Alexander Rodríguez

Wenhao Mu, Facundo Yan, Anik Mumssen et al.

Deep learning has enabled significant advances in time-series causal inference, yet progress remains constrained by the lack of realistic benchmarks with observable counterfactual outcomes. Existing datasets either rely on real-world observations without ground-truth counterfactuals or on simplified simulations that fail to capture complex causal dynamics. To address this gap, we develop a large-scale benchmark for counterfactual prediction in epidemic time series under dynamic interventions. Unlike existing benchmarks, it supports static and time-varying treatments, as well as both single-policy and multi-policy intervention settings, enabling evaluation of causal inference methods across a broad range of causal inference scenarios. Leveraging a calibrated agent-based model grounded in real-world demographic, mobility, epidemiological, and policy data, we generate realistic counterfactual trajectories across more than 150 U.S. counties. Using this benchmark, we evaluate widely used and state-of-the-art causal inference methods, revealing substantial performance differences and highlighting the challenges of realistic time-series causal reasoning.

Yuhan Yang, Ruipu Li, Alexander Rodríguez

Scientific simulators are increasingly being integrated into LLM-driven systems for high-stakes simulation-driven decision-making. However, existing frameworks primarily use LLMs to generate, calibrate, or execute simulators, treating them as black-box interfaces rather than as structured mechanistic systems that can be reasoned about. As a result, current approaches lack the ability to identify, represent, and reason about the assumptions and mechanisms underlying simulator behavior, limiting transparency, auditability, and decision justification. We introduce MechSim, a mechanism-grounded neuro-symbolic reasoning framework for executable scientific simulators. Unlike prior neuro-symbolic approaches that primarily reason over static symbolic structures, MechSim enables LLM agents to reason about the mechanisms, assumptions, and execution behavior of scientific simulators. Our framework represents simulators through a shared structured schema capturing assumptions, variables, mechanism dependencies, and execution traces. On top of this representation, LLM agents operate as constrained reasoning engines that generate structured, evidence-grounded explanations linking simulator outcomes to their underlying mechanisms. We evaluate our approach across multiple high-stakes domains and show that it improves mechanism-level explanation quality, simulator analysis, and downstream decision-making reliability.

Ayush Chopra, Alexander Rodríguez, Jayakumar Subramanian et al.

Mechanistic simulators are an indispensable tool for epidemiology to explore the behavior of complex, dynamic infections under varying conditions and navigate uncertain environments. Agent-based models (ABMs) are an increasingly popular simulation paradigm that can represent the heterogeneity of contact interactions with granular detail and agency of individual behavior. However, conventional ABM frameworks are not differentiable and present challenges in scalability; due to which it is non-trivial to connect them to auxiliary data sources. In this paper, we introduce GradABM: a scalable, differentiable design for agent-based modeling that is amenable to gradient-based learning with automatic differentiation. GradABM can quickly simulate million-size populations in few seconds on commodity hardware, integrate with deep neural networks and ingest heterogeneous data sources. This provides an array of practical benefits for calibration, forecasting, and evaluating policy interventions. We demonstrate the efficacy of GradABM via extensive experiments with real COVID-19 and influenza datasets.

Alexander Rodríguez, Harshavardhan Kamarthi, Pulak Agarwal et al.

The COVID-19 pandemic has brought forth the importance of epidemic forecasting for decision makers in multiple domains, ranging from public health to the economy as a whole. While forecasting epidemic progression is frequently conceptualized as being analogous to weather forecasting, however it has some key differences and remains a non-trivial task. The spread of diseases is subject to multiple confounding factors spanning human behavior, pathogen dynamics, weather and environmental conditions. Research interest has been fueled by the increased availability of rich data sources capturing previously unobservable facets and also due to initiatives from government public health and funding agencies. This has resulted, in particular, in a spate of work on 'data-centered' solutions which have shown potential in enhancing our forecasting capabilities by leveraging non-traditional data sources as well as recent innovations in AI and machine learning. This survey delves into various data-driven methodological and practical advancements and introduces a conceptual framework to navigate through them. First, we enumerate the large number of epidemiological datasets and novel data streams that are relevant to epidemic forecasting, capturing various factors like symptomatic online surveys, retail and commerce, mobility, genomics data and more. Next, we discuss methods and modeling paradigms focusing on the recent data-driven statistical and deep-learning based methods as well as on the novel class of hybrid models that combine domain knowledge of mechanistic models with the effectiveness and flexibility of statistical approaches. We also discuss experiences and challenges that arise in real-world deployment of these forecasting systems including decision-making informed by forecasts. Finally, we highlight some challenges and open problems found across the forecasting pipeline.

