arXiv subjects

Anil Vullikanti

Publications and source records attributed to Anil Vullikanti.

At least 19 recordsLinked to original sources

arXiv2026

EpiNarrate: Agentic Generation of Grounded Narratives from Epidemiological Scenario Projections

Generation of clear and accessible public health narratives is critical for communicating complex epidemiological projections to policymakers and the general public at large. Such narratives require more than simply reporting numbers: projections must be contextualized and quantitatively grounded across multiple dimensions. Further, projections are often derived from large ensemble datasets which combine intervention assumptions, geographic and demographic strata, outcomes, time horizons, and uncertainty quantiles. However, directly using large language models (LLMs) to summarize and contextualize such data often leads to inconsistencies, omissions, and fragile behavior. We introduce an agentic framework (EpiNarrate) for public health report generation that separates structured numerical reasoning from natural-language generation. The framework first extracts scenario axes and organizes them into a partial-order schema, enabling systematic traversal of the underlying multidimensional space. It then constructs an augmented dataset and derives valid quantitative statements through a comparison grammar that enforces semantic and arithmetic consistency. To balance coverage and non-redundancy, we introduce an interestingness-driven selection mechanism based on maximum-entropy principles. Experiments on the COVID-19 Scenario Modeling Hub demonstrate that our model produces narratives with improved factual grounding and broader coverage of salient epidemiological patterns, while preserving the style of expert-written reports.

cs.CL↗

arXiv2026

Robust Network Flow Interdiction Problems with Applications to Counter-Narcotics

Interdiction problems arise in a number of application areas, including global security, supply chains, and critical infrastructure protection - the goal is inhibit the movement of goods, people or information. An area of particular interest is counter-narcotics, where nodes or edges in a network are placed under surveillance or blocked to minimize the flow of illicit drugs from source to the destination. A fundamental challenge in this narco-traffic interdiction is data scarcity: available datasets are limited by the very nature of the problem and provide only partial and uncertain views of trafficking networks. Thus, developing robust interdiction methods that take this inherent lack of information is critical. In this paper we initiate the study of network flow interdiction problems under network uncertainty. First, using a limited real-world dataset, we generate an ensemble of plausible network realizations representing alternative trafficking scenarios. The method combines simulations with mathematical programming techniques to generate network ensembles that are consistent with the observed data. Second, we formulate the robust network flow interdiction problem and develop an integer linear program to solve the problem. We evaluate the optimal interdiction strategy and obtain the residual flows over the scenarios. Our analysis reveals that even modest budgets can yield significant flow reductions. However, optimal solutions vary substantially across scenarios, motivating the need for robust solutions. We show that the robust strategy achieves near-optimal performance across all near-real world realizations while remaining stable under structural uncertainty. This simulation-driven approach provides a principled basis for policy analysis and supports maximizing the return on interdiction investments in uncertain, data-limited environments.

cs.CE↗

arXiv2026

Cascading Impacts of the USA--China Trade War on Global Oilseed Supply Chain

Global supply chains are highly interconnected, making them vulnerable to cascading disruptions induced by trade policy shocks. Understanding how such disruptions propagate through production networks, and how mitigation mechanisms such as trade reallocation and production adjustment can alleviate their impacts, remains a central challenge. In this work, we develop a linear programming formulation of an Input-Output (IO) system that captures cascading supply-chain disruptions together with trade reallocation and production expansion. Our formulation yields a system-level equilibrium characterization that enables the joint analysis of disruption propagation and mitigation within a unified framework. We propose an efficient algorithm for computing approximate equilibrium solutions by minimizing total unmet demand in large IO systems. We apply our approach to tariff-induced disruptions in the global oilseeds supply chain arising from the U.S.-China trade war. Our results show that a localized 70% disruption to flows from the U.S. oilseeds sector to China leads to a 3.27% loss in global output, with China experiencing a disproportionate loss of 14.02%. As a counterfactual mitigation strategy, allowing a 20% reallocation from Brazil's oilseed sector to China significantly reduces global output losses to 1.36%, although pressure remains high on final-demand flows. We further investigate production expansion as an additional mitigation mechanism and show that it introduces tradeoffs between reducing global final-demand losses and protecting Brazil's domestic flows. Domestic reallocation disproportionately shifts losses toward smaller economies, while globally sourced expansion redistributes losses more broadly across the network.

