Inference Methodology Research Articles

Cyber threats in the age of artificial intelligence: Exploiting advanced technologies and strengthening cybersecurity

The rapid advancement in artificial intelligence (AI) technologies has led to the emergence of new and complex cyber threats. These threats rely on AI capabilities to target digital systems and infrastructures with greater precision and efficiency, making them more difficult to detect and counter. AI is being used to develop automated cyber-attacks, such as malware that can adapt and learn from its digital environment. Conversely, AI is also employed to enhance cyber security by enabling early threat detection, analyzing suspicious behaviors, and providing rapid responses to hacking incidents. Based on the above, the research idea we intend to present at this article on how to achieve a balance between leveraging AI technologies to protect digital systems and the growing risks associated with using these technologies to develop more sophisticated cyber-attacks. Research Methodologies: The study requires employing both the descriptive-analytical and inferential methodologies.

Impact of addressing modifiable risk factors on the 10-year risk of cardiovascular disease in individuals with familial hypercholesterolemia: a causal analysis utilising UK biobank

Abstract Background Familial hypercholesterolemia (FH) is a prevalent autosomal dominant disorder characterised by elevated low-density lipoprotein cholesterol (LDL-C) levels from birth. These elevated LDL-C levels significantly amplify the lifetime risk of cardiovascular disease (CVD). While the impact of early and effective initiation of lipid-lowering medication (LLM) on CVD risk is well documented in genetically confirmed FH, the additional impact of addressing modifiable lifestyle risk factors (MLRF) in that patient population remains largely unquantified. Methods This study quantified the potential effects of successfully managing 4 MLRF (smoking, obesity, alcohol consumption, and low physical activity) on the 10-year incidence of a first CVD diagnosis in adults with genetically confirmed FH treated with LLM within the UK Biobank. The synthesised causal estimates of these 4 MLF were obtained using two recent causal analysis frameworks, namely the doWhy causal calculus framework and the Causal Forest Double Machine Learning Method. Results In 660 FH individuals (mean age 56±8 years; 60.15% women), smoking cessation and reducing body mass index below 30 kg/m2 delivered the most substantial risk reductions (pooled estimates, adjusted for the 3 other MLRF: -6.5% and -3.2%, respectively; both p<0.001), followed by initiating moderate or high physical activity (-1.7%; p<0.001; Figure). Notably, cessation of alcohol consumption significantly increased CVD risk (+2.5%; p<0.001), aligning with existing literature. Conclusion In over 10 years, reductions in CVD risk ranging from 1.7% to 6.5% were achievable through smoking cessation, BMI reduction, and enhanced physical activity in FH individuals. Leveraging causal inference methodologies facilitates the discernment of which risk factors offer the most pronounced additional benefits beyond lipid-lowering interventions in this high-risk population.Forest Plot of Causal Effect Estimates

Tree sequences as a general-purpose tool for population genetic inference.

As population genetics data increases in size new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient, but are not interchangeable with existing data structures used for many population genetic inference methodologies such as the use of convolutional neural networks (CNNs) applied to population genetic alignments. To better utilize these new data structures we propose and implement a graph convolutional network (GCN) to directly learn from tree sequence topology and node data, allowing for the use of neural network applications without an intermediate step of converting tree sequences to population genetic alignment format. We then compare our approach to standard CNN approaches on a set of previously defined benchmarking tasks including recombination rate estimation, positive selection detection, introgression detection, and demographic model parameter inference. We show that tree sequences can be directly learned from using a GCN approach and can be used to perform well on these common population genetics inference tasks with accuracies roughly matching or even exceeding that of a CNN-based method. As tree sequences become more widely used in population genetics research we foresee developments and optimizations of this work to provide a foundation for population genetics inference moving forward.

