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Article ; Online: Parameter-insensitive Min Cut Clustering with Flexible Size Constrains.

Nie, Feiping / Xie, Fangyuan / Yu, Weizhong / Li, Xuelong

IEEE transactions on pattern analysis and machine intelligence

2024 Volume PP

Abstract: ... Means (KM) and min cut clustering are typical ones. However, they may produce empty or skewed clustering ... while in min cut clustering, it still needs to be developed. In this paper, we propose a parameter-insensitive ... min cut clustering with flexible size constraints. Specifically, we add lower limitations ...

Abstract	Clustering is a fundamental topic in machine learning and various methods are proposed, in which K-Means (KM) and min cut clustering are typical ones. However, they may produce empty or skewed clustering results, which are not as expected. In KM, the constrained clustering methods have been fully studied while in min cut clustering, it still needs to be developed. In this paper, we propose a parameter-insensitive min cut clustering with flexible size constraints. Specifically, we add lower limitations on the number of samples for each cluster, which can perfectly avoid the trivial solution in min cut clustering. As far as we are concerned, this is the first attempt of directly incorporating size constraints into min cut. However, it is a NP-hard problem and difficult to solve. Thus, the upper limits is also added in but it is still difficult to solve. Therefore, an additional variable that is equivalent to label matrix is introduced in and the augmented Lagrangian multiplier (ALM) is used to decouple the constraints. In the experiments, we find that the our algorithm is less sensitive to lower bound and is practical in image segmentation. A large number of experiments demonstrate the effectiveness of our proposed algorithm.
Language	English
Publishing date	2024-02-20
Publishing country	United States
Document type	Journal Article
ISSN	1939-3539
ISSN (online)	1939-3539
DOI	10.1109/TPAMI.2024.3367912
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Article ; Online: RART-LAMP: One-Step Extraction-Free Method for Genotyping within 40 min.

Zhang, Zhang / Guan, Luhao / Yao, Juan / Li, Lijia / Liu, Chunfang / Guo, Yongcan / Xie, Guoming

Analytical chemistry

2023 Volume 95, Issue 33, Page(s) 12487–12496

Abstract: Loop-mediated isothermal amplification (LAMP) is a commonly used alternative to PCR for point-of-care detection of nucleic acids due to its rapidity, sensitivity, specificity, and simpler instrumentation. While dual-labeled TaqMan probes are widely used ... ...

Abstract	Loop-mediated isothermal amplification (LAMP) is a commonly used alternative to PCR for point-of-care detection of nucleic acids due to its rapidity, sensitivity, specificity, and simpler instrumentation. While dual-labeled TaqMan probes are widely used in PCR for single-nucleotide polymorphism (SNP) genotyping, real-time LAMP primarily relies on turbidimetry or intercalator fluorescence measurements, which can be non-specific and generate false-positive results. In this study, we propose a closed-tube, dual-labeled RNA-modified probes and RNase H II-assisted real-time LAMP (RART-LAMP) method for SNP genotyping. Our findings indicate that (1) fluorescence signals were predominantly derived from probe hydrolysis rather than hybridization, (2) temperature-controlled hybridization between the probe and template ensured the specificity of SNP analysis, and (3) RNase H II hydrolysis between the target containing SNP sites and probes did not exhibit sequence specificity. Our RART-LAMP approach demonstrated excellent performance in genotyping C677T clinical samples, including gDNA extracted from blood, saliva, and swabs. More importantly, saliva and swab samples could be directly analyzed without any pretreatment, indicating promising prospects for nucleic acid analysis at the point of care in resource-limited settings.
MeSH term(s)	Genotype ; Sensitivity and Specificity ; Nucleic Acid Amplification Techniques/methods ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Nucleic Acid Hybridization
Language	English
Publishing date	2023-08-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c02232
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Book ; Online: Data-Driven Min-Max MPC for Linear Systems

Xie, Yifan / Berberich, Julian / Allgower, Frank

2023

Abstract: ... we propose a data-driven min-max model predictive control (MPC) scheme to design state-feedback controllers ... from noisy data for unknown linear time-invariant (LTI) system. The considered min-max problem minimizes ...