econ.GN↗

arXiv2026

Scalable K-clique Estimation with Differential Privacy

Counts of $k$-cliques are commonly used metrics in subgraph mining. Since graphs often have sensitive data, there also has been a lot of work on $k$-clique counts with differential privacy. However, these metrics have very high global sensitivity, and so more sophisticated techniques have been developed for counting $k$-cliques with privacy. Smooth sensitivity and ladder functions were developed for reducing the noise magnitude for private estimates of these metrics. However, these are computationally very inefficient to estimate. No polynomial time algorithms are known for smooth sensitivity of $k$-cliques for $k>3$, while the time complexity of ladder functions is lower bounded by the time for exact counts, which does not scale very well. In this paper, we develop a new highly scalable algorithm for estimating $k$-clique counts with differential privacy. Our algorithm adapts the ladder function to serve as a smooth upper bound on its local sensitivity, and utilizes the approximation sensitivity framework to calibrate noise with magnitude proportional to an approximation of the bound. This gives us a significant improvement in the running time. Experiments show that our method is several orders of magnitude faster than the ladder function based estimates of $k$-clique counts, while the accuracy is similar. Our algorithm is the first to scale to graphs with millions of edges, and for larger $k$, for which the ladder function algorithm doesn't complete.

cs.DS↗

arXiv2026

Are LLMs Ready for Neural-integrated Mechanistic Modeling? A Benchmark and Agentic Framework

Large language models (LLMs) have shown promise in constructing mechanistic models from data. However, existing evaluations largely focus on simplified settings and fail to capture the complexity of real-world scientific modeling. In practice, such modeling often involves neural-integrated formulations, where a mechanistic model component and a neural network component are jointly constructed, leading to a significantly more complex search space. Motivated by this gap, we introduce the Neural-Integrated Mechanistic Modeling (NIMM) benchmark, which evaluates LLM-generated neural-integrated mechanistic models across three scientific domains. Experiments on NIMM reveal that existing LLM-based approaches struggle to effectively explore this complex space, resulting in limited search stability and solution quality. To address this challenge, we propose NIMMGen, a tree-guided agentic framework that enables diversified exploration via branch-level search and improves solutions through atomic model refinement. Extensive experiments demonstrate that NIMMGen achieves state-of-the-art performance on NIMM, significantly improving search stability and solution quality.

cs.LG↗

arXiv2026

Large Language Models Lack Temporal Awareness of Medical Knowledge

The existing methods for evaluating the medical knowledge of Large Language Models (LLMs) are largely based on atemporal examination-style benchmarks, while in reality, medical knowledge is inherently dynamic and continuously evolves as new evidence emerges and treatments are approved. Consequently, evaluating medical knowledge without a temporal context may provide an incomplete assessment of whether LLMs can accurately reason about time-specific medical knowledge. Moreover, most medical data are historical, requiring the models not only to recall the correct knowledge, but also to know when that knowledge is correct. To bridge the gap, we built TempoMed-Bench, the first-of-its-kind benchmark for evaluating the temporal awareness of the LLMs in the medical domain through evolving guideline knowledge. Based on the TempoMed-Bench, our evaluation analysis first reveals that LLMs lack temporal awareness in medical knowledge through the key findings: (1) model performance on up-to-date medical knowledge exhibits a gradual linear decline over time rather than a sharp knowledge-cutoff behavior, suggesting that parametric medical knowledge is not strictly bounded by knowledge cutoffs; (2) LLMs consistently struggle more with recalling outdated historical medical knowledge than with up-to-date recommendations: accuracy of historical knowledge is only 25.37%-53.89% of up-to-date knowledge, indicating potential knowledge forgetting effects during training; and (3) LLMs often exhibit temporally inconsistent behaviors, where predictions fluctuate irregularly across neighboring years. We also show that the temporal awareness problem is a challenge that cannot be easily solved when integrated with agentic search tools (-3.15%-14.14%). This work highlights an important yet underexplored challenge and motivates future research on developing LLMs that can better encode time-specific medical knowledge.

cs.LG↗

arXiv2026

Estimating the cascading global impacts of gas disruptions in Qatar

This study examines the global impacts of a localized disruption in Qatar's gas sector using a multi-regional input-output framework and scenario-based analysis. While the direct impacts of this disruption on importing countries are clear, indirect and cascading impacts are not well understood. We use a Multiregional input-output (MRIO) model to assess the impact of this disruption and to determine whether trade reallocations and increased production can mitigate its effects. Our analysis shows that this disruption leads to significant gas supply losses in Asia and Europe, with the largest aggregate impacts observed in India, China, and South Korea. Allowing for trade reallocation partially mitigates these losses. Further expansion of production capacity among major gas-producing countries improves supply conditions and leads to broader output gains; however, these benefits remain concentrated in a few large economies. Even significant increases in production among top producers offer limited relief to economies such as India and Pakistan. Overall, the results highlight the uneven distribution of both vulnerabilities and recovery potential within global supply chains. While adaptive mechanisms such as trade reallocation and production expansion can alleviate the effects of supply shocks, their effectiveness is limited and heterogeneous. The findings underscore the importance of network structure in shaping shock propagation and resilience, offering insights for managing systemic risks in an interconnected global economy.