A Causal Inference Methodology to Support Research on Osteopenia for Breast Cancer Patients

A Causal Inference Methodology to Support Research on Osteopenia for Breast Cancer Patients

Realized Random Graphs, with an Application to the Interbank Network

Abstract We introduce a new inferential methodology for dynamic network models driven by latent state variables. The main idea is to obtain a noisy representation of the state variables dynamics by computing a sequence of cross-sectional estimates of the network model at each point in time. The dynamic modeling of these cross-sectional estimates, that we name realized random graphs, transforms the original nonlinear state-space network model into a linear time-series model that can be easily estimated. Under the assumption of a mixed-membership blockmodel structure, the model parameters and the unobservable state variables can be consistently estimated when both the size of the network and the time-series length are large. By allowing for an extremely rich parameterization of the model in high dimensions, the proposed methodology describes the heterogeneous topology of real-world networks. We corroborate our findings by using this novel framework to estimate and forecast the dynamic common factors driving the evolution of the Italian electronic market of interbank deposits, and we show that the interbank lending rate is a key factor determining the network topology.

Tree sequences as a general-purpose tool for population genetic inference.

As population genetics data increases in size new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient, but are not interchangeable with existing data structures used for many population genetic inference methodologies such as the use of convolutional neural networks (CNNs) applied to population genetic alignments. To better utilize these new data structures we propose and implement a graph convolutional network (GCN) to directly learn from tree sequence topology and node data, allowing for the use of neural network applications without an intermediate step of converting tree sequences to population genetic alignment format. We then compare our approach to standard CNN approaches on a set of previously defined benchmarking tasks including recombination rate estimation, positive selection detection, introgression detection, and demographic model parameter inference. We show that tree sequences can be directly learned from using a GCN approach and can be used to perform well on these common population genetics inference tasks with accuracies roughly matching or even exceeding that of a CNN-based method. As tree sequences become more widely used in population genetics research we foresee developments and optimizations of this work to provide a foundation for population genetics inference moving forward.

Activity-travel pattern inference based on multi-source big data

ABSTRACT We provide a comprehensive review of the literature on inferring activity-travel patterns (ATP) using multi-source big data; the increasing number of publications over time on this subject, demonstrates the importance of big data in this task. Our aims are to identify the advantages and research gaps in ATP inference and to promote further developments in this field. We clarify the fundamental concepts (i.e. ATP and its components), commonly used data sources, and inference processes employed in ATP inference studies. Emphasis is placed on two prominent big data sources: mobile phone data and smart card data. We outline the various approaches involved in the inference process, and we highlight existing shortcomings in data sources, ATP inference methodologies, and result validation. Based on the review, it is evident that future research should address several limitations in ATP inference. Firstly, it is necessary to improve the comprehensive understanding of ATP and understand the interrelationships among its different components. Secondly, it is necessary to integrate different data sources and leverage their respective strengths to gain deeper insights into activity-travel behaviour. Lastly, further investigation into emerging technologies such as artificial intelligence in ATP inference is warranted to improve inference accuracy. The findings of this study could provide valuable insights for policy makers, enabling them to gain a deeper understanding of activity-travel choice behaviour and develop more effective policies related to transportation system.

Bus travel feature inference with small samples based on multi-clustering topic model over Internet of Things

With the widespread application of Internet of Things (IoT) technology, there has been a shift from a broad-brush to a more refined approach in traffic optimization. An increasing amount of IoT data is being utilized in trajectory mining and inference, offering more precise characteristic information for optimizing public transportation. Services that optimize public transit based on inferred travel characteristics can enhance the appeal of public transport, increase its likelihood as a travel choice, alleviate traffic congestion, and reduce carbon emissions. However, the inherent complexities of disorganized and unstructured public transportation data pose significant challenges to extracting travel features. This study explores the enhancement of bus travel by integrating advanced technologies like positioning systems, IoT, and AI to infer features in public transportation data. It introduces the MK-LDA (MeanShift Kmeans Latent Dirichlet Allocation), a novel thematic modeling technique for deducing characteristics of public transit travel using limited travel trajectory data. The model employs a segmented inference methodology, initially leveraging the Mean-shift clustering algorithm to create POI seeds, followed by the P-K-means algorithm for discerning patterns in user travel behavior and extracting travel modalities. Additionally, a P-LDA (POI-Latent Dirichlet Allocation) inference algorithm is proposed to examine the interplay between travel characteristics and behaviors, specifically targeting attributes significantly correlated with public transit usage, including age, occupation, gender, activity levels, cost, safety, and personality traits. Empirical validation highlights the efficacy of this thematic modeling-based inference technique in identifying and predicting travel characteristics and patterns, boasting enhanced interpretability and outperforming conventional benchmarks.