Harshavardhan Kamarthi, Lingkai Kong, Alexander Rodríguez et al.

Probabilistic hierarchical time-series forecasting is an important variant of time-series forecasting, where the goal is to model and forecast multivariate time-series that have underlying hierarchical relations. Most methods focus on point predictions and do not provide well-calibrated probabilistic forecasts distributions. Recent state-of-art probabilistic forecasting methods also impose hierarchical relations on point predictions and samples of distribution which does not account for coherency of forecast distributions. Previous works also silently assume that datasets are always consistent with given hierarchical relations and do not adapt to real-world datasets that show deviation from this assumption. We close both these gap and propose PROFHiT, which is a fully probabilistic hierarchical forecasting model that jointly models forecast distribution of entire hierarchy. PROFHiT uses a flexible probabilistic Bayesian approach and introduces a novel Distributional Coherency regularization to learn from hierarchical relations for entire forecast distribution that enables robust and calibrated forecasts as well as adapt to datasets of varying hierarchical consistency. On evaluating PROFHiT over wide range of datasets, we observed 41-88% better performance in accuracy and significantly better calibration. Due to modeling the coherency over full distribution, we observed that PROFHiT can robustly provide reliable forecasts even if up to 10% of input time-series data is missing where other methods' performance severely degrade by over 70%.

Harshavardhan Kamarthi, Lingkai Kong, Alexander Rodríguez et al.

Probabilistic hierarchical time-series forecasting is an important variant of time-series forecasting, where the goal is to model and forecast multivariate time-series that have underlying hierarchical relations. Most methods focus on point predictions and do not provide well-calibrated probabilistic forecasts distributions. Recent state-of-art probabilistic forecasting methods also impose hierarchical relations on point predictions and samples of distribution which does not account for coherency of forecast distributions. Previous works also silently assume that datasets are always consistent with given hierarchical relations and do not adapt to real-world datasets that show deviation from this assumption. We close both these gap and propose PROFHiT, which is a fully probabilistic hierarchical forecasting model that jointly models forecast distribution of entire hierarchy. PROFHiT uses a flexible probabilistic Bayesian approach and introduces a novel Distributional Coherency regularization to learn from hierarchical relations for entire forecast distribution that enables robust and calibrated forecasts as well as adapt to datasets of varying hierarchical consistency. On evaluating PROFHiT over wide range of datasets, we observed 41-88% better performance in accuracy and significantly better calibration. Due to modeling the coherency over full distribution, we observed that PROFHiT can robustly provide reliable forecasts even if up to 10% of input time-series data is missing where other methods' performance severely degrade by over 70%.

Shangqing Xu, Zhiyuan Zhao, Megha Sharma et al.

Severe heatwaves in urban areas significantly threaten public health, calling for establishing early warning strategies. Despite predicting occurrence of heatwaves and attributing historical mortality, predicting an incoming deadly heatwave remains a challenge due to the difficulty in defining and estimating heat-related mortality. Furthermore, establishing an early warning system imposes additional requirements, including data availability, spatial and temporal robustness, and decision costs. To address these challenges, we propose DeepTherm, a modular early warning system for deadly heatwave prediction without requiring heat-related mortality history. By highlighting the flexibility of deep learning, DeepTherm employs a dual-prediction pipeline, disentangling baseline mortality in the absence of heatwaves and other irregular events from all-cause mortality. We evaluated DeepTherm on real-world data across Spain. Results demonstrate consistent, robust, and accurate performance across diverse regions, time periods, and population groups while allowing trade-off between missed alarms and false alarms.

Xiangrui Liu, Yuanyuan Zhang, Qianyu Shang et al.

Foundation models, first introduced in 2021, refer to large-scale pretrained models (e.g., large language models (LLMs) and vision-language models (VLMs)) that learn from extensive unlabeled datasets through unsupervised methods, enabling them to excel in diverse downstream tasks. These models, like GPT, can be adapted to various applications such as question answering and visual understanding, outperforming task-specific AI models and earning their name due to broad applicability across fields. The development of biomedical foundation models marks a significant milestone in the use of artificial intelligence (AI) to understand complex biological phenomena and advance medical research and practice. This survey explores the potential of foundation models in diverse domains within biomedical fields, including computational biology, drug discovery and development, clinical informatics, medical imaging, and public health. The purpose of this survey is to inspire ongoing research in the application of foundation models to health science.

Wenhao Mu, Zhi Cao, Mehmed Uludag et al.

