui

    Journal of the American Medical Informatics Association : JAMIA

    2024  

    Abstract: Objective: To solve major clinical natural language processing (NLP) tasks using a unified text-to-text learning architecture based on a generative large language model (LLM) via prompt tuning.: Methods: We formulated 7 key clinical NLP tasks as text- ...

    Abstract Objective: To solve major clinical natural language processing (NLP) tasks using a unified text-to-text learning architecture based on a generative large language model (LLM) via prompt tuning.
    Methods: We formulated 7 key clinical NLP tasks as text-to-text learning and solved them using one unified generative clinical LLM, GatorTronGPT, developed using GPT-3 architecture and trained with up to 20 billion parameters. We adopted soft prompts (ie, trainable vectors) with frozen LLM, where the LLM parameters were not updated (ie, frozen) and only the vectors of soft prompts were updated, known as prompt tuning. We added additional soft prompts as a prefix to the input layer, which were optimized during the prompt tuning. We evaluated the proposed method using 7 clinical NLP tasks and compared them with previous task-specific solutions based on Transformer models.
    Results and conclusion: The proposed approach achieved state-of-the-art performance for 5 out of 7 major clinical NLP tasks using one unified generative LLM. Our approach outperformed previous task-specific transformer models by ∼3% for concept extraction and 7% for relation extraction applied to social determinants of health, 3.4% for clinical concept normalization, 3.4%-10% for clinical abbreviation disambiguation, and 5.5%-9% for natural language inference. Our approach also outperformed a previously developed prompt-based machine reading comprehension (MRC) model, GatorTron-MRC, for clinical concept and relation extraction. The proposed approach can deliver the "one model for all" promise from training to deployment using a unified generative LLM.
    Language English
    Publishing date 2024-04-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 1205156-1
    ISSN 1527-974X ; 1067-5027
    ISSN (online) 1527-974X
    ISSN 1067-5027
    DOI 10.1093/jamia/ocae078
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Model tuning or prompt Tuning? a study of large language models for clinical concept and relation extraction.

    Peng, Cheng / Yang, Xi / Smith, Kaleb E / Yu, Zehao / Chen, Aokun / Bian, Jiang / Wu, Yonghui

    Journal of biomedical informatics

    2024  Volume 153, Page(s) 104630

    Abstract: Objective: To develop soft prompt-based learning architecture for large language models (LLMs), examine prompt-tuning using frozen/unfrozen LLMs, and assess their abilities in transfer learning and few-shot learning.: Methods: We developed a soft ... ...

    Abstract Objective: To develop soft prompt-based learning architecture for large language models (LLMs), examine prompt-tuning using frozen/unfrozen LLMs, and assess their abilities in transfer learning and few-shot learning.
    Methods: We developed a soft prompt-based learning architecture and compared 4 strategies including (1) fine-tuning without prompts; (2) hard-prompting with unfrozen LLMs; (3) soft-prompting with unfrozen LLMs; and (4) soft-prompting with frozen LLMs. We evaluated GatorTron, a clinical LLM with up to 8.9 billion parameters, and compared GatorTron with 4 existing transformer models for clinical concept and relation extraction on 2 benchmark datasets for adverse drug events and social determinants of health (SDoH). We evaluated the few-shot learning ability and generalizability for cross-institution applications.
    Results and conclusion: When LLMs are unfrozen, GatorTron-3.9B with soft prompting achieves the best strict F1-scores of 0.9118 and 0.8604 for concept extraction, outperforming the traditional fine-tuning and hard prompt-based models by 0.6 ∼ 3.1 % and 1.2 ∼ 2.9 %, respectively; GatorTron-345 M with soft prompting achieves the best F1-scores of 0.8332 and 0.7488 for end-to-end relation extraction, outperforming other two models by 0.2 ∼ 2 % and 0.6 ∼ 11.7 %, respectively. When LLMs are frozen, small LLMs have a big gap to be competitive with unfrozen models; scaling LLMs up to billions of parameters makes frozen LLMs competitive with unfrozen models. Soft prompting with a frozen GatorTron-8.9B model achieved the best performance for cross-institution evaluation. We demonstrate that (1) machines can learn soft prompts better than hard prompts composed by human, (2) frozen LLMs have good few-shot learning ability and generalizability for cross-institution applications, (3) frozen LLMs reduce computing cost to 2.5 ∼ 6 % of previous methods using unfrozen LLMs, and (4) frozen LLMs require large models (e.g., over several billions of parameters) for good performance.
    MeSH term(s) Humans ; Natural Language Processing ; Machine Learning ; Data Mining/methods ; Algorithms ; Social Determinants of Health ; Drug-Related Side Effects and Adverse Reactions
    Language English
    Publishing date 2024-03-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2057141-0
    ISSN 1532-0480 ; 1532-0464
    ISSN (online) 1532-0480
    ISSN 1532-0464
    DOI 10.1016/j.jbi.2024.104630
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: TransFuser: Imitation With Transformer-Based Sensor Fusion for Autonomous Driving.

