Tianrun Cai

BACKGROUND Renal cell carcinoma (RCC) recurrence after definitive therapy remains difficult to predict using conventional clinicopathologic risk models. Computed tomography (CT), electronic health record data, and radiology text may contain complementary prognostic signals, but many multimodal models are difficult to interpret. OBJECTIVE This study aimed to develop and evaluate an interpretable multimodal model that uses residual regression to identify imaging information not captured by known semantic features and to predict RCC recurrence after surgery. METHODS We conducted a retrospective cohort study using Mass General Brigham data from January 1, 2000, through September 1, 2022, with the public DeepLesion data set used for pretraining. The final RCC imaging cohort included 1615 patients. A CT contrastive language-image pretraining model aligned imaging and text embeddings; residual regression isolated an imaging component orthogonal to concept unique identifier–based text features. Baseline clinical, radiomic, natural language processing, and residual features were combined in XGBoost Cox models. Models were trained using algorithmically derived recurrence labels and evaluated using an expert-annotated subset. Discrimination was assessed at 12, 60, and 120 months, and predicted risk groups were compared using time-to-event analyses. RESULTS The ensemble model achieved area under the receiver operating characteristic curve values of 0.86 (95% CI 0.85-0.87) at 12 months, 0.78 (95% CI 0.77-0.80) at 60 months, and 0.82 (95% CI 0.81-0.83) at 120 months. The corresponding baseline-only values were 0.68 (95% CI 0.66-0.71), 0.73 (95% CI 0.72-0.75), and 0.79 (95% CI 0.78-0.81). At 60 months, ensemble-defined high- and low-risk groups had a hazard ratio of 6.34 (95% CI 2.70-14.91; P<.001). Residual features mapped to interpretable imaging phenotypes, including necrosis, infiltrative growth, and vascular characteristics. CONCLUSIONS Residual regression–derived imaging features added prognostic information to clinical, radiomic, and text-derived features while retaining an interpretable link to imaging phenotypes. External and prospective validation is needed before clinical use.

Background: The current landscape of emergency care (EC) is marked by high demand, leading to issues such as emergency department boarding, overcrowding, and subsequent delays that impact the quality and safety of patient care. Integrating data science into EC can enhance decision-making with predictive, preventative, personalized, and participatory approaches. However, gaps in adherence to fairness, accountability, interpretability, and responsibility are evident, particularly due to barriers to data-sharing, which often result in a lack of transparency and robust oversight in these applications. Objective: The FAIR-EC (Fair, Accountable, Interpretable, and Responsible-Emergency Care) collaboration adapts the existing Fair, Accountable, Interpretable, and Responsible principles to address emerging challenges as data science integrates with EC. This initiative aims to transform EC by establishing ethical artificial intelligence standards specifically tailored for this integration. By bridging the gap between EC professionals, data scientists, and other stakeholders, the collaboration promotes international cooperation that leverages advanced data science techniques to enhance EC outcomes across different care settings. Methods: We propose a federated research design to analyze extensive datasets from various global institutions without compromising patient privacy. This approach transforms epidemiological research with advanced data science techniques, emphasizing the harmonization of data for comprehensive analyses across different health care systems. Results: The FAIR-EC initiative has facilitated the identification and harmonization of datasets from diverse geographical regions, enabling the examination of regional variations in EC practices. As of paper submission, participating sites have identified retrospective EC datasets totaling >2 million records (eg, Duke Health >400,000 and Singapore General Hospital >1.7 million records). Initial projects have demonstrated feasibility and operational readiness, including implementation of federated workflows and ongoing development of a federated scoring system, cross-site evaluation, and adaptation of association studies and predictive models across various regions. Cross-site harmonization and pilot analyses are underway (with local ethics approvals in progress), and first multisite results are expected to be submitted in mid-late 2026, with additional project-level publications anticipated in 2027. These efforts highlight the feasibility of leveraging advanced data science techniques to address the complexities of EC while preserving patient privacy without centralizing individual-level data. This project was funded from September 1, 2022, to August 31, 2023. Conclusions: FAIR-EC integrates data science ethically and effectively into EC, addressing challenges such as fragmented data, real-time handoffs, and public health crises. Its federated design harmonizes diverse data streams while preserving privacy, and its emphasis on ethical artificial intelligence aligns with the dynamic nature of EC. Despite challenges in data variability and system complexity, FAIR-EC establishes a strong foundation for innovation in global EC.