Abstract	Designing data-driven controllers in the presence of noise is an important research problem, in particular when guarantees on stability, robustness, and constraint satisfaction are desired. In this paper, we propose a data-driven min-max model predictive control (MPC) scheme to design state-feedback controllers from noisy data for unknown linear time-invariant (LTI) system. The considered min-max problem minimizes the worst-case cost over the set of system matrices consistent with the data. We show that the resulting optimization problem can be reformulated as a semidefinite program (SDP). By solving the SDP, we obtain a state-feedback control law that stabilizes the closed-loop system and guarantees input and state constraint satisfaction. A numerical example demonstrates the validity of our theoretical results.
Keywords	Electrical Engineering and Systems Science - Systems and Control
Publishing date	2023-09-29
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Min-entropy estimation for semiconductor superlattice true random number generators.

Liu, Jing / Xie, Jianguo / Chao, Lu / Wu, Han / Ding, Peng / Chen, Xiaoming / Feng, Huamin

Scientific reports

2022 Volume 12, Issue 1, Page(s) 2948

Abstract: ... generators is closely related to the min-entropy of the raw output because feeding cryptographic applications ... focused on the min-entropy estimation based on the stochastic model for SSL-TRNG, which is a highly ... recommended method for evaluating the security of a specific TRNG structure. A min-entropy estimation method ...

Abstract	Semiconductor superlattice true random number generator (SSL-TRNG) has an outstanding practical property on high-throughput and high-security cryptographic applications. Security in random number generators is closely related to the min-entropy of the raw output because feeding cryptographic applications with insufficient entropy leads to poor security and vulnerability to malicious attacks. However, no research has focused on the min-entropy estimation based on the stochastic model for SSL-TRNG, which is a highly recommended method for evaluating the security of a specific TRNG structure. A min-entropy estimation method is proposed in this paper for the SSL-TRNG by extending the Markov stochastic model derived from the memory effects. By calculating the boundary of the transition matrix, the min-entropy result is the average value of each sample (1 bit) is 0.2487. Moreover, the experimental results show that the estimator is accurate enough to adjust compression rate dynamically in post-processing to reach the required security level, estimating entropy on the fly rather than off-line.
Language	English
Publishing date	2022-02-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-06815-2
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Book ; Online: Faster Min-Plus Product for Monotone Instances

Chi, Shucheng / Duan, Ran / Xie, Tianle / Zhang, Tianyi

2022

Abstract: In this paper, we show that the time complexity of monotone min-plus product of two $n\times n$ ... the min-plus product $C$ where $C_{i,j}=\min_k\{A_{i,k}+B_{k,j}\}$ takes $\tilde{O}(n^{(3+\omega)/2 ... Vassilevska Williams 2016]. Finally, we also consider the problem of min-plus convolution between two integral ...

Abstract	In this paper, we show that the time complexity of monotone min-plus product of two $n\times n$ matrices is $\tilde{O}(n^{(3+\omega)/2})=\tilde{O}(n^{2.687})$, where $\omega < 2.373$ is the fast matrix multiplication exponent [Alman and Vassilevska Williams 2021]. That is, when $A$ is an arbitrary integer matrix and $B$ is either row-monotone or column-monotone with integer elements bounded by $O(n)$, computing the min-plus product $C$ where $C_{i,j}=\min_k\{A_{i,k}+B_{k,j}\}$ takes $\tilde{O}(n^{(3+\omega)/2})$ time, which greatly improves the previous time bound of $\tilde{O}(n^{(12+\omega)/5})=\tilde{O}(n^{2.875})$ [Gu, Polak, Vassilevska Williams and Xu 2021]. Then by simple reductions, this means the following problems also have $\tilde{O}(n^{(3+\omega)/2})$ time algorithms: (1) $A$ and $B$ are both bounded-difference, that is, the difference between any two adjacent entries is a constant. The previous results give time complexities of $\tilde{O}(n^{2.824})$ [Bringmann, Grandoni, Saha and Vassilevska Williams 2016] and $\tilde{O}(n^{2.779})$ [Chi, Duan and Xie 2022]. (2) $A$ is arbitrary and the columns or rows of $B$ are bounded-difference. Previous result gives time complexity of $\tilde{O}(n^{2.922})$ [Bringmann, Grandoni, Saha and Vassilevska Williams 2016]. (3) The problems reducible to these problems, such as language edit distance, RNA-folding, scored parsing problem on BD grammars. [Bringmann, Grandoni, Saha and Vassilevska Williams 2016]. Finally, we also consider the problem of min-plus convolution between two integral sequences which are monotone and bounded by $O(n)$, and achieve a running time upper bound of $\tilde{O}(n^{1.5})$. Previously, this task requires running time $\tilde{O}(n^{(9+\sqrt{177})/12}) = O(n^{1.859})$ [Chan and Lewenstein 2015]. Comment: Add acknowledgment
Keywords	Computer Science - Data Structures and Algorithms ; F.2.2
Subject code	005
Publishing date	2022-04-09
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: [Safety and feasibility of 120 min rapid infusion regimen of daratumumab in patients with multiple myeloma].

