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Molecular Generation and Optimization of Molecular Properties Using a Transformer Model

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Big Data Mining and Analytics 2024年第1期7卷 142-155页

作者： Zhongyin Xu xiujuan Lei Mei ma Yi Pan school of Computer Science Shaanxi Normal UniversityXi'an 710119China Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China

Generating novel molecules to satisfy specific properties is a challenging task in modern drug discovery,which requires the optimization of a specific objective based on satisfying chemical ***,we aim to optimize the properties of a specific molecule to satisfy the specific properties of the generated *** matched Molecular Pairs(MMPs),which contain the source and target molecules,are used herein,and logD and solubility are selected as the optimization *** main innovative work lies in the calculation related to a specific transformer from the perspective of a matrix *** intervals and state changes are then used to encode logD and solubility for subsequent *** the experiments,we screen the data based on the proportion of heavy atoms to all atoms in the groups and select 12365,1503,and 1570 MMPs as the training,validation,and test sets,*** models are compared with the baseline models with respect to their abilities to generate molecules with specific *** show that the transformer model can accurately optimize the source molecules to satisfy specific properties.

关键词： molecular optimization transformer matched Molecular Pairs(MMPs) logD solubility

Quantitative estimation of global mean precipitation throughout the Phanerozoic era

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Science china Earth sciences 2024年第5期67卷 1616-1624页

作者： xiujuan BAO Yongyun HU Laboratory for Climate and Ocean-Atmospheric Studies Department of Atmospheric and Oceanic SciencesSchool of PhysicsPeking UniversityBeijing 100871China

Quantitatively estimating the global mean precipitation(GMP)throughout Earth's history is crucial for enhancing our understanding of long-term climate evolution and the hydrological ***,currently there is no established methodology for estimating global mean ***,we present the first study that estimates GMP in the Phanerozoic *** relationship between GMP and global mean surface temperature(GMST)is investigated by analyzing data from 23 models in the Coupled Model Intercomparison Project phase 6(CMIP6).The result reveals consistent and significant impact of temperature on precipitation,with a sensitivity range of 2–3%K^(-1).Additionally,we propose a method for accessing latitudinal variations in precipitation caused by land area distributions and paleo-Koppen climatic *** climatic belts are determined based on geological indicators such as coals,evaporites,and glacial *** GMP is thus quantitatively estimated by combining variations in GMST,land area distributions,and paleo-koppen climatic belts,spanning from 540 ma to the present *** quantitative GMP curve demonstrates fluctuations in GMP about 500 mm yr^(-1),with values ranging from 948 to1442 mm yr-1over the Phanerozoic *** curve aligns closely with findings derived from numerical *** presented paleoprecipitation variations facilitate a more comprehensive understanding of the interconnected geological and paleoclimatic developments.

关键词： Paleoprecipitation Paleoclimate K?ppen climatic belts Global mean precipitation Hydrological cycle

An Encoding-Decoding Framework Based on CNN for circ RNA-RBP Binding Sites Prediction

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Chinese Journal of Electronics 2024年第1期33卷 256-263页

作者： Yajing GUO xiujuan LEI Yi PAN school of Computer Science Shaanxi Normal University Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences Department of Computer Science Georgia State University

Predicting RNA binding protein(RBP) binding sites on circular RNAs(circ RNAs) is a fundamental step to understand their interaction mechanism. Numerous computational methods are developed to solve this problem, but they cannot fully learn the features. Therefore, we propose circ-CNNED, a convolutional neural network(CNN)-based encoding and decoding framework. We first adopt two encoding methods to obtain two original matrices. We preprocess them using CNN before fusion. To capture the feature dependencies, we utilize temporal convolutional network(TCN) and CNN to construct encoding and decoding blocks, respectively. Then we introduce global expectation pooling to learn latent information and enhance the robustness of circ-CNNED. We perform circ-CNNED across 37 datasets to evaluate its effect. The comparison and ablation experiments demonstrate that our method is superior. In addition, motif enrichment analysis on four datasets helps us to explore the reason for performance improvement of circ-CNNED.

关键词： Proteins RNA Neural networks Encoding Robustness Decoding Convolutional neural networks

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K_0-group and approximate similarity invariants of strongly irreducible operators

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Science china mathematics 2008年第12期51卷 2231-2252页

作者： HE Hua1, SHI Rui1,2 & ma xiujuan1 1 school of Science, hebei university of technology, tianjin 300130, china 2 school of mathematics and Information Science, hebei Normal university, Shijiazhuang 050016, china school of Science Hebei University of Technology Tianjin China school of mathematics and Information Science Hebei Normal University Shijiazhuang China

Let H olenote a complex separable Hilbert space and L(H) denote the collection of bounded linear operators on H. An operator T ∈ L(H) is said to be strongly irreducible if T does not commute with any nontrivial idempotent. Herrero and Jiang showed that the norm-closure of the class of all strongly irreducible operators is the class of all operators with connected spectrum. This result can be considered as an "approximate inverse" of the Riesz decomposition theorem. In the paper, we give a more precise characterization of approximate invariants of strongly irreducible operators. The main result is: For any T ∈ L(H) with connected spectrum and ε > 0, there exists a strongly irreducible operator A, such that A - T < ε, V (A (A)) =～ N, K0(A (A)) ～= Z, and A (A)/rad A (A) is commutative, where A (A) denotes the commutant of A and rad A (A) denotes the Jacobson radical of A (A). The research is inspired by the recent similarity classification technique of Cowen-Douglas operators of Jiang Chunlan.