Classical probabilistic graphical models face fundamental challenges in modern data environments, which are characterized by high dimensionality, source heterogeneity, and stringent data-sharing constraints. In this work, we revisit the Ising model, a well-established member of the Markov Random Field (MRF) family, and develop a distributed framework that enables scalable and privacy-preserving representation learning from large-scale binary data with inherent low-rank structure. Our approach optimizes a non-convex surrogate loss function via bi-factored gradient descent, offering substantial computational and communication advantages over conventional convex approaches. We evaluate our algorithm on multi-institutional electronic health record (EHR) datasets from 58,248 patients across the University of Pittsburgh Medical Center (UPMC) and Mass General Brigham (MGB), demonstrating superior performance in global representation learning and downstream clinical tasks, including relationship detection, patient phenotyping, and patient clustering. These results highlight a broader potential for statistical inference in federated, high-dimensional settings while addressing the practical challenges of data complexity and multi-institutional integration.

Managing chronic diseases requires ongoing monitoring of disease activity and therapeutic responses to optimize treatment plans. With the growing availability of disease-modifying therapies, it is crucial to investigate comparative effectiveness and long-term outcomes beyond those available from randomized clinical trials. We introduce a comprehensive pipeline for generating reproducible and generalizable real-world evidence on disease outcomes by leveraging electronic health record data. The pipeline first generates scalable disease outcomes by linking electronic health record data with registry data containing a small sample of labeled outcomes. It then applies causal analysis using these scalable outcomes to evaluate therapies for chronic diseases. The implementation of the pipeline is illustrated in a case study based on multiple sclerosis. Our approach addresses challenges in real-world evidence generation for disease activity of chronic conditions, specifically the lack of direct observations on key outcomes and biases arising from imperfect or incomplete data. We present advanced machine learning techniques such as semisupervised and ensemble methods to impute missing outcome data, further incorporating steps for calibrated causal analyses and bias correction.

UNSTRUCTURED Managing chronic diseases requires ongoing monitoring of disease activity and therapeutic responses to optimize treatment plans. With the growing availability of disease-modifying therapies, it is crucial to investigate comparative effectiveness and long-term outcomes beyond those available from randomized clinical trials. We introduce a comprehensive pipeline for generating reproducible and generalizable real-world evidence on disease outcomes by leveraging electronic health record data. The pipeline first generates scalable disease outcomes by linking electronic health record data with registry data containing a small sample of labeled outcomes. It then applies causal analysis using these scalable outcomes to evaluate therapies for chronic diseases. The implementation of the pipeline is illustrated in a case study based on multiple sclerosis. Our approach addresses challenges in real-world evidence generation for disease activity of chronic conditions, specifically the lack of direct observations on key outcomes and biases arising from imperfect or incomplete data. We present advanced machine learning techniques such as semisupervised and ensemble methods to impute missing outcome data, further incorporating steps for calibrated causal analyses and bias correction.

Objective: Patients with rheumatoid arthritis (RA) are at increased risk of cardiovascular disease (CVD) including heart failure (HF). However, little is known regarding the relative risks of HF subtypes such as HF with preserved ejection fraction (HFpEF) or reduced ejection fraction (HFrEF) in RA compared with non‐RA.Methods: We identified patients with RA and matched non‐RA comparators among participants consenting to broad research from two large academic centers. We identified incident HF and categorized HF subtypes based on EF closest to the HF incident date. Covariates included age, sex, and established CVD risk factors. Cox proportional hazards models were used to estimate the hazard ratios (HRs) for incident HF and HF subtypes.Results: We studied 1,445 patients with RA and 4,335 matched non‐RA comparators (mean age 51.4 and 51.7 years, respectively; 78.7% female). HFpEF was the most common HF subtype in both groups (65% in RA vs 59% in non‐RA). Patients with RA had an HR of 1.79 (95% confidence interval [CI] 1.38–2.32) for incident HF compared with those without RA after adjusting for CVD risk factors. Patients with RA had a higher rate of HFpEF (HR 1.99, 95% CI 1.43–2.77), but there was no statistical difference in the HFrEF rate (HR 1.45, 95% CI 0.81–2.60).Conclusion: RA was associated with a higher rate of HF overall compared with non‐RA, even after adjustment for established CVD risk factors. The elevated risk was driven by HFpEF, supporting a role for inflammation in HFpEF and highlighting potential opportunities to address this excess risk in RA.