Wang, T H / Hao, R / Xu, B N / Chang, L / Liu, Z B / Yao, J L / Wang, W / Xie, W J / Yan, W W / Xiao, Z J / Qiu, L G / An, G

Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi

2023 Volume 44, Issue 8, Page(s) 696–699

MeSH term(s)	Humans ; Multiple Myeloma/drug therapy ; Feasibility Studies ; Antibodies, Monoclonal/adverse effects ; Dexamethasone/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols
Chemical Substances	daratumumab (4Z63YK6E0E) ; Antibodies, Monoclonal ; Dexamethasone (7S5I7G3JQL)
Language	Chinese
Publishing date	2023-09-15
Publishing country	China
Document type	Journal Article
ZDB-ID	2997162-7
ISSN	0253-2727 ; 0253-2727
ISSN (online)	0253-2727
ISSN	0253-2727
DOI	10.3760/cma.j.issn.0253-2727.2023.08.017
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Article ; Online: RART-LAMP: One-Step Extraction-Free Method for Genotyping within 40 min

Zhang, Zhang / Guan, Luhao / Yao, Juan / Li, Lijia / Liu, Chunfang / Guo, Yongcan / Xie, Guoming

Analytical Chemistry. 2023 Aug. 03, v. 95, no. 33 p.12487-12496

2023

Abstract	Loop-mediated isothermal amplification (LAMP) is a commonly used alternative to PCR for point-of-care detection of nucleic acids due to its rapidity, sensitivity, specificity, and simpler instrumentation. While dual-labeled TaqMan probes are widely used in PCR for single-nucleotide polymorphism (SNP) genotyping, real-time LAMP primarily relies on turbidimetry or intercalator fluorescence measurements, which can be non-specific and generate false-positive results. In this study, we propose a closed-tube, dual-labeled RNA-modified probes and RNase H II-assisted real-time LAMP (RART-LAMP) method for SNP genotyping. Our findings indicate that (1) fluorescence signals were predominantly derived from probe hydrolysis rather than hybridization, (2) temperature-controlled hybridization between the probe and template ensured the specificity of SNP analysis, and (3) RNase H II hydrolysis between the target containing SNP sites and probes did not exhibit sequence specificity. Our RART-LAMP approach demonstrated excellent performance in genotyping C677T clinical samples, including gDNA extracted from blood, saliva, and swabs. More importantly, saliva and swab samples could be directly analyzed without any pretreatment, indicating promising prospects for nucleic acid analysis at the point of care in resource-limited settings.
Keywords	analytical chemistry ; blood ; fluorescence ; genotyping ; hybridization ; hydrolysis ; instrumentation ; loop-mediated isothermal amplification ; nucleic acids ; point-of-care systems ; ribonucleases ; saliva ; single nucleotide polymorphism ; turbidimetry
Language	English
Dates of publication	2023-0803
Size	p. 12487-12496.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c02232
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: Faster Algorithms for Bounded-Difference Min-Plus Product

Chi, Shucheng / Duan, Ran / Xie, Tianle

2021

Abstract: Min-plus product of two $n\times n$ matrices is a fundamental problem in algorithm research. It is ... we focus on the min-plus product on a special class of matrices, called $\delta$-bounded-difference ...

