Chemical machine learning with kernels: The key impact of loss functions

Machine learning promises to accelerate materials discovery by allowing computational efficient property predictions from a small number of reference calculations. As a result, the literature spent a considerable effort in designing representations that capture basic physical properties so far. In stark contrast, our work focuses on the less-studied learning formulations in this context in order to exploit inner structures in the prediction errors. In particular, we propose to directly optimize basic loss functions of the prediction error metrics typically used in the literature, such as the mean absolute error or the worst case error. We show that a proper choice of the loss function can directly improve the prediction performance in the desired metric, albeit at the cost of additional computations during training. To support this claim, we describe the statistical learning theoretic foundations and provide numerical evidence with the prediction of atomization energies for a database of small organic molecule

Forging Links between Human Mental Retardation–Associated CNVs and Mouse Gene Knockout Models

Rare copy number variants (CNVs) are frequently associated with common neurological disorders such as mental retardation (MR; learning disability), autism, and schizophrenia. CNV screening in clinical practice is limited because pathological CNVs cannot be distinguished routinely from benign CNVs, and because genes underlying patients' phenotypes remain largely unknown. Here, we present a novel, statistically robust approach that forges links between 148 MR–associated CNVs and phenotypes from ∼5,000 mouse gene knockout experiments. These CNVs were found to be significantly enriched in two classes of genes, those whose mouse orthologues, when disrupted, result in either abnormal axon or dopaminergic neuron morphologies. Additional enrichments highlighted correspondences between relevant mouse phenotypes and secondary presentations such as brain abnormality, cleft palate, and seizures. The strength of these phenotype enrichments (>100% increases) greatly exceeded molecular annotations (<30% increases) and allowed the identification of 78 genes that may contribute to MR and associated phenotypes. This study is the first to demonstrate how the power of mouse knockout data can be systematically exploited to better understand genetically heterogeneous neurological disorders

An investigation on climate responsive design strategies of vernacular housing in Vietnam

peer reviewedaudience: researcher, professional, studentEnergy conservation issues and environmental problems in recent years have increased interest in traditional architecture which is well known for its energy saving designs. This paper thoroughly investigates vernacular housing designs and evaluates on the aspect of building physics. A new research methodology which is adapted to the natural and social context of Vietnam was proposed and applied. The process was carried out step by step, including: climate zoning, systematic analysis, in-situ survey and building simulations. The results of this study indicate that vernacular housing in Vietnam is creatively adapted to the local natural conditions and uses various climate responsive strategies. Through this study, the most frequently used strategies and their effectiveness were derived. The authors also found that under extreme weather conditions, traditional designs might not be sufficient to maintain indoor thermal comfort

Development and validation of a new MRI simulation technique that can reliably estimate optimal in vivo scanning parameters in a glioblastoma murine model

BACKGROUND: Magnetic Resonance Imaging (MRI) relies on optimal scanning parameters to achieve maximal signal-to-noise ratio (SNR) and high contrast-to-noise ratio (CNR) between tissues resulting in high quality images. The optimization of such parameters is often laborious, time consuming, and user-dependent, making harmonization of imaging parameters a difficult task. In this report, we aim to develop and validate a computer simulation technique that can reliably provide optimal in vivo scanning parameters ready to be used for in vivo evaluation of disease models. METHODS: A glioblastoma murine model was investigated using several MRI imaging methods. Such MRI methods underwent a simulated and an in vivo scanning parameter optimization in pre- and post-contrast conditions that involved the investigation of tumor, brain parenchyma and cerebrospinal fluid (CSF) CNR values in addition to the time relaxation values of the related tissues. The CNR tissues information were analyzed and the derived scanning parameters compared in order to validate the simulated methodology as a reliable technique for optimal in vivo scanning parameters estimation. RESULTS: The CNRs and the related scanning parameters were better correlated when spin-echo-based sequences were used rather than the gradient-echo-based sequences due to augmented inhomogeneity artifacts affecting the latter methods. Optimal in vivo scanning parameters were generated successfully by the simulations after initial scanning parameter adjustments that conformed to some of the parameters derived from the in vivo experiment. CONCLUSION: Scanning parameter optimization using the computer simulation was shown to be a valid surrogate to the in vivo approach in a glioblastoma murine model yielding in a better delineation and differentiation of the tumor from the contralateral hemisphere. In addition to drastically reducing the time invested in choosing optimal scanning parameters when compared to an in vivo approach, this simulation program could also be used to harmonize MRI acquisition parameters across scanners from different vendors

