Robust Field-level Likelihood-free Inference with Galaxies

© 2023. The Author(s). Published by the American Astronomical Society. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY), https://creativecommons.org/licenses/by/4.0/We train graph neural networks to perform field-level likelihood-free inference using galaxy catalogs from state-of-the-art hydrodynamic simulations of the CAMELS project. Our models are rotational, translational, and permutation invariant and do not impose any cut on scale. From galaxy catalogs that only contain 3D positions and radial velocities of ∼1000 galaxies in tiny (25h−1Mpc)3 volumes our models can infer the value of Ωm with approximately 12% precision. More importantly, by testing the models on galaxy catalogs from thousands of hydrodynamic simulations, each having a different efficiency of supernova and active galactic nucleus feedback, run with five different codes and subgrid models—IllustrisTNG, SIMBA, Astrid, Magneticum, SWIFT-EAGLE—we find that our models are robust to changes in astrophysics, subgrid physics, and subhalo/galaxy finder. Furthermore, we test our models on 1024 simulations that cover a vast region in parameter space—variations in five cosmological and 23 astrophysical parameters—finding that the model extrapolates really well. Our results indicate that the key to building a robust model is the use of both galaxy positions and velocities, suggesting that the network has likely learned an underlying physical relation that does not depend on galaxy formation and is valid on scales larger than ∼10 h −1 kpc.Peer reviewe

A Universal Equation to Predict Ω m from Halo and Galaxy Catalogs

© 2023. The Author(s). Published by the American Astronomical Society. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY), https://creativecommons.org/licenses/by/4.0/We discover analytic equations that can infer the value of Ωm from the positions and velocity moduli of halo and galaxy catalogs. The equations are derived by combining a tailored graph neural network (GNN) architecture with symbolic regression. We first train the GNN on dark matter halos from Gadget N-body simulations to perform field-level likelihood-free inference, and show that our model can infer Ωm with ∼6% accuracy from halo catalogs of thousands of N-body simulations run with six different codes: Abacus, CUBEP3M, Gadget, Enzo, PKDGrav3, and Ramses. By applying symbolic regression to the different parts comprising the GNN, we derive equations that can predict Ωm from halo catalogs of simulations run with all of the above codes with accuracies similar to those of the GNN. We show that, by tuning a single free parameter, our equations can also infer the value of Ωm from galaxy catalogs of thousands of state-of-the-art hydrodynamic simulations of the CAMELS project, each with a different astrophysics model, run with five distinct codes that employ different subgrid physics: IllustrisTNG, SIMBA, Astrid, Magneticum, SWIFT-EAGLE. Furthermore, the equations also perform well when tested on galaxy catalogs from simulations covering a vast region in parameter space that samples variations in 5 cosmological and 23 astrophysical parameters. We speculate that the equations may reflect the existence of a fundamental physics relation between the phase-space distribution of generic tracers and Ωm, one that is not affected by galaxy formation physics down to scales as small as 10 h −1 kpc.Peer reviewe

Attitudes toward Precision Treatment of Smoking in the Southern Community Cohort Study

Background: Precision interventions using biological data may enhance smoking treatment, yet are understudied among smokers who are disproportionately burdened by smoking-related disease. Methods: We surveyed smokers in the NCI-sponsored Southern Community Cohort Study, consisting primarily of African-American, low-income adults. Seven items assessed attitudes toward aspects of precision smoking treatment, from undergoing tests to acting on results. Items were dichotomized as favorable (5 = strongly agree/4 = agree) versus less favorable (1 = strongly disagree/2 = disagree/3 = neutral); a summary score reflecting generalized attitudes was also computed. Multivariable logistic regression tested independent associations of motivation (precontemplation, contemplation, and preparation) and confidence in quitting (low, medium, and high) with generalized attitudes, controlling for sociodemographic factors and nicotine dependence. Results: More than 70% of respondents endorsed favorable generalized attitudes toward precision medicine, with individual item favorability ranging from 64% to 83%. Smokers holding favorable generalized attitudes reported higher income and education (P \u3c 0.05). Predicted probabilities of favorable generalized attitudes ranged from 63% to 75% across motivation levels [contemplation vs. precontemplation: adjusted odds ratio (AOR) = 2.10, 95% confidence interval (CI), 1.36–3.25, P = 0.001; preparation vs. precontemplation: AOR = 1.83, 95% CI, 1.20–2.78, P = 0.005; contemplation vs. preparation: AOR = 1.15, 95% CI, 0.75–1.77, P = 0.52] and from 59% to 78% across confidence (medium vs. low: AOR = 1.91, 95% CI, 1.19–3.07, P = 0.007; high vs. low: AOR = 2.62, 95% CI, 1.68–4.10, P \u3c 0.001; medium vs. high: AOR = 0.73, 95% CI, 0.48–1.11, P = 0.14). Conclusions: Among disproportionately burdened community smokers, most hold favorable attitudes toward precision smoking treatment. Individuals with lower motivation and confidence to quit may benefit from additional intervention to engage with precision smoking treatment. Impact: Predominantly favorable attitudes toward precision smoking treatment suggest promise for future research testing their effectiveness and implementation

