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  1. Article: Knowledge Graphs for COVID-19: An Exploratory Review of the Current Landscape.

    Chatterjee, Avishek / Nardi, Cosimo / Oberije, Cary / Lambin, Philippe

    Journal of personalized medicine

    2021  Volume 11, Issue 4

    Abstract: Background: Searching through the COVID-19 research literature to gain actionable clinical insight is a formidable task, even for experts. The usefulness of this corpus in terms of improving patient care is tied to the ability to see the big picture ... ...

    Abstract Background: Searching through the COVID-19 research literature to gain actionable clinical insight is a formidable task, even for experts. The usefulness of this corpus in terms of improving patient care is tied to the ability to see the big picture that emerges when the studies are seen in conjunction rather than in isolation. When the answer to a search query requires linking together multiple pieces of information across documents, simple keyword searches are insufficient. To answer such complex information needs, an innovative artificial intelligence (AI) technology named a knowledge graph (KG) could prove to be effective.
    Methods: We conducted an exploratory literature review of KG applications in the context of COVID-19. The search term used was "covid-19 knowledge graph". In addition to PubMed, the first five pages of search results for Google Scholar and Google were considered for inclusion. Google Scholar was used to include non-peer-reviewed or non-indexed articles such as pre-prints and conference proceedings. Google was used to identify companies or consortiums active in this domain that have not published any literature, peer-reviewed or otherwise.
    Results: Our search yielded 34 results on PubMed and 50 results each on Google and Google Scholar. We found KGs being used for facilitating literature search, drug repurposing, clinical trial mapping, and risk factor analysis.
    Conclusions: Our synopses of these works make a compelling case for the utility of this nascent field of research.
    Language English
    Publishing date 2021-04-14
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662248-8
    ISSN 2075-4426
    ISSN 2075-4426
    DOI 10.3390/jpm11040300
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Comparing Prognostic Factors of Cancers Identified by Artificial Intelligence (AI) and Human Readers in Breast Cancer Screening.

    Oberije, Cary J G / Sharma, Nisha / James, Jonathan J / Ng, Annie Y / Nash, Jonathan / Kecskemethy, Peter D

    Cancers

    2023  Volume 15, Issue 12

    Abstract: Invasiveness status, histological grade, lymph node stage, and tumour size are important prognostic factors for breast cancer survival. This evaluation aims to compare these features for cancers detected by AI and human readers using digital mammography. ...

    Abstract Invasiveness status, histological grade, lymph node stage, and tumour size are important prognostic factors for breast cancer survival. This evaluation aims to compare these features for cancers detected by AI and human readers using digital mammography. Women diagnosed with breast cancer between 2009 and 2019 from three UK double-reading sites were included in this retrospective cohort evaluation. Differences in prognostic features of cancers detected by AI and the first human reader (R1) were assessed using chi-square tests, with significance at
    Language English
    Publishing date 2023-06-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers15123069
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Artificial Intelligence as Supporting Reader in Breast Screening: A Novel Workflow to Preserve Quality and Reduce Workload.

    Ng, Annie Y / Glocker, Ben / Oberije, Cary / Fox, Georgia / Sharma, Nisha / James, Jonathan J / Ambrózay, Éva / Nash, Jonathan / Karpati, Edith / Kerruish, Sarah / Kecskemethy, Peter D

    Journal of breast imaging

    2024  Volume 5, Issue 3, Page(s) 267–276

    Abstract: Objective: To evaluate the effectiveness of a new strategy for using artificial intelligence (AI) as supporting reader for the detection of breast cancer in mammography-based double reading screening practice.: Methods: Large-scale multi-site, multi- ... ...

