arXiv subjects

Hiroshi Ohno

Publications and source records attributed to Hiroshi Ohno.

At least 37 records · Page 2Linked to original sources

arXiv2024

Machine Learning Estimation on the Trace of Inverse Dirac Operator using the Gradient Boosting Decision Tree Regression

We present our preliminary results on the machine learning estimation of $\text{Tr} \, M^{-n}$ from other observables with the gradient boosting decision tree regression, where $M$ is the Dirac operator. Ordinarily, $\text{Tr} \, M^{-n}$ is obtained by linear CG solver for stochastic sources which needs considerable computational cost. Hence, we explore the possibility of cost reduction on the trace estimation by the adoption of gradient boosting decision tree algorithm. We also discuss effects of bias and its correction.

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arXiv2024

Unified theory of upper confidence bound policies for bandit problems targeting total reward, maximal reward, and more

The upper confidence bound (UCB) policy is recognized as an order-optimal solution for the classical total-reward bandit problem. While similar UCB-based approaches have been applied to the max bandit problem, which aims to maximize the cumulative maximal reward, their order optimality remains unclear. In this study, we clarify the unified conditions under which the UCB policy achieves the order optimality in both total-reward and max bandit problems. A key concept of our theory is the oracle quantity, which identifies the best arm by its highest value. This allows a unified definition of the UCB policy as pulling the arm with the highest UCB of the oracle quantity. Additionally, under this setting, optimality analysis can be conducted by replacing traditional regret with the number of failures as a core measure. One consequence of our analysis is that the confidence interval of the oracle quantity must narrow appropriately as trials increase to ensure the order optimality of UCB policies. From this consequence, we prove that the previously proposed MaxSearch algorithm satisfies this condition and is an order-optimal policy for the max bandit problem. We also demonstrate that new bandit problems and their order-optimal UCB algorithms can be systematically derived by providing the appropriate oracle quantity and its confidence interval. Building on this, we propose PIUCB algorithms, which aim to pull the arm with the highest probability of improvement (PI). These algorithms can be applied to the max bandit problem in practice and perform comparably or better than the MaxSearch algorithm in toy examples. This suggests that our theory has the potential to generate new policies tailored to specific oracle quantities.

stat.ML↗

arXiv2024

Sparse modeling study to extract spectral functions from lattice QCD data

We present spectral functions extracted from Euclidean-time correlation functions by using sparse modeling. Sparse modeling is a method that solves inverse problems by considering only the sparseness of the solution we seek. To check applicability of the method, we firstly test it with mock data which imitate charmonium correlation functions on a fine lattice. We show that the method can reconstruct the resonance peaks in the spectral functions. Then, we extract charmonium spectral functions from correlation functions obtained from lattice QCD at temperatures below and above the critical temperature $T_{\mathrm{c}}$. We show that this method yields results like those obtained with MEM and other methods.

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arXiv2023

Sparse modeling approach to extract spectral functions with covariance of Euclidean-time correlators of lattice QCD

We present our sparse modeling study to extract spectral functions from Euclidean-time correlation functions. In this study covariance between different Euclidean times of the correlation function is taken into account, which was not done in previous studies. In order to check applicability of the method, we firstly test it with mock data which imitate possible charmonium spectral functions. Then, we extract spectral functions from correlation functions obtained from lattice QCD at finite temperature.

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arXiv2023

Antibiotic-dependent instability of homeostatic plasticity for growth and environmental load

Reducing antibiotic usage in livestock animals has become an urgent issue worldwide to prevent antimicrobial resistance. Here, abuse of chlortetracycline (CTC), a versatile antibacterial agent, on the performance, blood components, fecal microbiota, and organic acid concentration in calves was investigated. Japanese Black calves were fed milk replacer containing CTC at 10 g/kg (CON) or 0 g/kg (EXP). Growth performance was not affected by CTC administration. However, CTC administration altered the correlation between fecal organic acids and bacterial genera. Machine learning methods such as association analysis, linear discriminant analysis, and energy landscape analysis revealed that CTC administration affected according to certain rules the population of various types of fecal bacteria. It is particularly interesting that the population of several methane-producing bacteria was high in the CON, and that of Lachnospiraceae, a butyrate-producing bacteria, was high in the EXP at 60 d of age. Furthermore, statistical causal inference based on machine learning data estimated that CTC treatment affects the entire intestinal environment, inhibiting butyrate production for growth and biological defense, which may be attributed to methanogens in feces. Thus, these observations highlight the multiple harmful impacts of antibiotics on intestinal health and the potential production of greenhouse gas in the calves.

