Patients advise their peers on how to cope with their illness in daily life on online support groups. To date, no efforts have been made to automatically extract recommended coping strategies from... Show morePatients advise their peers on how to cope with their illness in daily life on online support groups. To date, no efforts have been made to automatically extract recommended coping strategies from online patient discussion groups. We introduce this new task, which poses a number of challenges including complex, long entities, a large long-tailed label space, and cross-document relations. We present an initial ontology for coping strategies as a starting point for future research on coping strategies, and the first end-to-end pipeline for extracting coping strategies for side effects. We also compared two possible computational solutions for this novel and highly challenging task; multi-label classification and named entity recognition (NER) with entity linking (EL). We evaluated our methods on the discussion forum from the Facebook group of the worldwide patient support organization ‘GIST support international’ (GSI); GIST support international donated the data to us. We found that coping strategy extraction is difficult and both methods attain limited performance (measured with score) on held out test sets; multi-label classification outperforms NER+EL ( vs ). An inspection of the multi-label classification output revealed that for some of the incorrect predictions, the reference label is close to the predicted label in the ontology (e.g. the predicted label ‘juice’ instead of the more specific reference label ‘grapefruit juice’). Performance increased to when we evaluated at a coarser level of the ontology. We conclude that our pipeline can be used in a semi-automatic setting, in interaction with domain experts to discover coping strategies for side effects from a patient forum. For example, we found that patients recommend ginger tea for nausea and magnesium and potassium supplements for cramps. This information can be used as input for patient surveys or clinical studies. Show less
Dirkson, A.; Hollander, D. den; Verberne, S.; Desar, I.; Husson, O.; Graaf, W. T A, van der; ... ; Kraaij, W. 2022
BACKGROUND\nOBJECTIVE\nMETHODS\nRESULTS\nCONCLUSIONS\nIncreasingly, social media is being recognized as a potential resource for patient-generated health data, for example, for pharmacovigilance.... Show moreBACKGROUND\nOBJECTIVE\nMETHODS\nRESULTS\nCONCLUSIONS\nIncreasingly, social media is being recognized as a potential resource for patient-generated health data, for example, for pharmacovigilance. Although the representativeness of the web-based patient population is often noted as a concern, studies in this field are limited.\nThis study aimed to investigate the sample bias of patient-centered social media in Dutch patients with gastrointestinal stromal tumor (GIST).\nA population-based survey was conducted in the Netherlands among 328 patients with GIST diagnosed 2-13 years ago to investigate their digital communication use with fellow patients. A logistic regression analysis was used to analyze clinical and demographic differences between forum users and nonusers.\nOverall, 17.9% (59/328) of survey respondents reported having contact with fellow patients via social media. Moreover, 78% (46/59) of forum users made use of GIST patient forums. We found no statistically significant differences for age, sex, socioeconomic status, and time since diagnosis between forum users (n=46) and nonusers (n=273). Patient forum users did differ significantly in (self-reported) treatment phase from nonusers (P=.001). Of the 46 forum users, only 2 (4%) were cured and not being monitored; 3 (7%) were on adjuvant, curative treatment; 19 (41%) were being monitored after adjuvant treatment; and 22 (48%) were on palliative treatment. In contrast, of the 273 patients who did not use disease-specific forums to communicate with fellow patients, 56 (20.5%) were cured and not being monitored, 31 (11.3%) were on curative treatment, 139 (50.9%) were being monitored after treatment, and 42 (15.3%) were on palliative treatment. The odds of being on a patient forum were 2.8 times as high for a patient who is being monitored compared with a patient that is considered cured. The odds of being on a patient forum were 1.9 times as high for patients who were on curative (adjuvant) treatment and 10 times as high for patients who were in the palliative phase compared with patients who were considered cured. Forum users also reported a lower level of social functioning (84.8 out of 100) than nonusers (93.8 out of 100; P=.008).\nForum users showed no particular bias on the most important demographic variables of age, sex, socioeconomic status, and time since diagnosis. This may reflect the narrowing digital divide. Overrepresentation and underrepresentation of patients with GIST in different treatment phases on social media should be taken into account when sourcing patient forums for patient-generated health data. A further investigation of the sample bias in other web-based patient populations is warranted. Show less
Dirkson, A.; Hollander, D. den; Verberne, S.; Desar, I.; Husson, O.; Graaf, W.T.A. van der; ... ; Kraaij, W. 2022
