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Article ; Online: Tessellating the Latent Space for Non-Adversarial Generative Auto-Encoders.

Gai, Kuo / Zhang, Shihua

IEEE transactions on pattern analysis and machine intelligence

2024 Volume 46, Issue 2, Page(s) 780–792

Abstract: Non-adversarial generative models are relatively easy to train and have less mode collapse than adversarial models. However, they are not very accurate in approximating the target distribution in latent space because they don't have a discriminator. To ... ...

Abstract	Non-adversarial generative models are relatively easy to train and have less mode collapse than adversarial models. However, they are not very accurate in approximating the target distribution in latent space because they don't have a discriminator. To this end, we develop a novel divide-and-conquer model called Tessellated Wasserstein Auto-Encoders (TWAE) which has less statistical error in approximating the target distribution. TWAE tessellates the support of the target distribution into a given number of regions using the centroidal Voronoi tessellation (CVT) technique and designs data batches according to the tessellation instead of random shuffling for accurate computation of discrepancy. Theoretically, we demonstrate that the error in estimating the discrepancy decreases as the number of samples n and the regions m of the tessellation increase at rates of [Formula: see text] and [Formula: see text], respectively. TWAE is very flexible to different non-adversarial metrics and can significantly enhance their generative performance in terms of Fréchet inception distance (FID) compared to existing ones. Furthermore, numerical results demonstrate that TWAE is competitive to the adversarial model and shows powerful generative ability.
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ISSN	1939-3539
ISSN (online)	1939-3539
DOI	10.1109/TPAMI.2023.3325282
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Article ; Online: High-density generation of spatial transcriptomics with STAGE.

Li, Shang / Gai, Kuo / Dong, Kangning / Zhang, Yiyang / Zhang, Shihua

Nucleic acids research

2024

Abstract: Spatial transcriptome technologies have enabled the measurement of gene expression while maintaining spatial location information for deciphering the spatial heterogeneity of biological tissues. However, they were heavily limited by the sparse spatial ... ...

Abstract	Spatial transcriptome technologies have enabled the measurement of gene expression while maintaining spatial location information for deciphering the spatial heterogeneity of biological tissues. However, they were heavily limited by the sparse spatial resolution and low data quality. To this end, we develop a spatial location-supervised auto-encoder generator STAGE for generating high-density spatial transcriptomics (ST). STAGE takes advantage of the customized supervised auto-encoder to learn continuous patterns of gene expression in space and generate high-resolution expressions for given spatial coordinates. STAGE can improve the low quality of spatial transcriptome data and smooth the generated manifold of gene expression through the de-noising function on the latent codes of the auto-encoder. Applications to four ST datasets, STAGE has shown better recovery performance for down-sampled data than existing methods, revealed significant tissue structure specificity, and enabled robust identification of spatially informative genes and patterns. In addition, STAGE can be extended to three-dimensional (3D) stacked ST data for generating gene expression at any position between consecutive sections for shaping high-density 3D ST configuration.
Language	English
Publishing date	2024-04-22
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkae294
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Article ; Online: Robust and self-lubricating polyvinyl alcohol tubes with a mucosa-like hierarchical architecture for endotracheal intubation.

Zhang, Tongrui / Gai, Kuo / Li, Ruyi / Liang, Yi / Li, Li / Chen, Junyu / Nie, Min

Journal of materials chemistry. B

2024 Volume 12, Issue 5, Page(s) 1330–1343

Abstract: Mechanical mismatch between interventional intubation tubes and human tissues often triggers inevitable friction and causes secondary injury to patients during interventional therapy. Herein, we propose a fabrication strategy of a self-lubricating ... ...

Abstract	Mechanical mismatch between interventional intubation tubes and human tissues often triggers inevitable friction and causes secondary injury to patients during interventional therapy. Herein, we propose a fabrication strategy of a self-lubricating polyvinyl alcohol (PVA) tube by industrial extrusion technology followed by simple infiltration with water. First, biocompatible glycerin was introduced to weaken the intrinsic hydrogen interaction of PVA by new molecular complexation, broadening the gap between the melting and decomposition temperatures and enabling the stable extrusion of the PVA tube. Subsequently, the as-prepared PVA tube was infiltrated with an aqueous solution to construct a strong hydrogen bonding network between PVA and water molecules, forming a soft hydration layer similar to the upper epithelium layer of mucosa. Benefiting from the solid and liquid properties of the hydration layer as well as the small proportion relative to the whole, the infiltrated PVA tube exhibited excellent hydration lubrication behavior and robust mechanical property. The friction coefficient, tensile strength and elongation at break were measured to be 0.05, 26.2 MPa and 654%, respectively, surpassing the values of 0.5, 16.4 MPa and 240% observed in a commercial polyvinyl chloride tube.
MeSH term(s)	Animals ; Humans ; Rabbits ; Polyvinyl Alcohol ; Tensile Strength ; Intubation, Intratracheal ; Mucous Membrane ; Water
Chemical Substances	Polyvinyl Alcohol (9002-89-5) ; Water (059QF0KO0R)
Language	English
Publishing date	2024-01-31
Publishing country	England
Document type	Journal Article
ZDB-ID	2702241-9
ISSN	2050-7518 ; 2050-750X
ISSN (online)	2050-7518
ISSN	2050-750X
DOI	10.1039/d3tb02402d
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Article ; Online: Generating bioactive and antiseptic interfaces with nano-silver hydroxyapatite-based coatings by pulsed electrochemical deposition for long-term efficient cervical soft tissue sealing.