    Abstract Objective: To evaluate the effectiveness of a new strategy for using artificial intelligence (AI) as supporting reader for the detection of breast cancer in mammography-based double reading screening practice.
    Methods: Large-scale multi-site, multi-vendor data were used to retrospectively evaluate a new paradigm of AI-supported reading. Here, the AI served as the second reader only if it agrees with the recall/no-recall decision of the first human reader. Otherwise, a second human reader made an assessment followed by the standard clinical workflow. The data included 280 594 cases from 180 542 female participants screened for breast cancer at seven screening sites in two countries and using equipment from four hardware vendors. The statistical analysis included non-inferiority and superiority testing of cancer screening performance and evaluation of the reduction in workload, measured as arbitration rate and number of cases requiring second human reading.
    Results: Artificial intelligence as a supporting reader was found to be superior or noninferior on all screening metrics compared with human double reading while reducing the number of cases requiring second human reading by up to 87% (245 395/280 594). Compared with AI as an independent reader, the number of cases referred to arbitration was reduced from 13% (35 199/280 594) to 2% (5056/280 594).
    Conclusion: The simulation indicates that the proposed workflow retains screening performance of human double reading while substantially reducing the workload. Further research should study the impact on the second human reader because they would only assess cases in which the AI prediction and first human reader disagree.
    MeSH term(s) Female ; Humans ; Artificial Intelligence ; Workload ; Retrospective Studies ; Workflow ; Breast Neoplasms/diagnosis ; Mammography
    Language English
    Publishing date 2024-02-28
    Publishing country United States
    Document type Journal Article
    ISSN 2631-6129
    ISSN (online) 2631-6129
    DOI 10.1093/jbi/wbad010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Improving shared decision making for lung cancer treatment by developing and validating an open-source web based patient decision aid for stage I-II non-small cell lung cancer.

    Halilaj, Iva / Ankolekar, Anshu / Lenaers, Anouk / Chatterjee, Avishek / Oberije, Cary J G / Eppings, Lisanne / Smit, Hans J M / Hendriks, Lizza E L / Jochems, Arthur / Lieverse, Relinde I Y / van Timmeren, Janita E / Wind, Anke / Lambin, Philippe

    Frontiers in digital health

    2024  Volume 5, Page(s) 1303261

    Abstract: The aim of this study was to develop and evaluate a proof-of-concept open-source individualized Patient Decision Aid (iPDA) with a group of patients, physicians, and computer scientists. The iPDA was developed based on the International Patient Decision ... ...

    Abstract The aim of this study was to develop and evaluate a proof-of-concept open-source individualized Patient Decision Aid (iPDA) with a group of patients, physicians, and computer scientists. The iPDA was developed based on the International Patient Decision Aid Standards (IPDAS). A previously published questionnaire was adapted and used to test the user-friendliness and content of the iPDA. The questionnaire contained 40 multiple-choice questions, and answers were given on a 5-point Likert Scale (1-5) ranging from "strongly disagree" to "strongly agree." In addition to the questionnaire, semi-structured interviews were conducted with patients. We performed a descriptive analysis of the responses. The iPDA was evaluated by 28 computer scientists, 21 physicians, and 13 patients. The results demonstrate that the iPDA was found valuable by 92% (patients), 96% (computer scientists), and 86% (physicians), while the treatment information was judged useful by 92%, 96%, and 95%, respectively. Additionally, the tool was thought to be motivating for patients to actively engage in their treatment by 92%, 93%, and 91% of the above respondents groups. More multimedia components and less text were suggested by the respondents as ways to improve the tool and user interface. In conclusion, we successfully developed and tested an iPDA for patients with stage I-II Non-Small Cell Lung Cancer (NSCLC).
    Language English
    Publishing date 2024-03-22
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2673-253X
    ISSN (online) 2673-253X
    DOI 10.3389/fdgth.2023.1303261
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Prospective implementation of AI-assisted screen reading to improve early detection of breast cancer.

    Ng, Annie Y / Oberije, Cary J G / Ambrózay, Éva / Szabó, Endre / Serfőző, Orsolya / Karpati, Edit / Fox, Georgia / Glocker, Ben / Morris, Elizabeth A / Forrai, Gábor / Kecskemethy, Peter D

    Nature medicine

    2023  Volume 29, Issue 12, Page(s) 3044–3049

    Abstract: Artificial intelligence (AI) has the potential to improve breast cancer screening; however, prospective evidence of the safe implementation of AI into real clinical practice is limited. A commercially available AI system was implemented as an additional ... ...

