Kimia Ghobadi

Nimeesha Chan, Felix Parker, William Bennett et al.

The complexity and heterogeneity of data in many real-world applications pose significant challenges for traditional machine learning and signal processing techniques. For instance, in medicine, effective analysis of diverse physiological signals is crucial for patient monitoring and clinical decision-making and yet highly challenging. We introduce MedTsLLM, a general multimodal large language model (LLM) framework that effectively integrates time series data and rich contextual information in the form of text to analyze physiological signals, performing three tasks with clinical relevance: semantic segmentation, boundary detection, and anomaly detection in time series. These critical tasks enable deeper analysis of physiological signals and can provide actionable insights for clinicians. We utilize a reprogramming layer to align embeddings of time series patches with a pretrained LLM's embedding space and make effective use of raw time series, in conjunction with textual context. Given the multivariate nature of medical datasets, we develop methods to handle multiple covariates. We additionally tailor the text prompt to include patient-specific information. Our model outperforms state-of-the-art baselines, including deep learning models, other LLMs, and clinical methods across multiple medical domains, specifically electrocardiograms and respiratory waveforms. MedTsLLM presents a promising step towards harnessing the power of LLMs for medical time series analysis that can elevate data-driven tools for clinicians and improve patient outcomes.

Farzin Ahmadi, Fardin Ganjkhanloo, Kimia Ghobadi

Linear constrained optimization techniques have been applied to many real-world settings. In recent years, inferring the unknown parameters and functions inside an optimization model has also gained traction. This inference is often based on existing observations and/or known parameters. Consequently, such models require reliable, easily accessed, and easily interpreted examples to be evaluated. To facilitate research in such directions, we provide a modified dataset based on dietary behaviors of different groups of people, their demographics, and pre-existing conditions, among other factors. This data is gathered from the National Health and Nutrition Examination Survey (NHANES) and complemented with the nutritional data from the United States Department of Agriculture (USDA). We additionally provide tailored datasets for hypertension and pre-diabetic patients as groups of interest who may benefit from targetted diets such as the Dietary Approaches to Stop Hypertension (DASH) eating plan. The data is compiled and curated in such a way that it is suitable as input to linear optimization models. We hope that this data and its supplementary, open-accessed materials can accelerate and simplify interpretations and research on linear optimization and constrained inference models. The complete dataset can be found in the following repository: https://github.com/CSSEHealthcare/InverseLearning

Fardin Ganjkhanloo, Emmett Springer, Erik H. Hoyer et al.

In this study, we aim to better align fall risk prediction from the Johns Hopkins Fall Risk Assessment Tool (JHFRAT) with additional clinically meaningful measures via a data-driven modelling approach. We conducted a retrospective cohort analysis of 54,209 inpatient admissions from three Johns Hopkins Health System hospitals between March 2022 and October 2023. A total of 20,208 admissions were included as high fall risk encounters, and 13,941 were included as low fall risk encounters. To incorporate clinical knowledge and maintain interpretability, we employed constrained score optimization (CSO) models to reweight the JHFRAT scoring weights, while preserving its additive structure and clinical thresholds. Recalibration refers to adjusting item weights so that the resulting score can order encounters more consistently by the study's risk labels, and without changing the tool's form factor or deployment workflow. The model demonstrated significant improvements in predictive performance over the current JHFRAT (CSO AUC-ROC=0.91, JHFRAT AUC-ROC=0.86). This performance improvement translates to protecting an additional 35 high-risk patients per week across the Johns Hopkins Health System. The constrained score optimization models performed similarly with and without the EHR variables. Although the benchmark black-box model (XGBoost), improves upon the performance metrics of the knowledge-based constrained logistic regression (AUC-ROC=0.94), the CSO demonstrates more robustness to variations in risk labeling. This evidence-based approach provides a robust foundation for health systems to systematically enhance inpatient fall prevention protocols and patient safety using data-driven optimization techniques, contributing to improved risk assessment and resource allocation in healthcare settings.

Fardin Gankhanloo, Emmett Springer, Erik H. Hoyer et al.

Risk assessment tools in healthcare commonly employ point-based scoring systems that map patients to ordinal risk categories via thresholds. While electronic health record (EHR) data presents opportunities for data-driven optimization of these tools, two fundamental challenges impede standard supervised learning: (1) partial supervision arising from intervention-censored outcomes, where only extreme categories can be reliably labeled, and (2) asymmetric misclassification costs that increase with ordinal distance. We propose a mixed-integer programming (MIP) framework that jointly optimizes scoring weights and category thresholds under these constraints. Our approach handles partial supervision through per-instance feasible label sets, incorporates asymmetric distance-aware objectives, and prevents middle-category collapse via minimum threshold gaps. We further develop a CSO relaxation using softplus losses that preserves the ordinal structure while enabling efficient optimization. The framework supports governance constraints including sign restrictions, sparsity, and minimal modifications to incumbent tools, ensuring practical deployability in clinical workflows.

Fardin Ganjkhanloo, Emmett Springer, Erik H. Hoyer et al.