Disruption of medical care among individuals in the southeastern United States during the COVID-19 pandemic

Background: Widespread disruptions of medical care to mitigate COVID-19 spread and reduce burden on healthcare systems may have deleterious public health consequences. Design and Methods: To examine factors contributing to healthcare interruptions during the pandemic, we conducted a COVID-19 impact survey between 10/7-12/14/2020 among participants of the Southern Community Cohort Study, which primarily enrolled low-income individuals in 12 southeastern states from 2002-2009. COVID survey data were combined with baseline and follow-up data. Results: Among 4,463 respondents, 40% reported having missed/delayed a health appointment during the pandemic; the common reason was provider-initiated cancellation or delay (63%). In a multivariable model, female sex was the strongest independent predictor of interrupted care, with odds ratio (OR) 1.63 (95% confidence interval [CI] 1.40-1.89). Those with higher education (OR 1.27; 95% CI 1.05-1.54 for college graduate vs ≤high school) and household income (OR 1.47; 95% CI 1.16-1.86 for >$50,000 vs <$15,000) were at significantly increased odds of missing healthcare.  Having greater perceived risk for acquiring (OR 1.42; 95% CI 1.17-1.72) or dying from COVID-19 (OR 1.25; 95% CI 1.04-1.51) also significantly increased odds of missed/delayed healthcare. Age was inversely associated with missed healthcare among men (OR for 5-year increase in age 0.88; 95% CI 0.80-0.96) but not women (OR 0.97; 95% CI 0.91-1.04; p-interaction=0.04). Neither race/ethnicity nor comorbidities were associated with interrupted healthcare. Conclusions: Disruptions to healthcare disproportionately affected women and were primarily driven by health system-initiated deferrals and individual perceptions of COVID-19 risk, rather than medical co-morbidities or other traditional barriers to healthcare access

Racial Differences in Hepatocellular Carcinoma Incidence and Risk Factors among a Low Socioeconomic Population

The purpose of this study was to examine differences in risk factors associated with hepatocellular carcinoma (HCC) among White and African Americans from low socioeconomic backgrounds in the Southern Community Cohort Study (SCCS). The SCCS is a prospective cohort study with participants from the southeastern US. HCC incidence rates were calculated. Multivariable Cox regression was used to calculate HCC-adjusted hazard ratios (aHR) associated with known baseline HCC risk factors for White and African Americans, separately. There were 294 incident HCC. The incidence rate ratio for HCC was higher (IRR = 1.4, 95%CI: 1.1–1.9) in African Americans compared to White Americans. White Americans saw a stronger association between self-reported hepatitis C virus (aHR = 19.24, 95%CI: 10.58–35.00) and diabetes (aHR = 3.55, 95%CI: 1.96–6.43) for the development of HCC compared to African Americans (aHR = 7.73, 95%CI: 5.71–10.47 and aHR = 1.48, 95%CI: 1.06–2.06, respectively) even though the prevalence of these risk factors was similar between races. Smoking (aHR = 2.91, 95%CI: 1.87–4.52) and heavy alcohol consumption (aHR = 1.59, 95%CI: 1.19–2.11) were significantly associated with HCC risk among African Americans only. In this large prospective cohort, we observed racial differences in HCC incidence and risk factors associated with HCC among White and African Americans

Baseline Prostate-specific Antigen Level in Midlife and Aggressive Prostate Cancer in Black Men

Background: Prostate-specific antigen (PSA) measurement in midlife predicts long-term prostate cancer (PCa) mortality among white men. Objective: To determine whether baseline PSA level during midlife predicts risk of aggressive PCa in black men. Design, setting, and participants: Nested case-control study among black men in the Southern Community Cohort Study recruited between 2002 and 2009. A prospective cohort in the southeastern USA with recruitment from community health centers. A total of 197 incident PCa patients aged 40–64 yr at study entry and 569 controls matched on age, date of blood draw, and site of enrollment. Total PSA was measured in blood collected and stored at enrollment. Outcome measurements and statistical analysis: Total and aggressive PCa (91 aggressive: Gleason ≥7, American Joint Committee on Cancer stage III/IV, or PCa-specific death). Exact conditional logistic regression estimated odds ratios (ORs) with 95% confidence intervals (CIs) for PCa by category of baseline PSA. Results and limitations: Median PSA among controls was 0.72, 0.80, 0.94, and 1.03 ng/ml for age groups 40–49, 50–54, 55–59, and 60–64 yr, respectively; 90th percentile levels were 1.68, 1.85, 2.73, and 3.33 ng/ml. Furthermore, 95% of total and 97% of aggressive cases had baseline PSA above the age-specific median. Median follow-up was 9 yr. The OR for total PCa comparing PSA >90th percentile versus ≤median was 83.6 (95% CI, 21.2–539) for 40–54 yr and 71.7 (95% CI, 23.3–288) for 55–64 yr. For aggressive cancer, ORs were 174 (95% CI, 32.3–infinity) for 40–54 yr and 51.8 (95% CI, 11.0–519) for 55–64 yr. A composite endpoint of aggressive PCa based on stage, grade, and mortality was used and is a limitation. Conclusions: PSA levels in midlife strongly predicted total and aggressive PCa among black men. PSA levels among controls were similar to those among white controls in prior studies. Patient summary: Prostate-specific antigen (PSA) level during midlife strongly predicted future development of aggressive prostate cancer among black men. Targeted screening based on a midlife PSA might identify men at high risk while minimizing screening in those men at low risk. Prostate-specific antigen (PSA) level during midlife strongly predicted total and aggressive prostate cancer among black men. Risk-stratified screening based on midlife PSA might retain the benefits of screening while reducing harms