    Chitta, Kashyap / Prakash, Aditya / Jaeger, Bernhard / Yu, Zehao / Renz, Katrin / Geiger, Andreas

    IEEE transactions on pattern analysis and machine intelligence

    2023  Volume 45, Issue 11, Page(s) 12878–12895

    Abstract: How should we integrate representations from complementary sensors for autonomous driving? Geometry-based fusion has shown promise for perception (e.g., object detection, motion forecasting). However, in the context of end-to-end driving, we find that ... ...

    Abstract How should we integrate representations from complementary sensors for autonomous driving? Geometry-based fusion has shown promise for perception (e.g., object detection, motion forecasting). However, in the context of end-to-end driving, we find that imitation learning based on existing sensor fusion methods underperforms in complex driving scenarios with a high density of dynamic agents. Therefore, we propose TransFuser, a mechanism to integrate image and LiDAR representations using self-attention. Our approach uses transformer modules at multiple resolutions to fuse perspective view and bird's eye view feature maps. We experimentally validate its efficacy on a challenging new benchmark with long routes and dense traffic, as well as the official leaderboard of the CARLA urban driving simulator. At the time of submission, TransFuser outperforms all prior work on the CARLA leaderboard in terms of driving score by a large margin. Compared to geometry-based fusion, TransFuser reduces the average collisions per kilometer by 48%.
    Language English
    Publishing date 2023-10-03
    Publishing country United States
    Document type Journal Article
    ISSN 1939-3539
    ISSN (online) 1939-3539
    DOI 10.1109/TPAMI.2022.3200245
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Clinical concept and relation extraction using prompt-based machine reading comprehension.

    Peng, Cheng / Yang, Xi / Yu, Zehao / Bian, Jiang / Hogan, William R / Wu, Yonghui

    Journal of the American Medical Informatics Association : JAMIA

    2023  Volume 30, Issue 9, Page(s) 1486–1493

    Abstract: Objective: To develop a natural language processing system that solves both clinical concept extraction and relation extraction in a unified prompt-based machine reading comprehension (MRC) architecture with good generalizability for cross-institution ... ...

    Abstract Objective: To develop a natural language processing system that solves both clinical concept extraction and relation extraction in a unified prompt-based machine reading comprehension (MRC) architecture with good generalizability for cross-institution applications.
    Methods: We formulate both clinical concept extraction and relation extraction using a unified prompt-based MRC architecture and explore state-of-the-art transformer models. We compare our MRC models with existing deep learning models for concept extraction and end-to-end relation extraction using 2 benchmark datasets developed by the 2018 National NLP Clinical Challenges (n2c2) challenge (medications and adverse drug events) and the 2022 n2c2 challenge (relations of social determinants of health [SDoH]). We also evaluate the transfer learning ability of the proposed MRC models in a cross-institution setting. We perform error analyses and examine how different prompting strategies affect the performance of MRC models.
    Results and conclusion: The proposed MRC models achieve state-of-the-art performance for clinical concept and relation extraction on the 2 benchmark datasets, outperforming previous non-MRC transformer models. GatorTron-MRC achieves the best strict and lenient F1-scores for concept extraction, outperforming previous deep learning models on the 2 datasets by 1%-3% and 0.7%-1.3%, respectively. For end-to-end relation extraction, GatorTron-MRC and BERT-MIMIC-MRC achieve the best F1-scores, outperforming previous deep learning models by 0.9%-2.4% and 10%-11%, respectively. For cross-institution evaluation, GatorTron-MRC outperforms traditional GatorTron by 6.4% and 16% for the 2 datasets, respectively. The proposed method is better at handling nested/overlapped concepts, extracting relations, and has good portability for cross-institute applications. Our clinical MRC package is publicly available at https://github.com/uf-hobi-informatics-lab/ClinicalTransformerMRC.
    MeSH term(s) Humans ; Comprehension ; Drug-Related Side Effects and Adverse Reactions ; Natural Language Processing
    Language English
    Publishing date 2023-06-15
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1205156-1
    ISSN 1527-974X ; 1067-5027
    ISSN (online) 1527-974X
    ISSN 1067-5027
    DOI 10.1093/jamia/ocad107
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Contextualized medication information extraction using Transformer-based deep learning architectures.