In this study we aim to better align fall risk prediction from the Johns Hopkins Fall Risk Assessment Tool (JHFRAT) with additional clinically meaningful measures via a data-driven modelling approach. We conducted a retrospective analysis of 54,209 inpatient admissions from three Johns Hopkins Health System hospitals between March 2022 and October 2023. A total of 20,208 admissions were included as high fall risk encounters, and 13,941 were included as low fall risk encounters. To incorporate clinical knowledge and maintain interpretability, we employed constrained score optimization (CSO) models on JHFRAT assessment data and additional electronic health record (EHR) variables. The model demonstrated significant improvements in predictive performance over the current JHFRAT (CSO AUC-ROC=0.91, JHFRAT AUC-ROC=0.86). The constrained score optimization models performed similarly with and without the EHR variables. Although the benchmark black-box model (XGBoost), improves upon the performance metrics of the knowledge-based constrained logistic regression (AUC-ROC=0.94), the CSO demonstrates more robustness to variations in risk labelling. This evidence-based approach provides a robust foundation for health systems to systematically enhance inpatient fall prevention protocols and patient safety using data-driven optimization techniques, contributing to improved risk assessment and resource allocation in healthcare settings.

Ha Manh Bui, Felix Parker, Kimia Ghobadi et al.

We study the Non-Stationary Reinforcement Learning (RL) under distribution shifts in both finite-horizon episodic and infinite-horizon discounted Markov Decision Processes (MDPs). In the finite-horizon case, the transition functions may suddenly change at a particular episode. In the infinite-horizon setting, such changes can occur at an arbitrary time step during the agent's interaction with the environment. While the Q-learning Upper Confidence Bound algorithm (QUCB) can discover a proper policy during learning, due to the distribution shifts, this policy can exploit sub-optimal rewards after the shift happens. To address this issue, we propose Density-QUCB (DQUCB), a shift-aware Q-learning~UCB algorithm, which uses a transition density function to detect distribution shifts, then leverages its likelihood to enhance the uncertainty estimation quality of Q-learning~UCB, resulting in a balance between exploration and exploitation. Theoretically, we prove that our oracle DQUCB achieves a better regret guarantee than QUCB. Empirically, our DQUCB enjoys the computational efficiency of model-free RL and outperforms QUCB baselines by having a lower regret across RL tasks, as well as a real-world COVID-19 patient hospital allocation task using a Deep-Q-learning architecture.

Felix Parker, Nimeesha Chan, Chi Zhang et al.

Complex numerical time series analysis often demands multi-step reasoning capabilities beyond current models' reach. Tasks like medical diagnosis and weather forecasting require sequential reasoning processes -- including counterfactual analysis, logical deduction, knowledge application, and multi-modal contextual integration -- that existing time series models cannot explicitly perform. While recent research has shown large language models (LLMs) can achieve sophisticated Chain-of-Thought (CoT) reasoning through reinforcement learning (RL), these advances have primarily focused on mathematical and coding domains, with LLMs still demonstrating poor performance on time series tasks. We introduce Chain Of thought for Understanding Numerical Time Series (COUNTS), the first framework that trains LLMs to perform CoT reasoning across diverse time series tasks using RL with verifiable rewards. Our approach employs a Residual Vector-Quantized VAE to create high-fidelity discrete tokens that seamlessly integrate into a pre-trained LLM's vocabulary. COUNTS undergoes a two-stage training process: first, supervised fine-tuning on time series analysis tasks to master our novel representations, followed by Group Relative Policy Optimization training on verifiable problems using prompting strategies that encourage explicit reasoning steps before producing final answers. Our experiments demonstrate that this RL-driven approach with intermediate CoT reasoning significantly enhances LLM performance across various time series analysis tasks, opening new possibilities for complex temporal data reasoning.

Felix Parker, Nimeesha Chan, Chi Zhang et al.

Time series data is fundamental to decision-making in many crucial domains including healthcare, finance, and environmental science. However, analyzing this data often requires incorporating unstructured contextual information, answering domain-specific questions, and generating natural language explanations -- capabilities that traditional time series models lack due to their inability to process text. While Large Language Models (LLMs) excel at contextual reasoning and knowledge integration, they struggle with numerical time series due to inefficient text-based representations and limited exposure to temporal data during pretraining. We address this gap by augmenting an LLM with specialized time series perception through a patch-based encoder-decoder architecture. We train this Time Series-augmented LLM (TsLLM) on a large corpus of over 2 million interleaved time series and text examples spanning diverse analysis tasks: forecasting with contextual information, time series question-answering, pattern explanation, classification with natural language outputs, and report generation. This training enables TsLLM to leverage both its language understanding and newly acquired temporal reasoning capabilities. While not designed to surpass specialized models on traditional benchmarks, TsLLM demonstrates strong performance on tasks requiring the integration of time series analysis with natural language -- capabilities that existing approaches cannot provide. Our work establishes a new paradigm for time series analysis that bridges numerical computation and natural language understanding, democratizing access to sophisticated temporal reasoning through natural language interaction.

Mathias Unberath, Kimia Ghobadi, Scott Levin et al.

The COVID-19 crisis has brought about new clinical questions, new workflows, and accelerated distributed healthcare needs. While artificial intelligence (AI)-based clinical decision support seemed to have matured, the application of AI-based tools for COVID-19 has been limited to date. In this perspective piece, we identify opportunities and requirements for AI-based clinical decision support systems and highlight challenges that impact "AI readiness" for rapidly emergent healthcare challenges.