Stable monomers in the ancestral sequence reconstruction of the last opisthokont common ancestor of dimeric triosephosphate isomerase.

Function and structure are strongly coupled in obligated oligomers such as Triosephosphate isomerase (TIM). In animals and fungi, TIM monomers are inactive and unstable. Previously, we used ancestral sequence reconstruction to study TIM evolution and found that before these lineages diverged, the last opisthokonta common ancestor of TIM (LOCATIM) was an obligated oligomer that resembles those of extant TIMs. Notably, calorimetric evidence indicated that ancestral TIM monomers are more structured than extant ones. To further increase confidence about the function, structure, and stability of the LOCATIM, in this work, we applied two different inference methodologies and the worst plausible case scenario for both of them, to infer four sequences of this ancestor and test the robustness of their physicochemical properties. The extensive biophysical characterization of the four reconstructed sequences of LOCATIM showed very similar hydrodynamic and spectroscopic properties, as well as ligand-binding energetics and catalytic parameters. Their 3D structures were also conserved. Although differences were observed in melting temperature, all LOCATIMs showed reversible urea-induced unfolding transitions, and for those that reached equilibrium, high conformational stability was estimated (ΔGTot = 40.6-46.2 kcal/mol). The stability of the inactive monomeric intermediates was also high (ΔGunf = 12.6-18.4 kcal/mol), resembling some protozoan TIMs rather than the unstable monomer observed in extant opisthokonts. A comparative analysis of the 3D structure of ancestral and extant TIMs shows a correlation between the higher stability of the ancestral monomers with the presence of several hydrogen bonds located in the "bottom" part of the barrel.

Studying Continuous, Time-varying, and/or Complex Exposures Using Longitudinal Modified Treatment Policies.

This tutorial discusses a methodology for causal inference using longitudinal modified treatment policies. This method facilitates the mathematical formalization, identification, and estimation of many novel parameters and mathematically generalizes many commonly used parameters, such as the average treatment effect. Longitudinal modified treatment policies apply to a wide variety of exposures, including binary, multivariate, and continuous, and can accommodate time-varying treatments and confounders, competing risks, loss to follow-up, as well as survival, binary, or continuous outcomes. Longitudinal modified treatment policies can be seen as an extension of static and dynamic interventions to involve the natural value of treatment and, like dynamic interventions, can be used to define alternative estimands with a positivity assumption that is more likely to be satisfied than estimands corresponding to static interventions. This tutorial aims to illustrate several practical uses of the longitudinal modified treatment policy methodology, including describing different estimation strategies and their corresponding advantages and disadvantages. We provide numerous examples of types of research questions that can be answered using longitudinal modified treatment policies. We go into more depth with one of these examples, specifically, estimating the effect of delaying intubation on critically ill COVID-19 patients' mortality. We demonstrate the use of the open-source R package lmtp to estimate the effects, and we provide code on https://github.com/kathoffman/lmtp-tutorial.

Evaluating attitudes on health-seeking behavior among a network of people who inject drugs

People who inject drugs (PWID) are often members of HIV/AIDS risk networks, where individuals engage in sexual and injection risk behavior. Engagement in HIV care is important for this population. Low socioeconomic status, stigmatization, and lack of access to medical care often complicate successful engagement in the HIV cascade of care for PWID. This study investigates how individual's attitudes about how much control they have over HIV/AIDS risk in their life (i.e., locus of control and self-blame) affect health-seeking behavior in PWID participants and their community members. We applied causal inference methodology to PWID HIV risk networks ascertained from the Social Factors and HIV Risk Study (SFHR) conducted between 1991 and 1993 in Bushwick, Brooklyn, New York. We estimated protective disseminated effects of attitudes toward HIV/AIDS on the health-seeking behaviors of others in the PWID community. In other words, a positive attitude toward controlling HIV/AIDS can improve the health-seeking behavior of other members of the community who report a pessimistic attitude toward HIV/AIDS control. Given this finding, we also discuss potential network interventions to improve health-seeking behavior among both PWID individuals who receive the intervention and others in the PWID network informed by our analysis of disseminated effects.