q-bio.QM↗

arXiv2023

Agricultural quality matrix-based multiomics structural analysis of carrots in soils fertilized with thermophile-fermented compost

Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, red color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that L-2-aminoadipate, phenylalanine, flavonoids and / or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus, L-2-aminoadipate and nicotinamide, and S-methyl L-cysteine were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen.

q-bio.QM↗

arXiv2022

Estimation of symbiotic bacterial structure in a sustainable seagrass ecosystem on recycled management

Seagrass meadows play an essential role in blue carbon and aquatic ecosystem services. However, methods for the flourishing of seagrass are still being explored. Here, data from 49 public coastal surveys on the distribution of seagrass and seaweed around the onshore aquaculture facilities are revalidated, and an exceptional area where the seagrass Zostera marina thrives was found. The bacterial population there showed an apparent decrease in the pathogen candidates belonging to the order Flavobacteriales. Moreover, structure equation modeling and a linear non-Gaussian acyclic model based on the machine learning data estimated an optimal symbiotic bacterial group candidate for seagrass growth as follows: the Lachnospiraceae and Ruminococcaceae families as gut-inhabitant bacteria, Rhodobacteraceae as photosynthetic bacteria, and Desulfobulbaceae as cable bacteria modulating oxygen or nitrate reduction and oxidation of sulfide. These observations confer a novel perspective on the seagrass symbiotic bacterial structures critical for blue carbon and low-pathogenic marine ecosystems in aquaculture.

q-bio.PE↗

arXiv2022

Materials Discovery using Max K-Armed Bandit

Search algorithms for the bandit problems are applicable in materials discovery. However, the objectives of the conventional bandit problem are different from those of materials discovery. The conventional bandit problem aims to maximize the total rewards, whereas materials discovery aims to achieve breakthroughs in material properties. The max K-armed bandit (MKB) problem, which aims to acquire the single best reward, matches with the discovery tasks better than the conventional bandit. Thus, here, we propose a search algorithm for materials discovery based on the MKB problem using a pseudo-value of the upper confidence bound of expected improvement of the best reward. This approach is pseudo-guaranteed to be asymptotic oracles that do not depends on the time horizon. In addition, compared with other MKB algorithms, the proposed algorithm has only one hyperparameter, which is advantageous in materials discovery. We applied the proposed algorithm to synthetic problems and molecular-design demonstrations using a Monte Carlo tree search. According to the results, the proposed algorithm stably outperformed other bandit algorithms in the late stage of the search process when the optimal arm of the MKB could not be determined based on its expectation reward.

stat.ML↗

arXiv2022

Symbiotic bacterial network structure involved in carbon and nitrogen metabolism of wood-utilizing insect larvae

Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive mechanism are expected to speculate a novel rule in wood biomass processing. Here, the relationships of inhabitant bacteria involved in carbon and nitrogen metabolism in the intestine of beetle larvae, an insect model, are investigated. Bacterial analysis of larval feces showed enrichment of members of which could include candidates for plant growth promotion, nitrogen cycle modulation, and/or environmental protection. The abundances of these bacteria were not necessarily positively correlated with the abundance in the habitat, suggesting that they might be selectively enriched in the intestines of larvae. Further association analysis predicted that carbon and nitrogen metabolism in the intestine was affected by the presence of the other common bacteria, the populations of which were not remarkably altered in the habitat and feces. Based on hypotheses targeting these selected bacterial groups, structural estimation modeling analyses statistically suggested that their metabolism of carbon and nitrogen and their stable isotopes, δ13C and δ15N, may be associated with fecal enriched bacteria and other common bacteria. In addition, other causal inference analyses, such as causal mediation analysis, linear non-Gaussian acyclic model (LiNGAM), and BayesLiNGAM, did not necessarily affirm the existence of prominent bacteria involved in metabolism, implying its importance as the bacterial groups for metabolism rather than a remarkable bacterium. Thus, these observations highlight a multifaceted view of symbiotic bacterial groups utilizing carbon and nitrogen from wood biomass in insect larvae as a cultivator of potentially environmentally beneficial bacteria.