physics.soc-ph↗

arXiv2026

Improving Epidemic Analyses with Privacy-Preserving Integration of Sensitive Data

Epidemic analyses increasingly rely on heterogeneous datasets, many of which are sensitive and require strong privacy protection. Although differential privacy (DP) has become a standard in machine learning and data sharing, its adoption in epidemiological modeling remains limited. In this work, we introduce DPEpiNN, a unified framework that integrates deep neural networks with a mechanistic SEIRM-based metapopulation model under formal DP guarantees. DPEpiNN supports multiple epidemic tasks (including multi-step forecasting, nowcasting, effective reproduction number $(R_t)$ estimation, and intervention analysis) within a single differentiable pipeline. The framework jointly learns epidemic parameters from heterogeneous public and sensitive datasets, while ensuring privacy via input perturbation mechanisms. We evaluate DPEpiNN using COVID-19 data from three regions. Results show that incorporating sensitive datasets substantially improves predictive performance even under strong privacy constraints. Compared with a deep learning baseline, DPEpiNN achieves higher accuracy in forecasting and nowcasting while producing reliable estimates of $R_t$. Furthermore, the learned epidemic transmission models remain inherently private due to the post-processing property of differential privacy, enabling downstream policy analyses such as simulation of social distancing interventions. Our work demonstrates that interpretability (through mechanistic modeling), predictive accuracy (through neural integration), and rigorous privacy guarantees can be jointly achieved in modern epidemic modeling.

cs.LG↗

arXiv2026

Differentially Private and Scalable Estimation of the Network Principal Component

Computing the principal component (PC) of the adjacency matrix of an undirected graph has several applications ranging from identifying key vertices for influence maximization and controlling diffusion processes, to discovering densely interconnected vertex subsets. However, many networked datasets are sensitive, which necessitates private computation of the PC for use in the aforementioned applications. Differential privacy has emerged as the gold standard in privacy-preserving data analysis, but existing DP algorithms for private PC suffer from low accuracy due to large noise injection or high complexity. Motivated by the large gap between the local and global sensitivities of the PC on real-graphs, we consider instance-specific mechanisms for privately computing the PC under edge-DP. These mechanisms guarantee privacy for all datasets, but provide good utility on ``well-behaved'' datasets by injecting smaller amounts of noise. More specifically, we consider the Propose-Test-Release (PTR) framework. Although computationally expensive in general, we design a novel approach for implementing a PTR variant in the same time as computation of a non-private PC, while offering good utility. Our framework tests in a differentially-private manner whether a given graph is ``well-behaved'' or not, and then tests whether its private to release a noisy PC with small noise. As a consequence, this also leads to the first DP algorithm for the Densest-$k$-subgraph problem, a key graph mining primitive. We run our method on diverse real-world networks, with the largest having 3 million vertices, and compare its utility to a pre-existing baseline based on the private power method (PPM). Although PTR requires a slightly larger privacy budget, on average, it achieves a 180-fold improvement in runtime over PPM.

cs.DS↗

arXiv2026

Agentic Framework for Epidemiological Modeling

Epidemic modeling is essential for public health planning, yet traditional approaches rely on fixed model classes that require manual redesign as pathogens, policies, and scenario assumptions evolve. We introduce EPIAGENT, an agentic framework that automatically synthesizes, calibrates, verifies, and refines epidemiological simulators by modeling disease progression as an iterative program synthesis problem. A central design choice is an explicit epidemiological flow graph intermediate representation that links scenario specifications to model structure and enables strong, modular correctness checks before code is generated. Verified flow graphs are then compiled into mechanistic models supporting interpretable parameter learning under physical and epidemiological constraints. Evaluation on epidemiological scenario case studies demonstrates that EPIAGENT captures complex growth dynamics and produces epidemiologically consistent counterfactual projections across varying vaccination and immune escape assumptions. Our results show that the agentic feedback loop prevents degeneration and significantly accelerates convergence toward valid models by mimicking professional expert workflows.