Comparing Diabetes Prevalence Between African Americans and Whites of Similar Socioeconomic Status

Objectives. We investigated whether racial disparities in the prevalence of type 2 diabetes exist beyond what may be attributable to differences in socioeconomic status (SES) and other modifiable risk factors

Healthy Eating and Risks of Total and Cause-Specific Death among Low-Income Populations of African-Americans and Other Adults in the Southeastern United States: A Prospective Cohort Study

Background: A healthy diet, as defined by the US Dietary Guidelines for Americans (DGA), has been associated with lower morbidity and mortality from major chronic diseases in studies conducted in predominantly non-Hispanic white individuals. It is unknown whether this association can be extrapolated to African-Americans and low-income populations. Methods and Findings: We examined the associations of adherence to the DGA with total and cause-specific mortality in the Southern Community Cohort Study, a prospective study that recruited 84,735 American adults, aged 40–79 y, from 12 southeastern US states during 2002–2009, mostly through community health centers that serve low-income populations. The present analysis included 50,434 African-Americans, 24,054 white individuals, and 3,084 individuals of other racial/ethnic groups, among whom 42,759 participants had an annual household income less than US$15,000. Usual dietary intakes were assessed using a validated food frequency questionnaire at baseline. Adherence to the DGA was measured by the Healthy Eating Index (HEI), 2010 and 2005 editions (HEI-2010 and HEI-2005, respectively). During a mean follow-up of 6.2 y, 6,906 deaths were identified, including 2,244 from cardiovascular disease, 1,794 from cancer, and 2,550 from other diseases. A higher HEI-2010 score was associated with lower risks of disease death, with adjusted hazard ratios (HRs) of 0.80 (95% CI, 0.73–0.86) for all-disease mortality, 0.81 (95% CI, 0.70–0.94) for cardiovascular disease mortality, 0.81 (95% CI, 0.69–0.95) for cancer mortality, and 0.77 (95% CI, 0.67–0.88) for other disease mortality, when comparing the highest quintile with the lowest (all p-values for trend 0.50). Several component scores in the HEI-2010, including whole grains, dairy, seafood and plant proteins, and ratio of unsaturated to saturated fatty acids, showed significant inverse associations with total mortality. HEI-2005 score was also associated with lower disease mortality, with a HR of 0.86 (95% CI, 0.79–0.93) when comparing extreme quintiles. Given the observational study design, however, residual confounding cannot be completely ruled out. In addition, future studies are needed to evaluate the generalizability of these findings to African-Americans of other socioeconomic status. Conclusions: Our results showed, to our knowledge for the first time, that adherence to the DGA was associated with lower total and cause-specific mortality in a low-income population, including a large proportion of African-Americans, living in the southeastern US

Associations of Dietary Intakes of Carotenoids and Vitamin A with Lung Cancer Risk in a Low-Income Population in the Southeastern United States

Observational studies found inverse associations of dietary carotenoids and vitamin A intakes with lung cancer risk. However, interventional trials among high-risk individuals showed that &beta;-carotene supplements increased lung cancer risk. Most of the previous studies were conducted among European descendants or Asians. We prospectively examined the associations of lung cancer risk with dietary intakes of carotenoids and vitamin A in the Southern Community Cohort Study, including 65,550 participants with 1204 incident lung cancer cases. Multivariate Cox regression was used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). Lung cancer cases had lower energy-adjusted dietary intakes of all carotenoids and vitamin A than non-cases. However, dietary intakes of carotenoids and vitamin A were not associated with overall lung cancer risk. A significant positive association of dietary vitamin A intake with lung cancer risk was observed among current smokers (HRQ4 vs. Q1 = 1.23; 95% CI: 1.02&ndash;1.49; Ptrend = 0.01). In addition, vitamin A intake was associated with an increased risk of adenocarcinoma among African Americans (HRQ4 vs. Q1 = 1.55; 95%CI: 1.08&ndash;2.21; Ptrend = 0.03). Dietary lycopene intake was associated with an increased risk of lung cancer among former smokers (HRQ4 vs. Q1 = 1.50; 95% CI: 1.04&ndash;2.17; Ptrend = 0.03). There are positive associations of dietary &beta;-cryptoxanthin intake with squamous carcinoma risk (HRQ4 vs. Q1 = 1.49; 95% CI: 1.03&ndash;2.15; Ptrend = 0.03). Further studies are warranted to confirm our findings