Objective: We aimed to examine the feasibility of applying natural language processing (NLP) to unstructured electronic health record (EHR) documents to detect the presence of financial insecurity among patients with rheumatologic disease enrolled in an integrated care management program (iCMP).Methods: We incorporated supervised, rule‐based NLP and statistical methods to identify financial insecurity among patients with rheumatic conditions enrolled in an iCMP (n = 20,395) in a multihospital EHR system. We constructed a lexicon for financial insecurity using data from available knowledge sources and then reviewed EHR notes from 538 randomly selected individuals (training cohort n = 366, validation cohort n = 172). We manually categorized records as having “definite,” “possible,” or “no” mention of financial insecurity. All available notes were processed using Narrative Information Linear Extraction, a rule‐based version of NLP. Models were trained using the NLP features for financial insecurity using logistic, least absolute shrinkage operator (LASSO), and random forest performance characteristic and were compared with the reference standard.Results: A total of 245,142 notes were processed from 538 individual patient records. Financial insecurity was present among 100 (27%) individuals in the training cohort and 63 (37%) in the validation cohort. The LASSO and random forest models performed identically and slightly better than logistic regression, with positive predictive values of 0.90, sensitivities of 0.29, and specificities of 0.98.Conclusion: The development of a context‐driven lexicon used with rule‐based NLP to extract data that identify financial insecurity is feasible for use and improved the capture for presence of financial insecurity with high accuracy. In the absence of a standard lexicon and construct definition for financial insecurity status, additional studies are needed to optimize the sensitivity of algorithms to categorize financial insecurity with construct validity.

Objective: Social determinants of health (SDoH), such as poverty, are associated with increased burden and severity of rheumatic and musculoskeletal diseases. This study was undertaken to study the prevalence and documentation of SDoH‐related needs in electronic health records (EHRs) of individuals with these conditions.Methods: We randomly selected individuals with ≥1 International Classification of Diseases, Ninth/Tenth Revision (ICD‐9/10) code for a rheumatic/musculoskeletal condition enrolled in a multihospital integrated care management program that coordinates care for medically and/or psychosocially complex individuals. We assessed SDoH documentation using terms for financial needs, food insecurity, housing instability, transportation, and medication access according to EHR note review and ICD‐10 SDoH billing codes (Z codes). We used multivariable logistic regression to examine associations between demographic factors (age, gender, race, ethnicity, insurance) and ≥1 (versus 0) SDoH need as the odds ratio (OR) with 95% confidence interval (95% CI).Results: Among 558 individuals with rheumatic/musculoskeletal conditions, 249 (45%) had ≥1 SDoH need documented in EHR notes by social workers, care coordinators, nurses, and physicians. A total of 171 individuals (31%) had financial insecurity, 105 (19%) had transportation needs, 94 (17%) had food insecurity; 5% had ≥1 related Z code. In the multivariable model, the odds of having ≥1 SDoH need was 2.45 times higher (95% CI 1.17–5.11) for Black versus White individuals and significantly higher for Medicaid or Medicare beneficiaries versus commercially insured individuals.Conclusion: Nearly half of this sample of complex care management patients with rheumatic/musculoskeletal conditions had SDoH documented within EHR notes; financial insecurity was the most prevalent. Only 5% of patients had representative billing codes suggesting that systematic strategies to extract SDoH from notes are needed.