cs.LG↗

arXiv2026

Reconstructing Network Outbreaks under Group Surveillance

A key public health problem during an outbreak is to reconstruct the disease cascade from a partial set of confirmed infections. This has been studied extensively under the Maximum Likelihood Estimation (MLE) formulation, which reduces the problem to finding some type of Steiner subgraph on a network. Group surveillance like wastewater or aerosol monitoring is a form of mass/pooled testing where samples from multiple individuals are pooled together and tested once for all. While a single negative test clears multiple individuals, a positive test does not reveal the infected individuals in the test pool. We introduce the POOLCASCADEMLE problem in the setting of a network propagation process, where the goal is to find a MLE cascade subgraph which is consistent with the pooled test outcomes. Previous work on reconstruction assumes that the test results are of individuals, i.e., pools of size one, and requires a consistent cascade to connect the positive testing nodes. In POOLCASCADEMLE, a consistent cascade must choose at least one node in each positive pool, adding another combinatorial layer. We show that, under the Independent Cascade (IC) model, POOLCASCADEMLE is NP-hard, and present an approximation algorithm based on a reduction to the Group Steiner Tree problem. We also consider a one-hop version of this problem, in which the disease can spread for one time step after being seeded. We show that even this restricted version is NP-hard, and develop a method using linear programming relaxation and rounding. We evaluate the performance of our methods on real and synthetic contact networks, in terms of missing infection recovery and prevalence estimation. We find that our approach outperforms meaningful baselines which correspond to pools of size one and use state-of-the-art methods.

cs.SI↗

arXiv2026

Information Theoretic Optimal Surveillance for Epidemic Prevalence in Networks

Estimating the true prevalence of an epidemic outbreak is a key public health problem. This is challenging because surveillance is usually resource intensive and biased. In the network setting, prior work on cost sensitive disease surveillance has focused on choosing a subset of individuals (or nodes) to minimize objectives such as probability of outbreak detection. Such methods do not give insights into the outbreak size distribution which, despite being complex and multi-modal, is very useful in public health planning. We introduce TESTPREV, a problem of choosing a subset of nodes which maximizes the mutual information with disease prevalence, which directly provides information about the outbreak size distribution. We show that, under the independent cascade (IC) model, solutions computed by all prior disease surveillance approaches are highly sub-optimal for TESTPREV in general. We also show that TESTPREV is hard to even approximate. While this mutual information objective is computationally challenging for general networks, we show that it can be computed efficiently for various network classes. We present a greedy strategy, called GREEDYMI, that uses estimates of mutual information from cascade simulations and thus can be applied on any network and disease model. We find that GREEDYMI does better than natural baselines in terms of maximizing the mutual information as well as reducing the expected variance in outbreak size, under the IC model.

physics.soc-ph↗

arXiv2025

Improving Hospital Risk Prediction with Knowledge-Augmented Multimodal EHR Modeling

Accurate prediction of clinical outcomes using Electronic Health Records (EHRs) is critical for early intervention, efficient resource allocation, and improved patient care. EHRs contain multimodal data, including both structured data and unstructured clinical notes that provide rich, context-specific information. In this work, we introduce a unified framework that seamlessly integrates these diverse modalities, leveraging all relevant available information through a two-stage architecture for clinical risk prediction. In the first stage, a fine-tuned Large Language Model (LLM) extracts crucial, task-relevant information from clinical notes, which is enhanced by graph-based retrieval of external domain knowledge from sources such as a medical corpus like PubMed, grounding the LLM's understanding. The second stage combines both unstructured representations and features derived from the structured data to generate the final predictions. This approach supports a wide range of clinical tasks. Here, we demonstrate its effectiveness on 30-day readmission and in-hospital mortality prediction. Experimental results show that our framework achieves strong performance, with AUC scores of $0.84$ and $0.92$, respectively, despite these tasks involving severely imbalanced datasets, with positive rates ranging from approximately $4\%$ to $13\%$. Moreover, it outperforms all existing baselines and clinical practices, including established risk scoring systems. To the best of our knowledge, this is one of the first frameworks for healthcare prediction which enhances the power of an LLM-based graph-guided knowledge retrieval method by combining it with structured data for improved clinical outcome prediction.

cs.LG↗

arXiv2025

CALYPSO: Forecasting and Analyzing MRSA Infection Patterns with Community and Healthcare Transmission Dynamics