Disease intervention specialist-delivered interventions and other partner services for HIV and sexually transmitted infections: A systematic review.

Disease intervention specialists (DIS) are critical for delivering partner services programs that provide partner notification, counseling, referral, and other services for HIV, sexually transmitted infections (STIs), and other infections. This systematic review of partner services and other DIS-delivered interventions for HIV and STIs was conducted to summarize the effectiveness of these programs and identify evidence gaps. A systematic literature review was conducted with a narrative synthesis. Articles were located using keyword searches in MEDLINE, Web of Science, CINAHL, and ProQuest through December 2022 and analyzed in 2023-2024. Included studies addressed an intervention of partner services or other DIS-delivered services for HIV or STIs; a United States setting; primary data collection; and an external comparison group or pre-post design. 1,915 unique records were screened for eligibility, with 30 studies included. Overall, DIS-delivered interventions improved clinical outcomes among index patients and population outcomes. Many studies focused on program process measures rather than population-level epidemiologic outcomes. All but one studies were scored as having low or medium strength of evidence. The evidence could be strengthened by establishing a streamlined set of core metrics, assessing impact using rigorous causal inference methodologies, linking program and clinical data systems, and supplementing impact evaluations with evidence on implementation strategies.

How to correctly fit an SIR model to data from an SEIR model?

In epidemiology, realistic disease dynamics often require Susceptible-Exposed-Infected-Recovered (SEIR)-like models because they account for incubation periods before individuals become infectious. However, for the sake of analytical tractability, simpler Susceptible-Infected-Recovered (SIR) models are commonly used, despite their lack of biological realism. Bridging these models is crucial for accurately estimating parameters and fitting models to observed data, particularly in population-level studies of infectious diseases.This paper investigates stochastic versions of the SEIR and SIR frameworks and demonstrates that the SEIR model can be effectively approximated by a SIR model with time-dependent infection and recovery rates. The validity of this approximation is supported by the derivation of a large-population Functional Law of Large Numbers (FLLN) limit and a finite-population concentration inequality.To apply this approximation in practice, the paper introduces a parameter inference methodology based on the Dynamic Survival Analysis (DSA) survival analysis framework. This method enables the fitting of the SIR model to data simulated from the more complex SEIR dynamics, as illustrated through simulated experiments.

Methodological approaches to assessing the genetic predisposition of osteochondrosis of the tarsocrural joint in the Pura Raza Española horses

Osteochondrosis (OC) is a developmental orthopaedic disease of significant concern in numerous sport horse breeds, with significant international relevance. Using digital radiographs, we assessed the occurrence of hock (tarsocrural joint) OC in 3 048 Pura Raza Española (PRE) horses which took part in a morpho-functional test, in three specific locations in the tarsus limbs: the Distal Intermediate Ridge of the Tibia (DIRT), the lateral trochlear ridges of the talus (LTT), and the medial trochlear ridges of the talus (MTT). An incidence rate of 13.3% was found for hock OC in the analysed sample, with the highest incidence rate observed in DIRT (10.0%) and the lowest in MTT (0.2%). Estimates of genetic predisposition to hock OC were carried out using three genetic approaches: 1a) a binomial threshold model based on the presence or absence of OC, 1b) a multinomial threshold model, on a scale from 0 (absence) to 3 (maximum), and 2) a linear model. The effects considered in the models included sex, genetic origin and stud class. All the analyses were based on the Bayesian inference methodology, using the THRGIBBS3F90 software. The binomial threshold model yielded the most suitable results, with an estimated heritability for Overall hock OC of 0.71 ± 0.055 on the underlying scale (0.53 on the observed scale), ranging in different locations from 0.48 ± 0.087 (LTT) to 0.66 ± 0.063 (DIRT) on the underlying scale (0.10 and 0.38 on the observed scale, respectively). The highest significative genetic correlation was observed between Overall and DIRT (0.97) for approach 1a, and the lowest significant genetic correlation was between Overall and LTT (0.49), for approach 2. This study contributes valuable insights into the genetic predisposition towards, as well as for the potential for selective breeding against, hock OC in PRE horses, and provides a basis for future research and breeding programmes aimed at minimising the occurrence of hock OC and promoting the overall health of this breed.