Chen, Jie / Gai, Kuo / He, Yuanyuan / Xu, Yuchan / Guo, Weihua

Journal of materials chemistry. B

2023 Volume 11, Issue 2, Page(s) 345–358

Abstract: Infections related to osseointegrated implants have sparked the interest in studying titanium modification for long-term effective soft tissue sealing. Constructing a silver (Ag)-hydroxyapatite (HA) coating is regarded as an effective strategy for ... ...

Abstract	Infections related to osseointegrated implants have sparked the interest in studying titanium modification for long-term effective soft tissue sealing. Constructing a silver (Ag)-hydroxyapatite (HA) coating is regarded as an effective strategy for integrating antibiosis with osteanagenesis; however, the outcome for long-term cervical soft tissue sealing
MeSH term(s)	Dogs ; Animals ; Durapatite/pharmacology ; Durapatite/chemistry ; Osteogenesis ; Coated Materials, Biocompatible/pharmacology ; Coated Materials, Biocompatible/chemistry ; Anti-Infective Agents, Local/pharmacology ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/chemistry
Chemical Substances	Durapatite (91D9GV0Z28) ; Coated Materials, Biocompatible ; Anti-Infective Agents, Local ; Anti-Bacterial Agents ; colloidal silver
Language	English
Publishing date	2023-01-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2702241-9
ISSN	2050-7518 ; 2050-750X
ISSN (online)	2050-7518
ISSN	2050-750X
DOI	10.1039/d2tb02098j
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Book ; Online: A Mathematical Principle of Deep Learning

Gai, Kuo / Zhang, Shihua

Learn the Geodesic Curve in the Wasserstein Space

2021

Abstract: Recent studies revealed the mathematical connection of deep neural network (DNN) and dynamic system. However, the fundamental principle of DNN has not been fully characterized with dynamic system in terms of optimization and generalization. To this end, ... ...

Abstract	Recent studies revealed the mathematical connection of deep neural network (DNN) and dynamic system. However, the fundamental principle of DNN has not been fully characterized with dynamic system in terms of optimization and generalization. To this end, we build the connection of DNN and continuity equation where the measure is conserved to model the forward propagation process of DNN which has not been addressed before. DNN learns the transformation of the input distribution to the output one. However, in the measure space, there are infinite curves connecting two distributions. Which one can lead to good optimization and generaliztion for DNN? By diving the optimal transport theory, we find DNN with weight decay attempts to learn the geodesic curve in the Wasserstein space, which is induced by the optimal transport map. Compared with plain network, ResNet is a better approximation to the geodesic curve, which explains why ResNet can be optimized and generalize better. Numerical experiments show that the data tracks of both plain network and ResNet tend to be line-shape in term of line-shape score (LSS), and the map learned by ResNet is closer to the optimal transport map in term of optimal transport score (OTS). In a word, we conclude a mathematical principle of deep learning is to learn the geodesic curve in the Wasserstein space; and deep learning is a great engineering realization of continuous transformation in high-dimensional space. Comment: 40 pages, 16 figures
Keywords	Computer Science - Machine Learning ; Statistics - Machine Learning
Subject code	006
Publishing date	2021-02-18
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Tessellated Wasserstein Auto-Encoders

Gai, Kuo / Zhang, Shihua

2020

Abstract: Non-adversarial generative models such as variational auto-encoder (VAE), Wasserstein auto-encoders with maximum mean discrepancy (WAE-MMD), sliced-Wasserstein auto-encoder (SWAE) are relatively easy to train and have less mode collapse compared to ... ...