Methicillin-resistant Staphylococcus aureus (MRSA) is a critical public health threat within hospitals as well as long-term care facilities. Better understanding of MRSA risks, evaluation of interventions and forecasting MRSA rates are important public health problems. Existing forecasting models rely on statistical or neural network approaches, which lack epidemiological interpretability, and have limited performance. Mechanistic epidemic models are difficult to calibrate and limited in incorporating diverse datasets. We present CALYPSO, a hybrid framework that integrates neural networks with mechanistic metapopulation models to capture the spread dynamics of infectious diseases (i.e., MRSA) across healthcare and community settings. Our model leverages patient-level insurance claims, commuting data, and healthcare transfer patterns to learn region- and time-specific parameters governing MRSA spread. This enables accurate, interpretable forecasts at multiple spatial resolutions (county, healthcare facility, region, state) and supports counterfactual analyses of infection control policies and outbreak risks. We also show that CALYPSO improves statewide forecasting performance by over 4.5% compared to machine learning baselines, while also identifying high-risk regions and cost-effective strategies for allocating infection prevention resources.

cs.LG↗

arXiv2025

Prediction of Hospital Associated Infections During Continuous Hospital Stays

The US Centers for Disease Control and Prevention (CDC), in 2019, designated Methicillin-resistant Staphylococcus aureus (MRSA) as a serious antimicrobial resistance threat. The risk of acquiring MRSA and suffering life-threatening consequences due to it remains especially high for hospitalized patients due to a unique combination of factors, including: co-morbid conditions, immuno suppression, antibiotic use, and risk of contact with contaminated hospital workers and equipment. In this paper, we present a novel generative probabilistic model, GenHAI, for modeling sequences of MRSA test results outcomes for patients during a single hospitalization. This model can be used to answer many important questions from the perspectives of hospital administrators for mitigating the risk of MRSA infections. Our model is based on the probabilistic programming paradigm, and can be used to approximately answer a variety of predictive, causal, and counterfactual questions. We demonstrate the efficacy of our model by comparing it against discriminative and generative machine learning models using two real-world datasets.

cs.LG↗

arXiv2025

Contrastive Explainable Clustering with Differential Privacy

This paper presents a novel approach to Explainable AI (XAI) that combines contrastive explanations with differential privacy for clustering algorithms. Focusing on k-median and k-means problems, we calculate contrastive explanations as the utility difference between original clustering and clustering with a centroid fixed to a specific data point. This method provides personalized insights into centroid placement. Our key contribution is demonstrating that these differentially private explanations achieve essentially the same utility bounds as non-private explanations. Experiments across various datasets show that our approach offers meaningful, privacy-preserving, and individually relevant explanations without significantly compromising clustering utility. This work advances privacy-aware machine learning by balancing data protection, explanation quality, and personalization in clustering tasks.

cs.LG↗

arXiv2025

Controlling the Spread of Epidemics on Networks with Differential Privacy

Designing effective strategies for controlling epidemic spread by vaccination is an important question in epidemiology, especially in the early stages when vaccines are limited. This is a challenging question when the contact network is very heterogeneous, and strategies based on controlling network properties, such as the degree and spectral radius, have been shown to be effective. Implementation of such strategies requires detailed information on the contact structure, which might be sensitive in many applications. Our focus here is on choosing effective vaccination strategies when the edges are sensitive and differential privacy guarantees are needed. Our main contributions are $(\varepsilon,δ)$-differentially private algorithms for designing vaccination strategies by reducing the maximum degree and spectral radius. Our key technique is a private algorithm for the multi-set multi-cover problem, which we use for controlling network properties. We evaluate privacy-utility tradeoffs of our algorithms on multiple synthetic and real-world networks, and show their effectiveness.

cs.DS↗

arXiv2025

Benign Samples Matter! Fine-tuning On Outlier Benign Samples Severely Breaks Safety

Recent studies have uncovered a troubling vulnerability in the fine-tuning stage of large language models (LLMs): even fine-tuning on entirely benign datasets can lead to a significant increase in the harmfulness of LLM outputs. Building on this finding, our red teaming study takes this threat one step further by developing a more effective attack. Specifically, we analyze and identify samples within benign datasets that contribute most to safety degradation, then fine-tune LLMs exclusively on these samples. We approach this problem from an outlier detection perspective and propose Self-Inf-N, to detect and extract outliers for fine-tuning. Our findings reveal that fine-tuning LLMs on 100 outlier samples selected by Self-Inf-N in the benign datasets severely compromises LLM safety alignment. Extensive experiments across seven mainstream LLMs demonstrate that our attack exhibits high transferability across different architectures and remains effective in practical scenarios. Alarmingly, our results indicate that most existing mitigation strategies fail to defend against this attack, underscoring the urgent need for more robust alignment safeguards. Codes are available at https://github.com/GuanZihan/Benign-Samples-Matter.

cs.LG↗