关键词： strongly irreducible operators Cowen-Douglas operators K0-group similarity orbit

Drug-Target Interactions Prediction Based on Signed Heterogeneous Graph Neural Networks

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Chinese Journal of Electronics 2024年第1期33卷 231-244页

作者： Ming CHEN Yajian JIANG xiujuan LEI Yi PAN Chunyan JI Wei JIANG College of Information Science and Engineering Hunan Normal University school of Computer Science Shaanxi Normal University Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences Computer Science Department BNU-HKBU United International College

Drug-target interactions(DTIs) prediction plays an important role in the process of drug *** computational methods treat it as a binary prediction problem, determining whether there are connections between drugs and targets while ignoring relational types information. Considering the positive or negative effects of DTIs will facilitate the study on comprehensive mechanisms of multiple drugs on a common target, in this work, we model DTIs on signed heterogeneous networks, through categorizing interaction patterns of DTIs and additionally extracting interactions within drug pairs and target protein pairs. We propose signed heterogeneous graph neural networks(SHGNNs), further put forward an end-to-end framework for signed DTIs prediction, called SHGNN-DTI,which not only adapts to signed bipartite networks, but also could naturally incorporate auxiliary information from drug-drug interactions(DDIs) and protein-protein interactions(PPIs). For the framework, we solve the message passing and aggregation problem on signed DTI networks, and consider different training modes on the whole networks consisting of DTIs, DDIs and PPIs. Experiments are conducted on two datasets extracted from Drug Bank and related databases, under different settings of initial inputs, embedding dimensions and training modes. The prediction results show excellent performance in terms of metric indicators, and the feasibility is further verified by the case study with two drugs on breast cancer.

关键词： Drugs Training Proteins Measurement Message passing Prediction methods Graph neural networks

Nd^(3)+:YAG-Al_(2)O_(3) nanocrystalline transparent ceramics with high inflexion concentration quenching of Nd^(3+) prepared by amorphous crystallization

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Journal of Advanced Ceramics 2024年第8期13卷 1242-1253页

作者： xiujuan Wan Guangfan Tan Liang Cai Jie Fu Jianqiang Li Yingchun Zhang school of materials Science and Engineering University of Science and Technology BeijingBeijing 100083China State Key Laboratory of New Ceramics and Fine Processing School of Materials Science and EngineeringTsinghua UniversityBeijing 100080China State Key Lab for Mesoscience and Engineering Institute of Process EngineeringChinese Academy of SciencesBeijing 100190China

Rare earth ion-doped Y_(3)Al_(5)O_(12)(YAG)-based transparent ceramics have been used as important laser gain media for a long time,yet the doping concentration of active ions is limited due to concentration quenching,wherein the inflexion concentration quenching of Nd^(3+)is recognized as 1.0 at%.In this work,YAG-Al_(2)O_(3) nanocrystalline transparent ceramics with a concentration of Nd^(3+)(O-5.0 at%)were fabricated via amorphous crystallization,and the crystal structure evolution,morphology,and optical properties were systematically investigated by differential scanning calorimetry(DSC),X-ray powder diffraction(XRD),transmission electron microscopy(TEM),magnetic resonation(maS),nuclear magnetic resonation(NMR),and fluorescence *** doping of Nd^(3+)can promote the transition of Al[5]and Al[6]to Al[14],indicating improvements in the ability of the amorphous material to form Nd^(3+):Y_(2)O_(3)-Al_(2)O_(3) vitrified beads,and 1.5 at%Nd^(3+):YAG-Al_(2)O_(3) nanocrystalline transparent ceramics can be obtained by crystallization at 1050℃ with a matrix composed of YAG and concomitant δ-Al_(2)O_(3) and θ-Al_(2)O_(3).The nanocrystalline transparent ceramics show an internal transmitance of 89.56%at 1064 nm,and the strongest emission peak corresponds to the energy transfer from 4F_(3/2) to 4l_(11/2) of Nd^(3+)with a fluorescence lifetime of 231μs when pumped by an 808 nm ***,spectral broadening begins to occur,indicating the onset of concentration quenching,when the concentration of Nd^(3+)exceeds 1.5 at%,substantially higher than the 1.0 at% observed in YAG ***-Al_(2)O_(3) nanocrystalline transparent ceramics obtained by amorphous crystalization can be utilized as the matrix to increase the inflexion point of doping concentration quenching of Nd^(3+),and this material may have great potential as a laser gain medium.