q-bio.QM↗

arXiv2021

Charm and beauty in the deconfined plasma from quenched lattice QCD

We present continuum extrapolated results of charmonium and bottomonium correlators in the vector channel at several temperatures below and above $T_c$. The continuum extrapolation jointly performed with the interpolations to have physical values of $J/ψ$ and $Υ$ masses in the confined phase is based on calculations on several large quenched isotropic lattices using clover-improved Wilson valence fermions carrying different quark masses. The extrapolated lattice correlators are confronted with perturbation theory results incorporating resummed thermal effects around the threshold from pNRQCD and vacuum asymptotics above the threshold. An additional transport peak is modelled below the threshold allowing for an estimate of the diffusion coefficients for charm and bottom quarks. We find that charmonium correlators in the vector channel can be well reproduced by perturbative spectral functions above $T_c$ where no resonance peaks for $J/ψ$ are needed at and above 1.1 $T_c$, while for bottomonium correlators a resonance peak for $Υ$ is still needed up to 1.5 $T_c$. By analyzing the transport contribution to the correlators we find that the drag coefficient of a charm quark is larger than that of a bottom quark.

hep-lat↗

arXiv2020

Nature of the phase transition for finite temperature $N_{\rm f}=3$ QCD with nonperturbatively O($a$) improved Wilson fermions at $N_{\rm t}=12$

We study the nature of the finite temperature phase transition for three-flavor QCD. In particular we investigate the location of the critical endpoint along the three flavor symmetric line in the light quark mass region of the Columbia plot. In the study, the Iwasaki gauge action and the nonperturvatively O($a$) improved Wilson-Clover fermion action are employed. We newly generate data at $N_{\rm t}=12$ and set an upper bound of the critical pseudoscalar meson mass in the continuum limit $m_{\rm PS,E}\lesssim 110$MeV.

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arXiv2020

Thermal modifications of quarkonia and heavy quark diffusion from a comparison of continuum-extrapolated lattice results to perturbative QCD

We investigate the in-medium modifications of heavy quarkonia in the vector channel and the heavy quark diffusion coefficient by comparing Euclidean correlators from the lattice to a perturbative spectral function. On the lattice side, we work with continuum extrapolated data from four different large and fine lattices with Clover-improved Wilson fermions in the quenched approximation at five temperatures (0.75, 1.1, 1.3, 1.5 and 2.25$T_c$). On the perturbative side, we use a combination of pNRQCD and vacuum asymptotics to describe the spectral function. After accounting for systematic errors, we obtain a spectral function that is suited to describe the bound state region. This spectral function describes charmonium well without a resonance peak at any of our analyzed temperatures above $T_c$, while we observe a thermally broadened resonance peak for bottomonium that is only melted at our largest temperature, $2.25T_c$. For the transport contribution we assume a Breit-Wigner shaped peak and find that the drag coefficient of charm quarks is larger than that of bottom quarks.

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arXiv2019

Critical endpoint in the continuum limit and critical endline at $N_{\rm T}=6$ of the finite temperature phase transition of QCD with clover fermions

We investigate the critical endpoints of the finite temperature phase transition of QCD at zero chemical potential. We employ the renormalization-group improved Iwasaki gauge action and non-perturbatively O(a)-improved Wilson-clover fermion action. The critical endpoints are determined by using the intersection point of kurtosis, employing the multi-parameter, multi-ensemble reweighting method. We present results for the critical endline at $N_{\rm T}$ = 6 and the continuum extrapolation for the critical endpoint of the SU(3)-flavor symmetric point.