Oil pollution in the Vietnamese waters

Enumeration of hydrocarbon-degrading microorganisms (HDM) and their degradative capacity studies were carried out in area IV of South China Sea (Vietnamese water). Microbial most probable number (MPN) varied from 101 to 105 cell/ ml of surface seawater or gram of sediment. Some microbial communities and bacterial strains isolated from 97 collected samples show high hydrocarbon degradation and surfactant producing abilities. Preliminary results of our microbial study indicated that oil pollution in IV area was not found in 30 research stations. Slight oil contamination was observed in 28 survey stations

Oil pollution in the Vietnamese waters

Enumeration of hydrocarbon-degrading microorganisms (HDM) and their degradative capacity studies were carried out in area IV of South China Sea (Vietnamese water). Microbial most probable number (MPN) varied from 101 to 105 cell/ ml of surface seawater or gram of sediment. Some microbial communities and bacterial strains isolated from 97 collected samples show high hydrocarbon degradation and surfactant producing abilities. Preliminary results of our microbial study indicated that oil pollution in IV area was not found in 30 research stations. Slight oil contamination was observed in 28 survey stations

Prevalence of Antibodies against Avian Influenza A (H5N1) Virus among Cullers and Poultry Workers in Ho Chi Minh City, 2005

Background: Between 2003 and 2005, highly pathogenic avian influenza A (H5N1) viruses caused large scale outbreaks in poultry in the Ho Chi Minh City area in Vietnam. We studied the prevalence of antibodies against H5N1 in poultry workers and cullers who were active in the program in Ho Chi Minh City in 2004 and 2005. Methodology/Principal Findings: Single sera from 500 poultry workers and poultry cullers exposed to infected birds were tested for antibodies to avian influenza H5N1, using microneutralization assays and hemagglutination inhibition assay with horse blood. All sera tested negative using microneutralization tests. Three samples showed a 1:80 titer in the hemagglutination inhibition assay. Conclusions/Significance: This study provides additional support for the low transmissibility of clade 1 H5N1 to humans, but limited transmission to highly exposed persons cannot be excluded given the presence of low antibody titers in some individuals. © 2009 Schultsz et al.published_or_final_versio

Exploring the feasibility of introducing triple artemisinin-based combination therapy in the malaria treatment policy in Vietnam

BACKGROUND: This study investigates the processes regarding changing malaria treatment policies in Vietnam. Moreover, it explores the feasibility of introducing triple artemisinin-based combination therapy (TACT) in Vietnam to support the national malaria control and elimination plan. METHODS: Data were collected via 12 in-depth interviews with key stakeholders, combined with a review of policy documents. RESULTS: TACT is considered as a useful backup strategy in case future treatment failures with current artemisinin-based combination therapy (ACT) would occur. Moreover, TACT is also considered as a promising strategy to prevent the re-establishment of malaria. However, regulatory procedures and implementation timelines for TACT were expected to be lengthy. Therefore, strategies to engage national decision-makers, regulators, and suppliers should be initiated soon, stipulating the benefits of TACT deployment. In Vietnam, a procedure to apply for an import permit without registration that has previously been applied to the introduction of artesunate-pyronaridine was proposed to accelerate the introduction of TACT. Global-level support through the World Health Organization recommendations and prequalification were considered critical for supporting the introduction of TACT in Vietnam. CONCLUSIONS: Appropriate approach strategies and early stakeholder engagement will be needed to accelerate the introduction of TACT in Vietnam