Predicting counterfactual distributions in complex dynamical systems is essential for scientific modeling and decision-making in domains such as public health and medicine. However, existing methods often rely on point estimates or purely data-driven models, which tend to falter under data scarcity. We propose a time series diffusion-based framework that incorporates guidance from imperfect expert models by extracting high-level signals to serve as structured priors for generative modeling. Our method, ODE-Diff, bridges mechanistic and data-driven approaches, enabling more reliable and interpretable causal inference. We evaluate ODE-Diff across semi-synthetic COVID-19 simulations, synthetic pharmacological dynamics, and real-world case studies, demonstrating that it consistently outperforms strong baselines in both point prediction and distributional accuracy.

Ruipu Li, Daniel Menacho, Alexander Rodríguez

Future trajectories play an important role across domains such as autonomous driving, hurricane forecasting, and epidemic modeling, where practitioners commonly generate ensemble paths by sampling probabilistic models or leveraging multiple autoregressive predictors. While these trajectories reflect inherent uncertainty, they are typically uncalibrated. We propose a unified framework based on conformal prediction that transforms sampled trajectories into calibrated prediction intervals with theoretical coverage guarantees. By introducing a novel online update step and an optimization step that captures inter-step dependencies, our method can produce discontinuous prediction intervals around each trajectory, naturally capture temporal dependencies, and yield sharper, more adaptive uncertainty estimates.

Ruipu Li, Alexander Rodríguez

We introduce a neural network conformal prediction method for time series that enhances adaptivity in non-stationary environments. Our approach acts as a neural controller designed to achieve desired target coverage, leveraging auxiliary multi-view data with neural network encoders in an end-to-end manner to further enhance adaptivity. Additionally, our model is designed to enhance the consistency of prediction intervals in different quantiles by integrating monotonicity constraints and leverages data from related tasks to boost few-shot learning performance. Using real-world datasets from epidemics, electric demand, weather, and others, we empirically demonstrate significant improvements in coverage and probabilistic accuracy, and find that our method is the only one that combines good calibration with consistency in prediction intervals.

Alexander Rodríguez, Jiaming Cui, Naren Ramakrishnan et al.

We introduce EINNs, a framework crafted for epidemic forecasting that builds upon the theoretical grounds provided by mechanistic models as well as the data-driven expressibility afforded by AI models, and their capabilities to ingest heterogeneous information. Although neural forecasting models have been successful in multiple tasks, predictions well-correlated with epidemic trends and long-term predictions remain open challenges. Epidemiological ODE models contain mechanisms that can guide us in these two tasks; however, they have limited capability of ingesting data sources and modeling composite signals. Thus, we propose to leverage work in physics-informed neural networks to learn latent epidemic dynamics and transfer relevant knowledge to another neural network which ingests multiple data sources and has more appropriate inductive bias. In contrast with previous work, we do not assume the observability of complete dynamics and do not need to numerically solve the ODE equations during training. Our thorough experiments on all US states and HHS regions for COVID-19 and influenza forecasting showcase the clear benefits of our approach in both short-term and long-term forecasting as well as in learning the mechanistic dynamics over other non-trivial alternatives.

Harshavardhan Kamarthi, Lingkai Kong, Alexander Rodríguez et al.

Probabilistic time-series forecasting enables reliable decision making across many domains. Most forecasting problems have diverse sources of data containing multiple modalities and structures. Leveraging information as well as uncertainty from these data sources for well-calibrated and accurate forecasts is an important challenging problem. Most previous work on multi-modal learning and forecasting simply aggregate intermediate representations from each data view by simple methods of summation or concatenation and do not explicitly model uncertainty for each data-view. We propose a general probabilistic multi-view forecasting framework CAMul, that can learn representations and uncertainty from diverse data sources. It integrates the knowledge and uncertainty from each data view in a dynamic context-specific manner assigning more importance to useful views to model a well-calibrated forecast distribution. We use CAMul for multiple domains with varied sources and modalities and show that CAMul outperforms other state-of-art probabilistic forecasting models by over 25\% in accuracy and calibration.

Harshavardhan Kamarthi, Alexander Rodríguez, B. Aditya Prakash

In real-time forecasting in public health, data collection is a non-trivial and demanding task. Often after initially released, it undergoes several revisions later (maybe due to human or technical constraints) - as a result, it may take weeks until the data reaches to a stable value. This so-called 'backfill' phenomenon and its effect on model performance has been barely studied in the prior literature. In this paper, we introduce the multi-variate backfill problem using COVID-19 as the motivating example. We construct a detailed dataset composed of relevant signals over the past year of the pandemic. We then systematically characterize several patterns in backfill dynamics and leverage our observations for formulating a novel problem and neural framework Back2Future that aims to refines a given model's predictions in real-time. Our extensive experiments demonstrate that our method refines the performance of top models for COVID-19 forecasting, in contrast to non-trivial baselines, yielding 18% improvement over baselines, enabling us obtain a new SOTA performance. In addition, we show that our model improves model evaluation too; hence policy-makers can better understand the true accuracy of forecasting models in real-time.

