Journal of Biomedical Informatics最新文献

Objective:

Methods:

Results:

Conclusion:

Objective

Methods

Results

Conclusion

Objective:

Disease severity scores, or endpoints, are routinely measured during Randomized Controlled Trials (RCTs) to closely monitor the effect of treatment. In real-world clinical practice, although a larger set of patients is observed, the specific RCT endpoints are often not captured, which makes it hard to utilize real-world data (RWD) to evaluate drug efficacy in larger populations.

Methods:

To overcome this challenge, we developed an ensemble technique which learns proxy models of disease endpoints in RWD. Using a multi-stage learning framework applied to RCT data, we first identify features considered significant drivers of disease available within RWD. To create endpoint proxy models, we use Explainable Boosting Machines (EBMs) which allow for both end-user interpretability and modeling of non-linear relationships.

Results:

We demonstrate our approach on two diseases, rheumatoid arthritis (RA) and atopic dermatitis (AD). As we show, our combined feature selection and prediction method achieves good results for both disease areas, improving upon prior methods proposed for predictive disease severity scoring.

Conclusion:

Having disease severity over time for a patient is important to further disease understanding and management. Our results open the door to more use cases in the space of RA and AD such as treatment effect estimates or prognostic scoring on RWD. Our framework may be extended beyond RA and AD to other diseases where the severity score is not well measured in electronic health records.

Objective:

The reading level of health educational materials significantly influences the understandability and accessibility of the information, particularly for minoritized populations. Many patient educational resources surpass widely accepted standards for reading level and complexity. There is a critical need for high-performing text simplification models for health information to enhance dissemination and literacy. This need is particularly acute in cancer education, where effective prevention and screening education can substantially reduce morbidity and mortality.

Methods:

We introduce Simplified Digestive Cancer (SimpleDC), a parallel corpus of cancer education materials tailored for health text simplification research, comprising educational content from the American Cancer Society, Centers for Disease Control and Prevention, and National Cancer Institute. The corpus includes 31 web pages with the corresponding manually simplified versions. It consists of 1183 annotated sentence pairs (361 train, 294 development, and 528 test). Utilizing SimpleDC and the existing Med-EASi corpus, we explore Large Language Model (LLM)-based simplification methods, including fine-tuning, reinforcement learning (RL), reinforcement learning with human feedback (RLHF), domain adaptation, and prompt-based approaches. Our experimentation encompasses Llama 2, Llama 3, and GPT-4. We introduce a novel RLHF reward function featuring a lightweight model adept at distinguishing between original and simplified texts when enables training on unlabeled data.

Results:

Fine-tuned Llama models demonstrated high performance across various metrics. Our RLHF reward function outperformed existing RL text simplification reward functions. The results underscore that RL/RLHF can achieve performance comparable to fine-tuning and improve the performance of fine-tuned models. Additionally, these methods effectively adapt out-of-domain text simplification models to a target domain. The best-performing RL-enhanced Llama models outperformed GPT-4 in both automatic metrics and manual evaluation by subject matter experts.

Conclusion:

The newly developed SimpleDC corpus will serve as a valuable asset to the research community, particularly in patient education simplification. The RL/RLHF methodologies presented herein enable effective training of simplification models on unlabeled text and the utilization of out-of-domain simplification corpora.

Objective

Digital behavior change interventions (DBCIs) are feasibly effective tools for addressing physical activity. However, in-depth understanding of participants’ long-term engagement with DBCIs remains sparse. Since the effectiveness of DBCIs to impact behavior change depends, in part, upon participant engagement, there is a need to better understand engagement as a dynamic process in response to an individual’s ever-changing biological, psychological, social, and environmental context.

Methods

The year-long micro-randomized trial (MRT) HeartSteps II provides an unprecedented opportunity to investigate DBCI engagement among ethnically diverse participants. We combined data streams from wearable sensors (Fitbit Versa, i.e., walking behavior), the HeartSteps II app (i.e. page views), and ecological momentary assessments (EMAs, i.e. perceived intrinsic and extrinsic motivation) to build the idiographic models. A system identification approach and a fluid analogy model were used to conduct autoregressive with exogenous input (ARX) analyses that tested hypothesized relationships between these variables inspired by Self-Determination Theory (SDT) with DBCI engagement through time.

Results

Data from 11 HeartSteps II participants was used to test aspects of the hypothesized SDT dynamic model. The average age was 46.33 (SD=7.4) years, and the average steps per day at baseline was 5,507 steps (SD=6,239). The hypothesized 5-input SDT-inspired ARX model for app engagement resulted in a 31.75 % weighted RMSEA (31.50 % on validation and 31.91 % on estimation), indicating that the model predicted app page views almost 32 % better relative to the mean of the data. Among Hispanic/Latino participants, the average overall model fit across inventories of the SDT fluid analogy was 34.22 % (SD=10.53) compared to 22.39 % (SD=6.36) among non-Hispanic/Latino Whites, a difference of 11.83 %. Across individuals, the number of daily notification prompts received by the participant was positively associated with increased app page views. The weekend/weekday indicator and perceived daily busyness were also found to be key predictors of the number of daily application page views.

Conclusions

This novel approach has significant implications for both personalized and adaptive DBCIs by identifying factors that foster or undermine engagement in an individual’s respective context. Once identified, these factors can be tailored to promote engagement and support sustained behavior change over time.