Although randomized controlled trials (RCTs) are the gold standard for establishing the efficacy and safety of a medical treatment, real-world evidence (RWE) generated from real-world data has been vital in postapproval monitoring and is being promoted for the regulatory process of experimental therapies. An emerging source of real-world data is electronic health records (EHRs), which contain detailed information on patient care in both structured (eg, diagnosis codes) and unstructured (eg, clinical notes and images) forms. Despite the granularity of the data available in EHRs, the critical variables required to reliably assess the relationship between a treatment and clinical outcome are challenging to extract. To address this fundamental challenge and accelerate the reliable use of EHRs for RWE, we introduce an integrated data curation and modeling pipeline consisting of 4 modules that leverage recent advances in natural language processing, computational phenotyping, and causal modeling techniques with noisy data. Module 1 consists of techniques for data harmonization. We use natural language processing to recognize clinical variables from RCT design documents and map the extracted variables to EHR features with description matching and knowledge networks. Module 2 then develops techniques for cohort construction using advanced phenotyping algorithms to both identify patients with diseases of interest and define the treatment arms. Module 3 introduces methods for variable curation, including a list of existing tools to extract baseline variables from different sources (eg, codified, free text, and medical imaging) and end points of various types (eg, death, binary, temporal, and numerical). Finally, module 4 presents validation and robust modeling methods, and we propose a strategy to create gold-standard labels for EHR variables of interest to validate data curation quality and perform subsequent causal modeling for RWE. In addition to the workflow proposed in our pipeline, we also develop a reporting guideline for RWE that covers the necessary information to facilitate transparent reporting and reproducibility of results. Moreover, our pipeline is highly data driven, enhancing study data with a rich variety of publicly available information and knowledge sources. We also showcase our pipeline and provide guidance on the deployment of relevant tools by revisiting the emulation of the Clinical Outcomes of Surgical Therapy Study Group Trial on laparoscopy-assisted colectomy versus open colectomy in patients with early-stage colon cancer. We also draw on existing literature on EHR emulation of RCTs together with our own studies with the Mass General Brigham EHR.

UNSTRUCTURED Although randomized controlled trials (RCTs) are the gold standard for establishing the efficacy and safety of a medical treatment, real-world evidence (RWE) generated from real-world data has been vital in postapproval monitoring and is being promoted for the regulatory process of experimental therapies. An emerging source of real-world data is electronic health records (EHRs), which contain detailed information on patient care in both structured (eg, diagnosis codes) and unstructured (eg, clinical notes and images) forms. Despite the granularity of the data available in EHRs, the critical variables required to reliably assess the relationship between a treatment and clinical outcome are challenging to extract. To address this fundamental challenge and accelerate the reliable use of EHRs for RWE, we introduce an integrated data curation and modeling pipeline consisting of 4 modules that leverage recent advances in natural language processing, computational phenotyping, and causal modeling techniques with noisy data. Module 1 consists of techniques for data harmonization. We use natural language processing to recognize clinical variables from RCT design documents and map the extracted variables to EHR features with description matching and knowledge networks. Module 2 then develops techniques for cohort construction using advanced phenotyping algorithms to both identify patients with diseases of interest and define the treatment arms. Module 3 introduces methods for variable curation, including a list of existing tools to extract baseline variables from different sources (eg, codified, free text, and medical imaging) and end points of various types (eg, death, binary, temporal, and numerical). Finally, module 4 presents validation and robust modeling methods, and we propose a strategy to create gold-standard labels for EHR variables of interest to validate data curation quality and perform subsequent causal modeling for RWE. In addition to the workflow proposed in our pipeline, we also develop a reporting guideline for RWE that covers the necessary information to facilitate transparent reporting and reproducibility of results. Moreover, our pipeline is highly data driven, enhancing study data with a rich variety of publicly available information and knowledge sources. We also showcase our pipeline and provide guidance on the deployment of relevant tools by revisiting the emulation of the Clinical Outcomes of Surgical Therapy Study Group Trial on laparoscopy-assisted colectomy versus open colectomy in patients with early-stage colon cancer. We also draw on existing literature on EHR emulation of RCTs together with our own studies with the Mass General Brigham EHR.