اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدInformation Extraction of Clinical Trial Eligibility Criteria
61
0
0.0
(
0
)
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
Clinical trials predicate subject eligibility on a diversity of criteria ranging from patient demographics to food allergies. Trials post their requirements as semantically complex, unstructured free-text. Formalizing trial criteria to a computer-interpretable syntax would facilitate eligibility determination. In this paper, we investigate an information extraction (IE) approach for grounding criteria from trials in ClinicalTrials(dot)gov to a shared knowledge base. We frame the problem as a novel knowledge base population task, and implement a solution combining machine learning and context free grammar. To our knowledge, this work is the first criteria extraction system to apply attention-based conditional random field architecture for named entity recognition (NER), and word2vec embedding clustering for named entity linking (NEL). We release the resources and core components of our system on GitHub at https://github.com/facebookresearch/Clinical-Trial-Parser. Finally, we report our per module and end to end performances; we conclude that our system is competitive with Criteria2Query, which we view as the current state-of-the-art in criteria extraction.
قيم البحث
اقرأ أيضاً
The Bidirectional Encoder Representations from Transformers (BERT) model has achieved the state-of-the-art performance for many natural language processing (NLP) tasks. Yet, limited research has been contributed to studying its effectiveness when the
target domain is shifted from the pre-training corpora, for example, for biomedical or clinical NLP applications. In this paper, we applied it to a widely studied a hospital information extraction (IE) task and analyzed its performance under the transfer learning setting. Our application became the new state-of-the-art result by a clear margin, compared with a range of existing IE models. Specifically, on this nursing handover data set, the macro-average F1 score from our model was 0.438, whilst the previous best deep learning models had 0.416. In conclusion, we showed that BERT based pre-training models can be transferred to health-related documents under mild conditions and with a proper fine-tuning process.
Clinical trials provide essential guidance for practicing Evidence-Based Medicine, though often accompanying with unendurable costs and risks. To optimize the design of clinical trials, we introduce a novel Clinical Trial Result Prediction (CTRP) tas
k. In the CTRP framework, a model takes a PICO-formatted clinical trial proposal with its background as input and predicts the result, i.e. how the Intervention group compares with the Comparison group in terms of the measured Outcome in the studied Population. While structured clinical evidence is prohibitively expensive for manual collection, we exploit large-scale unstructured sentences from medical literature that implicitly contain PICOs and results as evidence. Specifically, we pre-train a model to predict the disentangled results from such implicit evidence and fine-tune the model with limited data on the downstream datasets. Experiments on the benchmark Evidence Integration dataset show that the proposed model outperforms the baselines by large margins, e.g., with a 10.7% relative gain over BioBERT in macro-F1. Moreover, the performance improvement is also validated on another dataset composed of clinical trials related to COVID-19.
FDA has been promoting enrollment practices that could enhance the diversity of clinical trial populations, through broadening eligibility criteria. However, how to broaden eligibility remains a significant challenge. We propose an AI approach to Coh
ort Optimization (AICO) through transformer-based natural language processing of the eligibility criteria and evaluation of the criteria using real-world data. The method can extract common eligibility criteria variables from a large set of relevant trials and measure the generalizability of trial designs to real-world patients. It overcomes the scalability limits of existing manual methods and enables rapid simulation of eligibility criteria design for a disease of interest. A case study on breast cancer trial design demonstrates the utility of the method in improving trial generalizability.
The best evidence concerning comparative treatment effectiveness comes from clinical trials, the results of which are reported in unstructured articles. Medical experts must manually extract information from articles to inform decision-making, which
is time-consuming and expensive. Here we consider the end-to-end task of both (a) extracting treatments and outcomes from full-text articles describing clinical trials (entity identification) and, (b) inferring the reported results for the former with respect to the latter (relation extraction). We introduce new data for this task, and evaluate models that have recently achieved state-of-the-art results on similar tasks in Natural Language Processing. We then propose a new method motivated by how trial results are typically presented that outperforms these purely data-driven baselines. Finally, we run a fielded evaluation of the model with a non-profit seeking to identify existing drugs that might be re-purposed for cancer, showing the potential utility of end-to-end evidence extraction systems.
Clinical case reports are written descriptions of the unique aspects of a particular clinical case, playing an essential role in sharing clinical experiences about atypical disease phenotypes and new therapies. However, to our knowledge, there has be
en no attempt to develop an end-to-end system to annotate, index, or otherwise curate these reports. In this paper, we propose a novel computational resource platform, CREATe, for extracting, indexing, and querying the contents of clinical case reports. CREATe fosters an environment of sustainable resource support and discovery, enabling researchers to overcome the challenges of information science. An online video of the demonstration can be viewed at https://youtu.be/Q8owBQYTjDc.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