    Abstract Artificial intelligence (AI) has the potential to improve breast cancer screening; however, prospective evidence of the safe implementation of AI into real clinical practice is limited. A commercially available AI system was implemented as an additional reader to standard double reading to flag cases for further arbitration review among screened women. Performance was assessed prospectively in three phases: a single-center pilot rollout, a wider multicenter pilot rollout and a full live rollout. The results showed that, compared to double reading, implementing the AI-assisted additional-reader process could achieve 0.7-1.6 additional cancer detection per 1,000 cases, with 0.16-0.30% additional recalls, 0-0.23% unnecessary recalls and a 0.1-1.9% increase in positive predictive value (PPV) after 7-11% additional human reads of AI-flagged cases (equating to 4-6% additional overall reading workload). The majority of cancerous cases detected by the AI-assisted additional-reader process were invasive (83.3%) and small-sized (≤10 mm, 47.0%). This evaluation suggests that using AI as an additional reader can improve the early detection of breast cancer with relevant prognostic features, with minimal to no unnecessary recalls. Although the AI-assisted additional-reader workflow requires additional reads, the higher PPV suggests that it can increase screening effectiveness.
    MeSH term(s) Female ; Humans ; Artificial Intelligence ; Breast Neoplasms/diagnosis ; Early Detection of Cancer/methods ; Mammography/methods ; Observer Variation ; Prospective Studies ; Retrospective Studies
    Language English
    Publishing date 2023-11-16
    Publishing country United States
    Document type Journal Article ; Multicenter Study
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-023-02625-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Open Source Repository and Online Calculator of Prediction Models for Diagnosis and Prognosis in Oncology.

    Halilaj, Iva / Oberije, Cary / Chatterjee, Avishek / van Wijk, Yvonka / Rad, Nastaran Mohammadian / Galganebanduge, Prabash / Lavrova, Elizaveta / Primakov, Sergey / Widaatalla, Yousif / Wind, Anke / Lambin, Philippe

    Biomedicines

    2022  Volume 10, Issue 11

    Abstract: 1) Background: The main aim was to develop a prototype application that would serve as an open-source repository for a curated subset of predictive and prognostic models regarding oncology, and provide a user-friendly interface for the included models ... ...

    Abstract (1) Background: The main aim was to develop a prototype application that would serve as an open-source repository for a curated subset of predictive and prognostic models regarding oncology, and provide a user-friendly interface for the included models to allow online calculation. The focus of the application is on providing physicians and health professionals with patient-specific information regarding treatment plans, survival rates, and side effects for different expected treatments. (2) Methods: The primarily used models were the ones developed by our research group in the past. This selection was completed by a number of models, addressing the same cancer types but focusing on other outcomes that were selected based on a literature search in PubMed and Medline databases. All selected models were publicly available and had been validated TRIPOD (Transparent Reporting of studies on prediction models for Individual Prognosis Or Diagnosis) type 3 or 2b. (3) Results: The open source repository currently incorporates 18 models from different research groups, evaluated on datasets from different countries. Model types included logistic regression, Cox regression, and recursive partition analysis (decision trees). (4) Conclusions: An application was developed to enable physicians to complement their clinical judgment with user-friendly patient-specific predictions using models that have received internal/external validation. Additionally, this platform enables researchers to display their work, enhancing the use and exposure of their models.
    Language English
    Publishing date 2022-10-23
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720867-9
    ISSN 2227-9059
    ISSN 2227-9059
    DOI 10.3390/biomedicines10112679
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Clinician perspectives on clinical decision support systems in lung cancer: Implications for shared decision-making.

    Ankolekar, Anshu / van der Heijden, Britt / Dekker, Andre / Roumen, Cheryl / De Ruysscher, Dirk / Reymen, Bart / Berlanga, Adriana / Oberije, Cary / Fijten, Rianne

    Health expectations : an international journal of public participation in health care and health policy

    2022  Volume 25, Issue 4, Page(s) 1342–1351

    Abstract: Background: Lung cancer treatment decisions are typically made among clinical experts in a multidisciplinary tumour board (MTB) based on clinical data and guidelines. The rise of artificial intelligence and cultural shifts towards patient autonomy are ... ...