hep-lat↗

arXiv2019

Meson Screening Masses in (2+1)-Flavor QCD

We present lattice QCD results for mesonic screening masses in the temperature range 140 MeV $\lesssim T \lesssim$ 2500 MeV. Our calculations were carried out using (2+1)-flavors of the Highly Improved Staggered Quark (HISQ) action, with a physical value for the strange quark mass and two values of the light quark mass corresponding to pion masses of 160 MeV and 140 MeV. Continuum-extrapolated results were obtained using calculations with a variety of lattice spacings corresponding to temporal lattice extents $N_τ= 6 - 16$. We discuss the implications of these results for the effective restoration of various symmetries in the high temperature phase of QCD, as well as the approach toward the perturbative limit.

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arXiv2018

Continuum extrapolation of the critical endpoint in 4-flavor QCD with Wilson-Clover fermions

We report our study on the critical endpoint of the finite temperature phase transition in 4-flavor QCD with Wilson-Clover fermions. Using the kurtosis intersection method, we determined the critical endpoint on lattices with $N_t$ = 4, 6 and 8. Our continuum extrapolated results show that the pseudo-scalar meson mass at the critical endpoint, $m_\mathrm{PS,E}$, for 4-flavor is clearly larger than that for 3-flavor. We also compared our results to those with staggered fermions and found that $m_\mathrm{PS,E}/T_E$ for 4-flavor with Wilson fermions might remain finite even in the continuum limit in contrast to that with staggered fermions, where $m_\mathrm{PS,E}/T_E$ is very close to zero, which suggests that the difference between Wilson and staggered fermions is at least not due to the rooting.

hep-lat↗

arXiv2018

Continuum extrapolation of quarkonium correlators at non-zero temperature

In the investigation of in-medium modifications of quarkonia and for determining heavy quark diffusion coefficients, correlation functions play a crucial role. For the first time we perform a continuum extrapolation of charmonium and bottomonium correlators in the vector channel based on non-perturbatively clover-improved Wilson fermions in quenched lattice QCD. Calculations were done at 4 different lattice spacings, spatial extents between 96 and 192, aspect ratio from 1/6 to 1/2, for 5 temperatures between $T/T_c = 0.75$ and $T/T_c = 2.2$. We interpolate between different quark masses to match to the same vector meson mass over different lattice setups. Afterwards we extrapolate the renormalized correlators to the continuum. While we find a strong temperature dependence for charmonium, bottomonium states are only slightly affected at higher temperatures.

hep-lat↗

arXiv2018

Charmonium and bottomonium spectral functions in the vector channel

In this paper we report our results on quarkonium spectral functions in the vector channel obtained from quenched lattice QCD simulations at $T\in[0.75, 2.25]~T_c$. The calculations have been performed on very large and fine isotropic lattices where both charm and bottom quarks can be treated relativistically. The spectral functions are reconstructed using the Maximum Entropy Method. We study the dissociation of quarkonium states from the temperature dependence of the spectral functions and estimate heavy quark diffusion coefficients using the low-frequency behavior of the vector spectral functions.

hep-lat↗

arXiv2018

Stochastic reconstructions of spectral functions: Application to lattice QCD

We present a detailed study of the applications of two stochastic approaches, stochastic optimization method (SOM) and stochastic analytical inference (SAI), to extract spectral functions from Euclidean correlation functions. SOM has the advantage that it does not require prior information. On the other hand, SAI is a more generalized method based on Bayesian inference. Under mean field approximation SAI reduces to the often-used maximum entropy method (MEM), and for a specific choice of the prior SAI becomes equivalent to SOM. To test the applicability of these two stochastic methods to lattice QCD, firstly, we apply these methods to various reasonably chosen model correlation functions, and present detailed comparisons of the reconstructed spectral functions obtained from SOM, SAI and MEM. Next, we present similar studies for charmonia correlation functions obtained from lattice QCD computations using clover-improved Wilson fermions on large, fine, isotropic lattices at $0.75$ and $1.5T_c$, $T_c$ being the deconfinement transition temperature of a pure gluon plasma. We find that SAI and SOM give consistent results to MEM at these two temperatures.

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