关键词： Y_(3)Al_(5)O_(12)(YAG)-Al_(2)O_(3) nanocrystalline transparent ceramics laser gain medium Nd^(3+)

Uniqueness and local stability for the inverse scattering problem of determining the cavity

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Science china mathematics 2005年第8期48卷 1113-1123页

作者： FENG Lixin & ma Fuming LmaM, school of mathematical sciences, Peking university, Beijing 100871, china school of mathematical sciences, Heilongjiang university, Harbin 150080, china school of mathematical sciences, Jilin university, Changchun 130012, china LmaM School of Mathematical Sciences Peking University Beijing China school of mathematical sciences Heilongjiang University Harbin China school of mathematical sciences Jilin University Changchun China

Considering a time-harmonic electromagnetic plane wave incident on an arbitrarily shaped open cavity embedded in infinite ground plane, the physical process is modelled by maxwell's equations. We investigate the inverse problem of determining the shape of the open cavity from the information of the measured scattered field. Results on the uniqueness and the local stability of the inverse problem in the 2-dimensional TM (transverse magnetic) polarization are proved in this paper.

关键词： uniqueness, stability, maxwell's equations, inverse scattering problem.

Achieving Negatively Charged Pt Single Atoms on Amorphous Ni(OH)_(2)Nanosheets with Promoted Hydrogen Absorption in Hydrogen Evolution

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Nano-Micro Letters 2024年第10期16卷 213-224页

作者： Yue Liu Gui Liu Xiangyu Chen Chuang Xue Mingke Sun Yifei Liu Jianxin Kang xiujuan Sun Lin Guo school of Chemistry Beijing Advanced Innovation Center for Biomedical EngineeringKey Laboratory of Bio-inspired Smart Interfacial Science and TechnologyBeihang UniversityBeijing 100191People's Republic of China school of Chemistry Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of EducationXiangtan UniversityXiangtan 411105HunanPeople'Republic of China

Single-atom(SA)catalysts with nearly 100%atom utilization have been widely employed in electrolysis for decades,due to the outperforming catalytic activity and ***,most of the reported SA catalysts are fixed through the strong bonding between the dispersed single metallic atoms with nonmetallic atoms of the substrates,which greatly limits the controllable regulation of electrocatalytic activity of SA *** this work,Pt-Ni bonded Pt SA catalyst with adjustable electronic states was successfully constructed through a controllable electrochemical reduction on the coordination unsaturated amorphous Ni(OH)_(2)nanosheet *** on the X-ray absorption fine structure analysis and first-principles calculations,Pt SA was bonded with Ni sites of amorphous Ni(OH)_(2),rather than conventional O sites,resulting in negatively charged Pt^(δ-).In situ Raman spectroscopy revealed that the changed configuration and electronic states greatly enhanced absorbability for activated hydrogen atoms,which were the essential intermediate for alkaline hydrogen evolution *** hydrogen spillover process was revealed from amorphous Ni(OH)_(2)that effectively cleave the H-O-H bond of H_(2)O and produce H atom to the Pt SA sites,leading to a low overpotential of 48 mV in alkaline electrolyte at-1000 ma cm^(-2)mg^(-1)_(Pt),evidently better than commercial Pt/C *** work provided new strategy for the control-lable modulation of the local structure of SA catalysts and the systematic regulation of the electronic states.

关键词： Hydrogen evolution reaction Amorphous Pt single atoms Hydrogen spillover

Split-plot designs with general minimum lower-order confounding

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Science china mathematics 2010年第4期53卷 939-952页

作者： WEI JiaLin 1,4,YANG JianFeng 1,LI Peng 3 & ZHANG RunChu 1,2,1 school of mathematical sciences and LPMC,Nankai university,tianjin 300071,china 2 KLAS and school of mathematics and Statistics,Northeast Normal university,Changchun 130024,china 3 school of mathematical sciences,Capital Normal university,Beijing 100037,china 4 school of sciences,tianjin university of Commerce,tianjin 300134,china school of mathematical sciences and LPMC Nankai University Tianjin China school of sciences Tianjin University of Commerce Tianjin China school of mathematical sciences Capital Normal University Beijing China KLAS and school of mathematics and Statistics Northeast Normal University Changchun China

Split-plot designs have been widely used in industrial *** to now,most methods for choosing this kind of designs are based on the minimum aberration (ma) ***,by introducing a new pattern,called aliased effect-number pattern (AENP),Zhang et *** a general minimum lowerorder confounding (denoted by GMC for short) criterion and established a general minimum confounding (also denoted by GMC for saving notations) *** is proved that,the GMC criterion selects optimal designs in a more elaborate manner than the existing ones,and when an experimenter has a prior about the importance ordering of factors in experiments the GMC designs are better than other optimal *** this paper we extend the GMC criterion to the split-plot design case and give a GMC-FFSP criterion for ranking split-plot *** comparisons of the new criterion with the ma-MSA-FFSP criterion are given,and the optimal 32-run split-plot designs up to 14 factors under the two criteria are tabulated for comparison and application.

关键词： fractional factorial design GMC criterion minimum aberration split-plot