Background: Increasingly, social media is being recognized as a potential resource for patient-generated health data, for example, for pharmacovigilance. Although the representativeness of the web... Show moreBackground: Increasingly, social media is being recognized as a potential resource for patient-generated health data, for example, for pharmacovigilance. Although the representativeness of the web-based patient population is often noted as a concern, studies in this field are limited.Objective: This study aimed to investigate the sample bias of patient-centered social media in Dutch patients with gastrointestinal stromal tumor (GIST).Methods: A population-based survey was conducted in the Netherlands among 328 patients with GIST diagnosed 2-13 years ago to investigate their digital communication use with fellow patients. A logistic regression analysis was used to analyze clinical and demographic differences between forum users and nonusers.Results: Overall, 17.9% (59/328) of survey respondents reported having contact with fellow patients via social media. Moreover, 78% (46/59) of forum users made use of GIST patient forums. We found no statistically significant differences for age, sex, socioeconomic status, and time since diagnosis between forum users (n=46) and nonusers (n=273). Patient forum users did differ significantly in (self-reported) treatment phase from nonusers (P=.001). Of the 46 forum users, only 2 (4%) were cured and not being monitored; 3 (7%) were on adjuvant, curative treatment; 19 (41%) were being monitored after adjuvant treatment; and 22 (48%) were on palliative treatment. In contrast, of the 273 patients who did not use disease-specific forums to communicate with fellow patients, 56 (20.5%) were cured and not being monitored, 31 (11.3%) were on curative treatment, 139 (50.9%) were being monitored after treatment, and 42 (15.3%) were on palliative treatment. The odds of being on a patient forum were 2.8 times as high for a patient who is being monitored compared with a patient that is considered cured. The odds of being on a patient forum were 1.9 times as high for patients who were on curative (adjuvant) treatment and 10 times as high for patients who were in the palliative phase compared with patients who were considered cured. Forum users also reported a lower level of social functioning (84.8 out of 100) than nonusers (93.8 out of 100; P=.008).Conclusions: Forum users showed no particular bias on the most important demographic variables of age, sex, socioeconomic status, and time since diagnosis. This may reflect the narrowing digital divide. Overrepresentation and underrepresentation of patients with GIST in different treatment phases on social media should be taken into account when sourcing patient forums for patient-generated health data. A further investigation of the sample bias in other web-based patient populations is warranted. Show less
Dirkson, A.; Verberne, S.; Oortmerssen, G. van; Gelderblom, H.; Kraaij, W. 2022
Patients advise their peers on how to cope with their illness in daily life on online support groups. To date, no efforts have been made to automatically extract recommended coping strategies from... Show morePatients advise their peers on how to cope with their illness in daily life on online support groups. To date, no efforts have been made to automatically extract recommended coping strategies from online patient discussion groups. We introduce this new task, which poses a number of challenges including complex, long entities, a large long-tailed label space, and cross-document relations. We present an initial ontology for coping strategies as a starting point for future research on coping strategies, and the first end-to-end pipeline for extracting coping strategies for side effects. We also compared two possible computational solutions for this novel and highly challenging task; multi-label classification and named entity recognition (NER) with entity linking (EL). We evaluated our methods on the discussion forum from the Facebook group of the worldwide patient support organization 'GIST support international' (GSI); GIST support international donated the data to us. We found that coping strategy extraction is difficult and both methods attain limited performance (measured with F1 score) on held out test sets; multi-label classification outperforms NER+EL (F1=0.220 vs F1=0.155). An inspection of the multi-label classification output revealed that for some of the incorrect predictions, the reference label is close to the predicted label in the ontology (e.g. the predicted label 'juice' instead of the more specific reference label 'grapefruit juice'). Performance increased to F1=0.498 when we evaluated at a coarser level of the ontology. We conclude that our pipeline can be used in a semi-automatic setting, in interaction with domain experts to discover coping strategies for side effects from a patient forum. For example, we found that patients recommend ginger tea for nausea and magnesium and potassium supplements for cramps.This information can be used as input for patient surveys or clinical studies. Show less
Dirkson, A.; Verberne, S.; Kraaij, W.; Oortmerssen, G. van; Gelderblom, H. 2022
