GeoPhy: Differentiable Phylogenetic Inference via Geometric Gradients of Tree Topologies

Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies and evolutionary distances on branches, is crucial for accurately inferring species relationships from molecular data and tasks requiring variable marginalization. Variational Bayesian methods are key to developing scalable, practical models; however, it remains challenging to conduct phylogenetic inference without restricting the combinatorially vast number of possible tree topologies. In this work, we introduce a novel, fully differentiable formulation of phylogenetic inference that leverages a unique representation of topological distributions in continuous geometric spaces. Through practical considerations on design spaces and control variates for gradient estimations, our approach, GeoPhy, enables variational inference without limiting the topological candidates. In experiments using real benchmark datasets, GeoPhy significantly outperformed other approximate Bayesian methods that considered whole topologies.Comment: 23 pages, 5 figure

12Epi -9deacetoxyxenicin, new cytotoxic diterpenoid from a Bornean soft coral Xenia sp

One new compound, 12-epi-9-deacetoxyxenicin (1) along with a hydroperoxide product, 12-epi-9-deacetoxy-8-hydroperoxyxenicin (2) and two known sesquiterpenoids (3–4) were isolated from a population of Bornean soft coral Xenia sp. The structures of these secondary metabolites were elucidated based on their spectroscopic data. Compounds 1 and 2 showed cytotoxic activity against ATL cell line, S1T. In addition, compound 3 exhibited hyphal inhibition of Lagenidium thermophilum

Explicitly Multi-Modal Benchmarks for Multi-Objective Optimization

In multi-objective optimization, designing good benchmark problems is an important issue for improving solvers. Although many benchmark problems have been proposed and some of them became de facto standards, designing multimodal problems that have a controllable landscape is still an open problem especially for high-dimensional cases. We thus propose the Benchmark with Explicit Multimodality (BEM), which lets the benchmark designer specify the basins of attraction using a graph structure known as the reachability graph. In this article, we focus on the mathematical formulation of the BEM. We will see that the BEM has preferable characteristics such as (i) realizing user-specified local Pareto set, (ii) allowing high-dimensional design spaces and (iii) possessing nonseparability

Effects of Olopatadine Hydrochloride, a Histamine H1 Receptor Antagonist, on Histamine-Induced Skin Responses

Effects of olopatadine hydrochloride, a histamine H1 receptor antagonist, on histamine-induced skin responses were evaluated in 10 healthy subjects in comparison with placebo, fexofenadine hydrochloride, and bepotastine besilate. Olopatadine significantly suppressed histamine-induced wheal, flare, and itch, starting 30 minutes after oral administration. Olopatadine was more effective than fexofenadine and bepotastine. None of the drugs studied impaired performance of word processing tasks. These results suggest that olopatadine can suppress skin symptoms caused by histamine soon after administration

Household income relationship with health services utilization and healthcare expenditures in people aged 75 years or older in Japan: A population-based study using medical and long-term care insurance claims data

Background: This study aimed to determine whether there are disparities in healthcare services utilization according to household income among people aged 75 years or older in Japan.Methods: We used data on medical and long-term care (LTC) insurance claims and on LTC insurance premiums and needs levels for people aged 75 years or older in a suburban city. Data on people receiving public welfare were not available. Participants were categorized according to household income level using LTC insurance premiums data. The associations of low income with physician visit frequency, length of hospital stay (LOS), and medical and LTC expenditures were evaluated and adjusted for 5-year age groups and LTC needs level.Results: The study analyzed 12,852 men and 18,020 women, among which 13.3% and 41.5%, respectively, were categorized as low income. Participants with low income for both genders were more likely to be functionally dependent. In the adjusted analyses, lower income was associated with fewer physician visits (incidence rate ratio [IRR] 0.90; 95% confidence interval [CI], 0.87–0.92 for men and IRR 0.97; 95% CI, 0.95–0.99 for women), longer LOS (IRR 1.98; 95% CI, 1.54–2.56 and IRR 1.42; 95% CI, 1.20–1.67, respectively), and higher total expenditures (exp(β) 1.09; 95% CI, 1.01–1.18 and exp(β) 1.09; 95% CI, 1.05–1.14, respectively).Conclusions: This study suggests that older people with lower income had fewer consultations with physicians but an increased use of inpatient services. The income categorization used in this study may be an appropriate proxy of socioeconomic status

Fluid Mode Spectroscopy for measuring dynamic viscosity of fluids in open cylindrical containers

On a daily basis we stir tee or coffee with a spoon and leave it to rest. We know empirically the larger the stickiness, viscosity, of the fluid, more rapidly its velocity slows down. It is surprising, therefore, that the variation has not been utilized for measuring (dynamic) viscosity of fluids. This study shows that a spectroscopy decomposing a velocity field into fluid modes (Stokes eigenmodes) allows us to measure accurately the dynamic viscosity. The method, Fluid Mode Spectroscopy (FMS), is based on the fact that each Stokes eigenmode has its inherent decay rate of eigenvalue and that the dimensionless rate of the slowest decaying mode (SDM) is constant, dependent only on the normalized shape of a fluid container, obtained analytically for some shapes including cylindrical containers. The FMS supplements major conventional measuring methods with each other, particularly useful for measuring low dynamic viscosity.Comment: 18 pagese, 6 figure