Marginal inference for hierarchical generalized linear mixed models with patterned covariance matrices using the Laplace approximation

AbstractWe develop hierarchical models and methods in a fully parametric approach to generalized linear mixed models for any patterned covariance matrix. The Laplace approximation is used to marginally estimate covariance parameters by integrating over all fixed and latent random effects. The Laplace approximation relies on Newton–Raphson updates, which also leads to predictions for the latent random effects. We develop methodology for complete marginal inference, from estimating covariance parameters and fixed effects to making predictions for unobserved data. The marginal likelihood is developed for six distributions that are often used for binary, count, and positive continuous data, and our framework is easily extended to other distributions. We compare our methods to fully Bayesian methods, automatic differentiation, and integrated nested Laplace approximations (INLA) for bias, mean‐squared (prediction) error, and interval coverage, and all methods yield very similar results. However, our methods are much faster than Bayesian methods, and more general than INLA. Examples with binary and proportional data, count data, and positive‐continuous data are used to illustrate all six distributions with a variety of patterned covariance structures that include spatial models (both geostatistical and areal models), time series models, and mixtures with typical random intercepts based on grouping.

Comparing traditional and causal inference methodologies for evaluating impacts of long-term air pollution exposure on hospitalization with Alzheimer's disease and related dementias.

Alzheimer's disease and related dementias (ADRD) present a growing public health burden in the United States. One actionable risk factor for ADRD is air pollution: multiple studies have found associations between air pollution and exacerbation of ADRD. Our study builds on previous studies by applying modern statistical causal inference methodologies-generalized propensity score (GPS) weighting and matching-on a large, longitudinal dataset. We follow 50 million Medicare enrollees to investigate impacts of three air pollutants-fine particular matter (PM${}_{2.5}$), nitrogen dioxide (NO${}_2$), and summer ozone (O${}_3$)-on elderly patients' rate of first hospitalization with ADRD diagnosis. Similar to previous studies using traditional statistical models, our results found increased hospitalization risks due to increased PM${}_{2.5}$ and NO${}_2$ exposure, with less conclusive results for O${}_3$. In particular, our GPS weighting analysis finds IQR increases in PM${}_{2.5}$, NO${}_2$, or O${}_3$ exposure results in hazard ratios of 1.108 (95% CI: 1.097-1.119), 1.058 (1.049-1.067), or 1.045 (1.036-1.054), respectively. GPS matching results are similar for PM${}_{2.5}$ and NO${}_2$ with attenuated effects for O${}_3$. Our results strengthen arguments that long-term PM${}_{2.5}$ and NO${}_2$ exposure increases risk of hospitalization with ADRD diagnosis. Additionally, we highlight strengths and limitations of causal inference methodologies in observational studies with continuous treatments. Keywords: Alzheimer's disease and related dementias, air pollution, Medicare, causal inference, generalized propensity score.

Bayesian inference methodology for primordial power spectrum reconstructions from Large Scale Structure

We use Bayesian inference to develop a non-parametric method to reconstruct the primordial power spectrum Pℛ (k) from Large Scale Structure (LSS) data. The performance of the method is assessed by testing it against simulations of the clustering of high-z (QSOs) objects. Their clustering is derived from different templates of the primordial power spectrum motivated by models of inflation: the Standard Model power law characterized by the two parameters As and ns ; a local feature template; and a global oscillatory template. The primordial power spectrum is reconstructed using N knots in the log {k, Pℛ (k)} plane while sampling the cosmological parameters {H 0, Ω b , Ω c }. We use two statistical tests to examine the reconstructions for signs of primordial features: a global test comparing the evidences and a novel local test quantifying the power of the hypothesis test between the power law model and the marginalized probability over N model. We also discuss results of an application to low-z (ELGs) objects with two different photometric errors keeping the cosmology fixed. The method shows good performance in all scenarios considered. In particular, the tests show no feature detection for the standard power-law primordial power spectrum; yet, the method is able to detect power spectrum deviations at a percent level for all considered features, combining either the low-z or the high-z redshift bins. In addition, we include a test proof-of-concept application to real data from the Sloan Digital Sky Survey Luminous Red Galaxy Data Release 4 (SDSS LRG 04), finding no preference for deviations from the primordial power law. The method is flexible, model independent, and suitable for its application to existing and future LSS surveys.