    Abstract Background: Lung cancer treatment decisions are typically made among clinical experts in a multidisciplinary tumour board (MTB) based on clinical data and guidelines. The rise of artificial intelligence and cultural shifts towards patient autonomy are changing the nature of clinical decision-making towards personalized treatments. This can be supported by clinical decision support systems (CDSSs) that generate personalized treatment information as a basis for shared decision-making (SDM). Little is known about lung cancer patients' treatment decisions and the potential for SDM supported by CDSSs. The aim of this study is to understand to what extent SDM is done in current practice and what clinicians need to improve it.
    Objective: To explore (1) the extent to which patient preferences are taken into consideration in non-small-cell lung cancer (NSCLC) treatment decisions; (2) clinician perspectives on using CDSSs to support SDM.
    Design: Mixed methods study consisting of a retrospective cohort study on patient deviation from MTB advice and reasons for deviation, qualitative interviews with lung cancer specialists and observations of MTB discussions and patient consultations.
    Setting and participants: NSCLC patients (N = 257) treated at a single radiotherapy clinic and nine lung cancer specialists from six Dutch clinics.
    Results: We found a 10.9% (n = 28) deviation rate from MTB advice; 50% (n = 14) were due to patient preference, of which 85.7% (n = 12) chose a less intensive treatment than MTB advice. Current MTB recommendations are based on clinician experience, guidelines and patients' performance status. Most specialists (n = 7) were receptive towards CDSSs but cited barriers, such as lack of trust, lack of validation studies and time. CDSSs were considered valuable during MTB discussions rather than in consultations.
    Conclusion: Lung cancer decisions are heavily influenced by clinical guidelines and experience, yet many patients prefer less intensive treatments. CDSSs can support SDM by presenting the harms and benefits of different treatment options rather than giving single treatment advice. External validation of CDSSs should be prioritized.
    Patient or public contribution: This study did not involve patients or the public explicitly; however, the study design was informed by prior interviews with volunteers of a cancer patient advocacy group. The study objectives and data collection were supported by Dutch health care insurer CZ for a project titled 'My Best Treatment' that improves patient-centeredness and the lung cancer patient pathway in the Netherlands.
    MeSH term(s) Artificial Intelligence ; Carcinoma, Non-Small-Cell Lung/therapy ; Decision Making ; Decision Support Systems, Clinical ; Humans ; Lung Neoplasms/therapy ; Patient Participation/methods ; Qualitative Research ; Retrospective Studies
    Language English
    Publishing date 2022-05-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2119434-8
    ISSN 1369-7625 ; 1369-6513
    ISSN (online) 1369-7625
    ISSN 1369-6513
    DOI 10.1111/hex.13457
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Covid19Risk.ai: An open source repository and online calculator of prediction models for early diagnosis and prognosis of Covid-19

    Halilaj, Iva / Chatterjee, Avishek / Wijk, Yvonka van / Wu, Guangyao / Eeckhout, Brice van / Oberije, Cary / Lambin, Philippe

    bioRxiv

    Abstract: Objective The current pandemic has led to a proliferation of predictive models being developed to address various aspects of COVID-19 patient care. We aimed to develop an online platform that would serve as an open source repository for a curated subset ... ...

    Abstract Objective The current pandemic has led to a proliferation of predictive models being developed to address various aspects of COVID-19 patient care. We aimed to develop an online platform that would serve as an open source repository for a curated subset of such models, and provide a simple interface for included models to allow for online calculation. This platform would support doctors during decision-making regarding diagnoses, prognoses, and follow-up of COVID-19 patients, expediting the models’ transition from research to clinical practice. Methods In this proof-of-principle study, we performed a literature search in PubMed and WHO database to find suitable models for implementation on our platform. All selected models were publicly available (peer reviewed publications or open source repository) and had been validated (TRIPOD type 3 or 2b). We created a method for obtaining the regression coefficients if only the nomogram was available in the original publication. All predictive models were transcribed on a practical graphical user interface using PHP 8.0.0, and published online together with supporting documentation and links to the associated articles. Results The open source website https :// covid 19 risk . ai /   currently incorporates nine models from six different research groups, evaluated on datasets from different countries. The website will continue to be populated with other models related to COVID-19 prediction as these become available. This dynamic platform allows COVID-19 researchers to contact us to have their model curated and included on our website, thereby increasing the reach and real-world impact of their work. Conclusion We have successfully demonstrated in this proof-of-principle study that our website provides an inclusive platform for predictive models related to COVID-19. It enables doctors to supplement their judgment with patient-specific predictions from externally-validated models in a user-friendly format. Additionally, this platform supports researchers in showcasing their work, which will increase the visibility and use of their models.
    Keywords covid19
    Language English
    Publishing date 2021-01-05
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.01.05.425384
    Database COVID19

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  9. Article ; Online: Lessons From a Systematic Literature Search on Diagnostic DNA Methylation Biomarkers for Colorectal Cancer: How to Increase Research Value and Decrease Research Waste?