Objective:

The paper introduces a framework for the evaluation of the encoding of factual scientific knowledge, designed to streamline the manual evaluation process typically conducted by domain experts. Inferring over and extracting information from Large Language Models (LLMs) trained on a large corpus of scientific literature can potentially define a step change in biomedical discovery, reducing the barriers for accessing and integrating existing medical evidence. This work explores the potential of LLMs for dialoguing with biomedical background knowledge, using the context of antibiotic discovery.

Methods:

The framework involves three evaluation steps, each assessing different aspects sequentially: fluency, prompt alignment, semantic coherence, factual knowledge, and specificity of the generated responses. By splitting these tasks between non-experts and experts, the framework reduces the effort required from the latter. The work provides a systematic assessment on the ability of eleven state-of-the-art LLMs, including ChatGPT, GPT-4 and Llama 2, in two prompting-based tasks: chemical compound definition generation and chemical compound–fungus relation determination.

Results:

Although recent models have improved in fluency, factual accuracy is still low and models are biased towards over-represented entities. The ability of LLMs to serve as biomedical knowledge bases is questioned, and the need for additional systematic evaluation frameworks is highlighted.

Conclusion:

While LLMs are currently not fit for purpose to be used as biomedical factual knowledge bases in a zero-shot setting, there is a promising emerging property in the direction of factuality as the models become domain specialised, scale up in size and level of human feedback.

Objective:

As new knowledge is produced at a rapid pace in the biomedical field, existing biomedical Knowledge Graphs (KGs) cannot be manually updated in a timely manner. Previous work in Natural Language Processing (NLP) has leveraged link prediction to infer the missing knowledge in general-purpose KGs. Inspired by this, we propose to apply link prediction to existing biomedical KGs to infer missing knowledge. Although Knowledge Graph Embedding (KGE) methods are effective in link prediction tasks, they are less capable of capturing relations between communities of entities with specific attributes (Fanourakis et al., 2023).

Methods:

To address this challenge, we proposed an entity distance-based method for abstracting a Community Knowledge Graph (CKG) from a simplified version of the pre-existing PubMed Knowledge Graph (PKG) (Xu et al., 2020). For link prediction on the abstracted CKG, we proposed an extension approach for the existing KGE models by linking the information in the PKG to the abstracted CKG. The applicability of this extension was proved by employing six well-known KGE models: TransE, TransH, DistMult, ComplEx, SimplE, and RotatE. Evaluation metrics including Mean Rank (MR), Mean Reciprocal Rank (MRR), and Hits@$k$ were used to assess the link prediction performance. In addition, we presented a backtracking process that traces the results of CKG link prediction back to the PKG scale for further comparison.

Results:

Six different CKGs were abstracted from the PKG by using embeddings of the six KGE methods. The results of link prediction in these abstracted CKGs indicate that our proposed extension can improve the existing KGE methods, achieving a top-10 accuracy of 0.69 compared to 0.5 for TransE, 0.7 compared to 0.54 for TransH, 0.67 compared to 0.6 for DistMult, 0.73 compared to 0.57 for ComplEx, 0.73 compared to 0.63 for SimplE, and 0.85 compared to 0.76 for RotatE on their CKGs, respectively. These improved performances also highlight the wide applicability of the extension approach.

Conclusion:

This study proposed novel insights into abstracting CKGs from the PKG. The extension approach indicated enhanced performance of the existing KGE methods and has applicability. As an interesting future extension, we plan to conduct link prediction for entities that are newly introduced to the PKG.

Background

In oncology, electronic health records contain textual key information for the diagnosis, staging, and treatment planning of patients with cancer. However, text data processing requires a lot of time and effort, which limits the utilization of these data. Recent advances in natural language processing (NLP) technology, including large language models, can be applied to cancer research. Particularly, extracting the information required for the pathological stage from surgical pathology reports can be utilized to update cancer staging according to the latest cancer staging guidelines.

Objectives

This study has two main objectives. The first objective is to evaluate the performance of extracting information from text-based surgical pathology reports and determining pathological stages based on the extracted information using fine-tuned generative language models (GLMs) for patients with lung cancer. The second objective is to determine the feasibility of utilizing relatively small GLMs for information extraction in a resource-constrained computing environment.

Methods

Lung cancer surgical pathology reports were collected from the Common Data Model database of Seoul National University Bundang Hospital (SNUBH), a tertiary hospital in Korea. We selected 42 descriptors necessary for tumor-node (TN) classification based on these reports and created a gold standard with validation by two clinical experts. The pathology reports and gold standard were used to generate prompt-response pairs for training and evaluating GLMs which then were used to extract information required for staging from pathology reports.

Results

We evaluated the information extraction performance of six trained models as well as their performance in TN classification using the extracted information. The Deductive Mistral-7B model, which was pre-trained with the deductive dataset, showed the best performance overall, with an exact match ratio of 92.24% in the information extraction problem and an accuracy of 0.9876 (predicting T and N classification concurrently) in classification.

Conclusion

This study demonstrated that training GLMs with deductive datasets can improve information extraction performance, and GLMs with a relatively small number of parameters at approximately seven billion can achieve high performance in this problem. The proposed GLM-based information extraction method is expected to be useful in clinical decision-making support, lung cancer staging and research.