Abstract	Non-adversarial generative models such as variational auto-encoder (VAE), Wasserstein auto-encoders with maximum mean discrepancy (WAE-MMD), sliced-Wasserstein auto-encoder (SWAE) are relatively easy to train and have less mode collapse compared to Wasserstein auto-encoder with generative adversarial network (WAE-GAN). However, they are not very accurate in approximating the target distribution in the latent space because they don't have a discriminator to detect the minor difference between real and fake. To this end, we develop a novel non-adversarial framework called Tessellated Wasserstein Auto-encoders (TWAE) to tessellate the support of the target distribution into a given number of regions by the centroidal Voronoi tessellation (CVT) technique and design batches of data according to the tessellation instead of random shuffling for accurate computation of discrepancy. Theoretically, we demonstrate that the error of estimate to the discrepancy decreases when the numbers of samples $n$ and regions $m$ of the tessellation become larger with rates of $\mathcal{O}(\frac{1}{\sqrt{n}})$ and $\mathcal{O}(\frac{1}{\sqrt{m}})$, respectively. Given fixed $n$ and $m$, a necessary condition for the upper bound of measurement error to be minimized is that the tessellation is the one determined by CVT. TWAE is very flexible to different non-adversarial metrics and can substantially enhance their generative performance in terms of Fr\'{e}chet inception distance (FID) compared to VAE, WAE-MMD, SWAE. Moreover, numerical results indeed demonstrate that TWAE is competitive to the adversarial model WAE-GAN, demonstrating its powerful generative ability. Comment: 38 pages, 8 figures
Keywords	Statistics - Machine Learning ; Computer Science - Machine Learning ; Mathematics - Optimization and Control ; 90-08 ; 68T01 ; I.2.6 ; I.5.1 ; I.4.0
Publishing date	2020-05-20
Publishing country	us
Document type	Book ; Online
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Article: Comparison of Failure and Complication Risks of Porcelain Laminate and Indirect Resin Veneer Restorations: A Meta-Analysis.

Liu, Mengqi / Gai, Kuo / Chen, Junyu / Jiang, Li

The International journal of prosthodontics

2019 Volume 32, Issue 1, Page(s) 59–65

Abstract: Purpose: To evaluate and compare the failure and complication risks of porcelain laminate and indirect resin veneer restorations (VRs) by means of a meta-analysis.: Methods: An electronic database search was performed in MEDLINE (PubMed), EMBASE ( ... ...

Abstract	Purpose: To evaluate and compare the failure and complication risks of porcelain laminate and indirect resin veneer restorations (VRs) by means of a meta-analysis. Methods: An electronic database search was performed in MEDLINE (PubMed), EMBASE (Ovid), and the Cochrane Central Register of Controlled Trials (CENTRAL) databases, and a gray literature search was performed on OpenGrey. All database searches were completed by March 2018. Two authors individually screened the literature according to the inclusion and exclusion criteria. The quality and risk of bias of the included studies were evaluated using the Newcastle-Ottawa scale (NOS) and the Cochrane Handbook for Systematic Reviews of Interventions (CHSRI). The Mantel-Haenszel method was used to synthesize the data of the included studies. All statistical analyses were performed using the software Stata 14.0, and the results were expressed as risk ratio (RR) with 95% confidence interval (CI). Results: Five studies-two randomized controlled trials (RCTs) and three clinical controlled trials (CCTs)-were included in this review. Of the three CCTs, two were assessed to be low quality, and the third was considered high quality. The two RCTs were rated as unclear risk of bias. The meta-analysis results showed the risk of failure for indirect resin VRs was higher than for porcelain laminate VRs (RR: 0.15, 95% CI: 0.06-0.40; P = .000). Fracture and debonding were the main complications leading to failure. For risk of fracture, an RR of 0.18 (95% CI: 0.04-0.71) and a statistically significant difference (P = .015) were found in favor of porcelain laminate VRs. For risk of debonding, there was no statistically significant difference (P = .108) found between the two types of VRs. The results of the sensitivity analysis (RR: 0.09, 95% CI: 0.02-0.45; P = .004) suggested that this conclusion was reliable. Conclusion: The survival rate of porcelain laminate VRs was higher than indirect resin VRs, and the latter had a higher risk of fracture. However, there was no statistically significant difference in the risk of debonding between the two types of VRs. Porcelain laminate VRs have a better prognosis compared to indirect resin VRs, which provides an evidence-based reference for the selection of VRs in clinical practice.
MeSH term(s)	Dental Porcelain ; Dental Restoration Failure ; Dental Restoration Repair ; Resins, Synthetic
Chemical Substances	Resins, Synthetic ; Dental Porcelain (12001-21-7)
Language	English
Publishing date	2019-01-24
Publishing country	United States
Document type	Journal Article ; Meta-Analysis ; Review
ZDB-ID	645046-5
ISSN	1942-4426 ; 0893-2174
ISSN (online)	1942-4426
ISSN	0893-2174
DOI	10.11607/ijp.6099
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Zs.A 2430: Show issues

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Article ; Online: Synthesis of obeticholic acid, a farnesoid X receptor agonist, and its major metabolites labeled with deuterium.