    Feng, Zheng / Oberije, Cary J G / van de Wetering, Alouisa J P / Koch, Alexander / Wouters, Kim A D / Vaes, Nathalie / Masclee, Ad A M / Carvalho, Beatriz / Meijer, Gerrit A / Zeegers, Maurice P / Herman, James G / Melotte, Veerle / van Engeland, Manon / Smits, Kim M

    Clinical and translational gastroenterology

    2022  Volume 13, Issue 6, Page(s) e00499

    Abstract: Objectives: To improve colorectal cancer (CRC) survival and lower incidence rates, colonoscopy and/or fecal immunochemical test screening are widely implemented. Although candidate DNA methylation biomarkers have been published to improve or complement ... ...

    Abstract Objectives: To improve colorectal cancer (CRC) survival and lower incidence rates, colonoscopy and/or fecal immunochemical test screening are widely implemented. Although candidate DNA methylation biomarkers have been published to improve or complement the fecal immunochemical test, clinical translation is limited. We describe technical and methodological problems encountered after a systematic literature search and provide recommendations to increase (clinical) value and decrease research waste in biomarker research. In addition, we present current evidence for diagnostic CRC DNA methylation biomarkers.
    Methods: A systematic literature search identified 331 diagnostic DNA methylation marker studies published before November 2020 in PubMed, EMBASE, Cochrane Library, and Google Scholar. For 136 bodily fluid studies, extended data extraction was performed. STARD criteria and level of evidence were registered to assess reporting quality and strength for clinical translation.
    Results: Our systematic literature search revealed multiple issues that hamper the development of DNA methylation biomarkers for CRC diagnosis, including methodological and technical heterogeneity and lack of validation or clinical translation. For example, clinical translation and independent validation were limited, with 100 of 434 markers (23%) studied in bodily fluids, 3 of 434 markers (0.7%) translated into clinical tests, and independent validation for 92 of 411 tissue markers (22%) and 59 of 100 bodily fluids markers (59%).
    Discussion: This systematic literature search revealed that major requirements to develop clinically relevant diagnostic CRC DNA methylation markers are often lacking. To avoid the resulting research waste, clinical needs, intended biomarker use, and independent validation should be better considered before study design. In addition, improved reporting quality would facilitate meta-analysis, thereby increasing the level of evidence and enabling clinical translation.
    MeSH term(s) Biomarkers, Tumor/genetics ; Colonoscopy ; Colorectal Neoplasms/diagnosis ; Colorectal Neoplasms/genetics ; DNA Methylation ; Humans ; Occult Blood
    Chemical Substances Biomarkers, Tumor
    Language English
    Publishing date 2022-06-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2581516-7
    ISSN 2155-384X ; 2155-384X
    ISSN (online) 2155-384X
    ISSN 2155-384X
    DOI 10.14309/ctg.0000000000000499
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Modeling-Based Decision Support System for Radical Prostatectomy Versus External Beam Radiotherapy for Prostate Cancer Incorporating an

    van Wijk, Yvonka / Ramaekers, Bram / Vanneste, Ben G L / Halilaj, Iva / Oberije, Cary / Chatterjee, Avishek / Marcelissen, Tom / Jochems, Arthur / Woodruff, Henry C / Lambin, Philippe

    Cancers

    2021  Volume 13, Issue 11

    Abstract: The aim of this study is to build a decision support system (DSS) to select radical prostatectomy (RP) or external beam radiotherapy (EBRT) for low- to intermediate-risk prostate cancer patients. We used an individual state-transition model based on ... ...

    Abstract The aim of this study is to build a decision support system (DSS) to select radical prostatectomy (RP) or external beam radiotherapy (EBRT) for low- to intermediate-risk prostate cancer patients. We used an individual state-transition model based on predictive models for estimating tumor control and toxicity probabilities. We performed analyses on a synthetically generated dataset of 1000 patients with realistic clinical parameters, externally validated by comparison to randomized clinical trials, and set up an in silico clinical trial for elderly patients. We assessed the cost-effectiveness (CE) of the DSS for treatment selection by comparing it to randomized treatment allotment. Using the DSS, 47.8% of synthetic patients were selected for RP and 52.2% for EBRT. During validation, differences with the simulations of late toxicity and biochemical failure never exceeded 2%. The in silico trial showed that for elderly patients, toxicity has more influence on the decision than TCP, and the predicted QoL depends on the initial erectile function. The DSS is estimated to result in cost savings (EUR 323 (95% CI: EUR 213-433)) and more quality-adjusted life years (QALYs; 0.11 years, 95% CI: 0.00-0.22) than randomized treatment selection.
    Language English
    Publishing date 2021-05-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers13112687
    Database MEDical Literature Analysis and Retrieval System OnLINE

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