Bayesian inference methodology to characterize the dust emissivity at far-infrared and submillimeter frequencies

ABSTRACT We present a Bayesian inference method to characterize the dust emission properties using the well-known dust-${\rm H\,{\small I}}$ correlation in the diffuse interstellar medium at Planck frequencies $\nu \ge 217$ GHz. We use the Galactic ${\rm H\,{\small I}}$ map from the Galactic All-Sky Survey (GASS) as a template to trace the Galactic dust emission. We jointly infer the pixel-dependent dust emissivity and the zero level present in the Planck intensity maps. We use the Hamiltonian Monte Carlo technique to sample the high-dimensional parameter space ($D \sim 10^3$). We demonstrate that the methodology leads to unbiased recovery of dust emissivity per pixel and the zero level when applied to realistic Planck sky simulations over a 6300 $\rm {deg}^2$ area around the Southern Galactic pole. As an application on data, we analyse the Planck intensity map at 353 GHz to jointly infer the pixel-dependent dust emissivity at $N_{\rm side}=32$ resolution (1.8° pixel size) and the global offset. We find that the spatially varying dust emissivity has a mean of 0.031 MJy sr$^{-1}$$(10^{20} \, \mathrm{cm^{-2}})^{-1}$ and $1\sigma$ standard deviation of 0.007 MJy sr$^{-1}$$(10^{20} \, \mathrm{cm^{-2}})^{-1}$. The mean dust emissivity increases monotonically with increasing mean ${\rm H\,{\small I}}$ column density. We find that the inferred global offset is consistent with the expected level of cosmic infrared background (CIB) monopole added to the Planck data at 353 GHz. This method is useful in studying the line-of-sight variations of dust spectral energy distribution in the multiphase interstellar medium.

Universal Inference Meets Random Projections: A Scalable Test for Log-Concavity

Shape constraints yield flexible middle grounds between fully nonparametric and fully parametric approaches to modeling distributions of data. The specific assumption of log-concavity is motivated by applications across economics, survival modeling, and reliability theory. However, there do not currently exist valid tests for whether the underlying density of given data is log-concave. The recent universal inference methodology provides a valid test. The universal test relies on maximum likelihood estimation (MLE), and efficient methods already exist for finding the log-concave MLE. This yields the first test of log-concavity that is provably valid in finite samples in any dimension, for which we also establish asymptotic consistency results. Empirically, we find that a random projections approach that converts the d-dimensional testing problem into many one-dimensional problems can yield high power, leading to a simple procedure that is statistically and computationally efficient.

Brief of Amici Curiae economists in support of respondents in Dobbs v. Jackson Women's Health Organization.

A pillar of Mississippi's argument in Dobbs v. Jackson Women's Health was that there is no evidence of "societal reliance" on abortion, meaning no reason to believe that access to abortion impacts the ability of women to participate in the economic and social life of the nation. Led by economist Caitlin Myers and attorney Anjali Srinivasan, more than 150 economists filed an amicus brief seeking to assist the Court in understanding that this assertion is erroneous. The economists describe developments in causal inference methodologies over the last three decades, and the ways in which these tools have been used to isolate the measure of the effects of abortion legalization in the 1970s and of abortion policies and access over the ensuing decades. The economists argue that there is a substantial body of well-developed and credible research that shows that abortion access has had and continues to have a significant effect on birth rates as well as broad downstream social and economic effects, including on women's educational attainment and job opportunities. What follows is a reprint of this brief.