    Chen, Aokun / Yu, Zehao / Yang, Xi / Guo, Yi / Bian, Jiang / Wu, Yonghui

    Journal of biomedical informatics

    2023  Volume 142, Page(s) 104370

    Abstract: Objective: To develop a natural language processing (NLP) system to extract medications and contextual information that help understand drug changes. This project is part of the 2022 n2c2 challenge.: Materials and methods: We developed NLP systems ... ...

    Abstract Objective: To develop a natural language processing (NLP) system to extract medications and contextual information that help understand drug changes. This project is part of the 2022 n2c2 challenge.
    Materials and methods: We developed NLP systems for medication mention extraction, event classification (indicating medication changes discussed or not), and context classification to classify medication changes context into 5 orthogonal dimensions related to drug changes. We explored 6 state-of-the-art pretrained transformer models for the three subtasks, including GatorTron, a large language model pretrained using > 90 billion words of text (including > 80 billion words from > 290 million clinical notes identified at the University of Florida Health). We evaluated our NLP systems using annotated data and evaluation scripts provided by the 2022 n2c2 organizers.
    Results: Our GatorTron models achieved the best F1-scores of 0.9828 for medication extraction (ranked 3rd), 0.9379 for event classification (ranked 2nd), and the best micro-average accuracy of 0.9126 for context classification. GatorTron outperformed existing transformer models pretrained using smaller general English text and clinical text corpora, indicating the advantage of large language models.
    Conclusion: This study demonstrated the advantage of using large transformer models for contextual medication information extraction from clinical narratives.
    MeSH term(s) Deep Learning ; Natural Language Processing ; Information Storage and Retrieval
    Language English
    Publishing date 2023-04-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 2057141-0
    ISSN 1532-0480 ; 1532-0464
    ISSN (online) 1532-0480
    ISSN 1532-0464
    DOI 10.1016/j.jbi.2023.104370
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online: Mip-Splatting

    Yu, Zehao / Chen, Anpei / Huang, Binbin / Sattler, Torsten / Geiger, Andreas

    Alias-free 3D Gaussian Splatting

    2023  

    Abstract: Recently, 3D Gaussian Splatting has demonstrated impressive novel view synthesis results, reaching high fidelity and efficiency. However, strong artifacts can be observed when changing the sampling rate, \eg, by changing focal length or camera distance. ... ...

    Abstract Recently, 3D Gaussian Splatting has demonstrated impressive novel view synthesis results, reaching high fidelity and efficiency. However, strong artifacts can be observed when changing the sampling rate, \eg, by changing focal length or camera distance. We find that the source for this phenomenon can be attributed to the lack of 3D frequency constraints and the usage of a 2D dilation filter. To address this problem, we introduce a 3D smoothing filter which constrains the size of the 3D Gaussian primitives based on the maximal sampling frequency induced by the input views, eliminating high-frequency artifacts when zooming in. Moreover, replacing 2D dilation with a 2D Mip filter, which simulates a 2D box filter, effectively mitigates aliasing and dilation issues. Our evaluation, including scenarios such a training on single-scale images and testing on multiple scales, validates the effectiveness of our approach.

    Comment: Project page: https://niujinshuchong.github.io/mip-splatting/
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Publishing date 2023-11-27
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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