Gai, Kuo / Huang, Yu / Liu, Baomin / Zhang, Yinsheng

Journal of labelled compounds & radiopharmaceuticals

2018

Abstract: Simple and facile methods for the synthesis of deuterium-labeled obeticholic acid and its 2 metabolites, glycine and taurine conjugates of obeticholic acid, are described herein. The 3 deuterated compounds were applicable for use as internal standards in ...

Abstract	Simple and facile methods for the synthesis of deuterium-labeled obeticholic acid and its 2 metabolites, glycine and taurine conjugates of obeticholic acid, are described herein. The 3 deuterated compounds were applicable for use as internal standards in drug development.
Language	English
Publishing date	2018-05-29
Publishing country	England
Document type	Journal Article
ZDB-ID	196095-7
ISSN	1099-1344 ; 0362-4803 ; 0022-2135
ISSN (online)	1099-1344
ISSN	0362-4803 ; 0022-2135
DOI	10.1002/jlcr.3643
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Article ; Online: Identification of unexpected unlabeled N,N-dimethylamide formation in the synthesis of deuterated fragment of ribociclib by a HATU-mediated coupling reaction.

Gai, Kuo / Liu, Baomin / Zhang, Yinsheng

Journal of labelled compounds & radiopharmaceuticals

2018 Volume 62, Issue 2, Page(s) 62–66

Abstract: Starting from N,N-dimethylamine and ... ...

Abstract	Starting from N,N-dimethylamine and D
MeSH term(s)	Aminopyridines/chemical synthesis ; Deuterium/chemistry ; Mass Spectrometry/standards ; Purines/chemical synthesis ; Pyridinium Compounds/chemistry ; Triazoles/chemistry
Chemical Substances	Aminopyridines ; Purines ; Pyridinium Compounds ; Triazoles ; Deuterium (AR09D82C7G) ; ribociclib (TK8ERE8P56)
Language	English
Publishing date	2018-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	196095-7
ISSN	1099-1344 ; 0362-4803 ; 0022-2135
ISSN (online)	1099-1344
ISSN	0362-4803 ; 0022-2135
DOI	10.1002/jlcr.3690
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Article ; Online: Biomimetic Peridontium Patches for Functional Periodontal Regeneration.

Ma, Yue / Yang, Xueting / Chen, Yan / Zhang, Jiumeng / Gai, Kuo / Chen, Jinlong / Huo, Fangjun / Guo, Qiang / Guo, Weihua / Gou, Maling / Yang, Bo / Tian, Weidong

Advanced healthcare materials

2023 Volume 12, Issue 7, Page(s) e2202169

Abstract: The unique structure of the periodontium, including the alveolar bone, cementum, and periodontal ligament (PDL), presents difficulties for the regeneration of its intricate organization. Irreversible structural breakdown of the periodontium increases the ...

Abstract	The unique structure of the periodontium, including the alveolar bone, cementum, and periodontal ligament (PDL), presents difficulties for the regeneration of its intricate organization. Irreversible structural breakdown of the periodontium increases the risk of tooth loosening and loss. Although the current therapies can restore the periodontal hard tissues to a certain extent, the PDL with its high directionality of multiple groups with different orientations and functions cannot be reconstructed. Here, biomimetic peridontium patches (BPPs) for functional periodontal regeneration using a microscale continuous digital light projection bioprinting method is reported. Orthotopic transplantation in the mandibles shows effective periodontal reconstruction. The resulting bioengineered tissues closely resembles natural periodontium in terms of the "sandwich structures," especially the correctly oriented fibers, showing different and specific orientation in different regions of the tooth root, which has never been found in previous studies. Furthermore, after the assessment of clinically functional properties it is found that the regenerative periodontium can achieve stable tooth movement under orthodontic migration force with no adverse consequences. Overall, the BPPs promote reconstruction of the functional periodontium and the complex microstructure of the periodontal tissue, providing a proof of principle for the clinical functional treatment of periodontal defects.
MeSH term(s)	Biomimetics ; Periodontal Ligament ; Periodontium ; Tooth Root
Language	English
Publishing date	2023-01-18
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649576-4
ISSN	2192-2659 ; 2192-2640
ISSN (online)	2192-2659
ISSN	2192-2640
DOI	10.1002/adhm.202202169
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