Harshavardhan Kamarthi, Lingkai Kong, Alexander Rodríguez et al.

Accurate and trustworthy epidemic forecasting is an important problem that has impact on public health planning and disease mitigation. Most existing epidemic forecasting models disregard uncertainty quantification, resulting in mis-calibrated predictions. Recent works in deep neural models for uncertainty-aware time-series forecasting also have several limitations; e.g. it is difficult to specify meaningful priors in Bayesian NNs, while methods like deep ensembling are computationally expensive in practice. In this paper, we fill this important gap. We model the forecasting task as a probabilistic generative process and propose a functional neural process model called EPIFNP, which directly models the probability density of the forecast value. EPIFNP leverages a dynamic stochastic correlation graph to model the correlations between sequences in a non-parametric way, and designs different stochastic latent variables to capture functional uncertainty from different perspectives. Our extensive experiments in a real-time flu forecasting setting show that EPIFNP significantly outperforms previous state-of-the-art models in both accuracy and calibration metrics, up to 2.5x in accuracy and 2.4x in calibration. Additionally, due to properties of its generative process,EPIFNP learns the relations between the current season and similar patterns of historical seasons,enabling interpretable forecasts. Beyond epidemic forecasting, the EPIFNP can be of independent interest for advancing principled uncertainty quantification in deep sequential models for predictive analytics

Alexander Rodríguez, Bijaya Adhikari, Naren Ramakrishnan et al.

Forecasting influenza like illnesses (ILI) has rapidly progressed in recent years from an art to a science with a plethora of data-driven methods. While these methods have achieved qualified success, their applicability is limited due to their inability to incorporate expert feedback and guidance systematically into the forecasting framework. We propose a new approach leveraging the Seldonian optimization framework from AI safety and demonstrate how it can be adapted to epidemic forecasting. We study two types of guidance: smoothness and regional consistency of errors, where we show that by its successful incorporation, we are able to not only bound the probability of undesirable behavior to happen, but also to reduce RMSE on test data by up to 17%.

Alexander Rodríguez, Bijaya Adhikari, Andrés D. González et al.

Can we infer all the failed components of an infrastructure network, given a sample of reachable nodes from supply nodes? One of the most critical post-disruption processes after a natural disaster is to quickly determine the damage or failure states of critical infrastructure components. However, this is non-trivial, considering that often only a fraction of components may be accessible or observable after a disruptive event. Past work has looked into inferring failed components given point probes, i.e. with a direct sample of failed components. In contrast, we study the harder problem of inferring failed components given partial information of some `serviceable' reachable nodes and a small sample of point probes, being the first often more practical to obtain. We formulate this novel problem using the Minimum Description Length (MDL) principle, and then present a greedy algorithm that minimizes MDL cost effectively. We evaluate our algorithm on domain-expert simulations of real networks in the aftermath of an earthquake. Our algorithm successfully identify failed components, especially the critical ones affecting the overall system performance.

Alexander Rodríguez, Nikhil Muralidhar, Bijaya Adhikari et al.

Forecasting influenza in a timely manner aids health organizations and policymakers in adequate preparation and decision making. However, effective influenza forecasting still remains a challenge despite increasing research interest. It is even more challenging amidst the COVID pandemic, when the influenza-like illness (ILI) counts are affected by various factors such as symptomatic similarities with COVID-19 and shift in healthcare seeking patterns of the general population. Under the current pandemic, historical influenza models carry valuable expertise about the disease dynamics but face difficulties adapting. Therefore, we propose CALI-Net, a neural transfer learning architecture which allows us to 'steer' a historical disease forecasting model to new scenarios where flu and COVID co-exist. Our framework enables this adaptation by automatically learning when it should emphasize learning from COVID-related signals and when it should learn from the historical model. Thus, we exploit representations learned from historical ILI data as well as the limited COVID-related signals. Our experiments demonstrate that our approach is successful in adapting a historical forecasting model to the current pandemic. In addition, we show that success in our primary goal, adaptation, does not sacrifice overall performance as compared with state-of-the-art influenza forecasting approaches.