Current methods of pharmacovigilance result in severe under-reporting of adverse drug events (ADEs). Patient forums have the potential to complement current pharmacovigilance practices by providing... Show moreCurrent methods of pharmacovigilance result in severe under-reporting of adverse drug events (ADEs). Patient forums have the potential to complement current pharmacovigilance practices by providing real-time uncensored and unsolicited information. We are the first to explore the value of patient forums for rare cancers. To this end, we conduct a case study on a patient forum for Gastrointestinal Stromal Tumor patients. We have developed machine learning algorithms to automatically extract and aggregate side effects from messages on open online discussion forums. We show that patient forum data can provide suggestions for which ADEs impact quality of life the most: For many side effects the relative reporting rate differs decidedly from that of the registration trials, including for example cognitive impairment and alopecia as side effects of avapritinib. We also show that our methods can provide real-world data for long-term ADEs, such as osteoporosis and tremors for imatinib, and novel ADEs not found in registration trials, such as dry eyes and muscle cramping for imatinib. We thus posit that automated pharmacovigilance from patient forums can provide real-world data for ADEs and should be employed as input for medical hypotheses for rare cancers. Show less
Hollander, D. den; Dirkson, A.; Verberne, S.; Kraaij, W.; Oortmerssen, G. van; Gelderblom, H.; ... ; Husson, O. 2022
Purpose European Reference Network on Rare Endocrine Conditions' (Endo-ERN) mission is to reduce and ultimately abolish inequalities in care for patients with rare endocrine conditions in Europe.... Show morePurpose European Reference Network on Rare Endocrine Conditions' (Endo-ERN) mission is to reduce and ultimately abolish inequalities in care for patients with rare endocrine conditions in Europe. This study assesses which themes related to rare endocrine conditions are prioritized by patients for clinical research. Methods A survey was developed, translated into 22 different European languages, and distributed to patients with rare endocrine conditions. Patients were asked to give priority scores to listed prespecified topics: fertility, heritability, tiredness, daily medicine intake, sleep quality, physical discomfort, and ability to work, partake in social life, and sports. They were also asked to suggest further important areas for research in open fields. Results After data cleaning, 1378 survey responses were analyzed. Most responses were received from Northern (47%) and Western Europeans (39%), while Southern (11%) and Eastern Europe (2%) were underrepresented. Respondents were most interested in research concerning ability to participate in social life and work. Patients suggested key areas to work: long-term side effects of medical treatments and quality of life. Some priorities differed between disease groups, both for prespecified and open topics and reflected aspects of patients' individual conditions. Conclusions With this large survey, Endo-ERN gained insight into patients' unmet needs in scientific research. Patients prioritized research on ability to work and participation in social activities, though needs differ between the disease groups. Clinical experts should incorporate the results of this survey into the design of future studies on rare endocrine conditions. We aim to utilize these results in designing patient-reported outcome measures for the disease areas covered by Endo-ERN. Show less
The unprompted patient experiences shared on patient forums contain a wealth of unexploited knowledge. Mining this knowledge and cross-linking it with biomedical literature, could expose novel... Show moreThe unprompted patient experiences shared on patient forums contain a wealth of unexploited knowledge. Mining this knowledge and cross-linking it with biomedical literature, could expose novel insights, which could subsequently provide hypotheses for further clinical research. As of yet, automated methods for open knowledge discovery on patient forum text are lacking. Thus, in this research proposal, we outline future research into methods for mining, aggregating and cross-linking patient knowledge from online forums. Additionally, we aim to address how one could measure the credibility of this extracted knowledge. Show less
The unprompted patient experiences shared on patient forums contain a wealth of unexploited knowledge. Mining this knowledge and cross-linking it with biomedical literature, could expose novel... Show moreThe unprompted patient experiences shared on patient forums contain a wealth of unexploited knowledge. Mining this knowledge and cross-linking it with biomedical literature, could expose novel insights, which could subsequently provide hypotheses for further clinical research. As of yet, automated methods for open knowledge discovery on patient forum text are lacking. Thus, in this research proposal, we outline future research into methods for mining, aggregating and cross-linking patient knowledge from online forums. Additionally, we aim to address how one could measure the credibility of this extracted knowledge. Show less