Abstract	Min-plus product of two $n\times n$ matrices is a fundamental problem in algorithm research. It is known to be equivalent to APSP, and in general it has no truly subcubic algorithms. In this paper, we focus on the min-plus product on a special class of matrices, called $\delta$-bounded-difference matrices, in which the difference between any two adjacent entries is bounded by $\delta=O(1)$. Our algorithm runs in randomized time $O(n^{2.779})$ by the fast rectangular matrix multiplication algorithm [Le Gall \& Urrutia 18], better than $\tilde{O}(n^{2+\omega/3})=O(n^{2.791})$ ($\omega<2.373$ [Alman \& V.V.Williams 20]). This improves previous result of $\tilde{O}(n^{2.824})$ [Bringmann et al. 16]. When $\omega=2$ in the ideal case, our complexity is $\tilde{O}(n^{2+2/3})$, improving Bringmann et al.'s result of $\tilde{O}(n^{2.755})$. Comment: 13 pages
Keywords	Computer Science - Data Structures and Algorithms ; 68W05 ; F.2.2
Publishing date	2021-10-17
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: A Clinical-Radiomic Model for Predicting Indocyanine Green Retention Rate at 15 Min in Patients With Hepatocellular Carcinoma.

Wu, Ji / Xie, Feng / Ji, Hao / Zhang, Yiyang / Luo, Yi / Xia, Lei / Lu, Tianfei / He, Kang / Sha, Meng / Zheng, Zhigang / Yong, Junekong / Li, Xinming / Zhao, Di / Yang, Yuting / Xia, Qiang / Xue, Feng

Frontiers in surgery

2022 Volume 9, Page(s) 857838

Abstract: Purpose: The indocyanine green retention rate at 15 min (ICG-R15) is of great importance ...

Abstract	Purpose: The indocyanine green retention rate at 15 min (ICG-R15) is of great importance in the accurate assessment of hepatic functional reserve for safe hepatic resection. To assist clinicians to evaluate hepatic functional reserve in medical institutions that lack expensive equipment, we aimed to explore a novel approach to predict ICG-R15 based on CT images and clinical data in patients with hepatocellular carcinoma (HCC). Methods: In this retrospective study, 350 eligible patients were enrolled and randomly assigned to the training cohort (245 patients) and test cohort (105 patients). Radiomics features and clinical factors were analyzed to pick out the key variables, and based on which, we developed the random forest regression, extreme gradient boosting regression (XGBR), and artificial neural network models for predicting ICG-R15, respectively. Pearson's correlation coefficient (R) was adopted to evaluate the performance of the models. Results: We extracted 660 CT image features in total from each patient. Fourteen variables significantly associated with ICG-R15 were picked out for model development. Compared to the other two models, the XGBR achieved the best performance in predicting ICG-R15, with a mean difference of 1.59% (median, 1.53%) and an Conclusion: The proposed approach that incorporates the optimal radiomics features and clinical factors can allow for individualized prediction of ICG-R15 value of patients with HCC, regardless of the specific equipment and detection reagent (NO. ChiCTR2100053042; URL, http://www.chictr.org.cn).
Language	English
Publishing date	2022-03-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2773823-1
ISSN	2296-875X
ISSN	2296-875X
DOI	10.3389/fsurg.2022.857838
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Article ; Online: Min-entropy estimation for semiconductor superlattice true random number generators

Jing Liu / Jianguo Xie / Lu Chao / Han Wu / Peng Ding / Xiaoming Chen / Huamin Feng

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 9

Abstract: ... number generators is closely related to the min-entropy of the raw output because feeding cryptographic ... However, no research has focused on the min-entropy estimation based on the stochastic model for SSL-TRNG ... which is a highly recommended method for evaluating the security of a specific TRNG structure. A min ...

Abstract	Abstract Semiconductor superlattice true random number generator (SSL-TRNG) has an outstanding practical property on high-throughput and high-security cryptographic applications. Security in random number generators is closely related to the min-entropy of the raw output because feeding cryptographic applications with insufficient entropy leads to poor security and vulnerability to malicious attacks. However, no research has focused on the min-entropy estimation based on the stochastic model for SSL-TRNG, which is a highly recommended method for evaluating the security of a specific TRNG structure. A min-entropy estimation method is proposed in this paper for the SSL-TRNG by extending the Markov stochastic model derived from the memory effects. By calculating the boundary of the transition matrix, the min-entropy result is the average value of each sample (1 bit) is 0.2487. Moreover, the experimental results show that the estimator is accurate enough to adjust compression rate dynamically in post-processing to reach the required security level, estimating entropy on the fly rather than off-line.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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