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10 results on '"Chen, Zuxu"'

1. Breaking the Hourglass Phenomenon of Residual Quantization: Enhancing the Upper Bound of Generative Retrieval

Author

Kuai, Zhirui, Chen, Zuxu, Wang, Huimu, Li, Mingming, Miao, Dadong, Wang, Binbin, Chen, Xusong, Kuang, Li, Han, Yuxing, Wang, Jiaxing, Tang, Guoyu, Liu, Lin, Wang, Songlin, and Zhuo, Jingwei

Subjects
Computer Science - Information Retrieval, Computer Science - Artificial Intelligence
Abstract

Generative retrieval (GR) has emerged as a transformative paradigm in search and recommender systems, leveraging numeric-based identifier representations to enhance efficiency and generalization. Notably, methods like TIGER employing Residual Quantization-based Semantic Identifiers (RQ-SID), have shown significant promise in e-commerce scenarios by effectively managing item IDs. However, a critical issue termed the "\textbf{Hourglass}" phenomenon, occurs in RQ-SID, where intermediate codebook tokens become overly concentrated, hindering the full utilization of generative retrieval methods. This paper analyses and addresses this problem by identifying data sparsity and long-tailed distribution as the primary causes. Through comprehensive experiments and detailed ablation studies, we analyze the impact of these factors on codebook utilization and data distribution. Our findings reveal that the "Hourglass" phenomenon substantially impacts the performance of RQ-SID in generative retrieval. We propose effective solutions to mitigate this issue, thereby significantly enhancing the effectiveness of generative retrieval in real-world E-commerce applications.

Published
2024

2. Generative Retrieval with Preference Optimization for E-commerce Search

Author

Li, Mingming, Wang, Huimu, Chen, Zuxu, Nie, Guangtao, Qiu, Yiming, Tang, Guoyu, Liu, Lin, and Zhuo, Jingwei

Subjects
Computer Science - Information Retrieval, Computer Science - Artificial Intelligence
Abstract

Generative retrieval introduces a groundbreaking paradigm to document retrieval by directly generating the identifier of a pertinent document in response to a specific query. This paradigm has demonstrated considerable benefits and potential, particularly in representation and generalization capabilities, within the context of large language models. However, it faces significant challenges in E-commerce search scenarios, including the complexity of generating detailed item titles from brief queries, the presence of noise in item titles with weak language order, issues with long-tail queries, and the interpretability of results. To address these challenges, we have developed an innovative framework for E-commerce search, called generative retrieval with preference optimization. This framework is designed to effectively learn and align an autoregressive model with target data, subsequently generating the final item through constraint-based beam search. By employing multi-span identifiers to represent raw item titles and transforming the task of generating titles from queries into the task of generating multi-span identifiers from queries, we aim to simplify the generation process. The framework further aligns with human preferences using click data and employs a constrained search method to identify key spans for retrieving the final item, thereby enhancing result interpretability. Our extensive experiments show that this framework achieves competitive performance on a real-world dataset, and online A/B tests demonstrate the superiority and effectiveness in improving conversion gains.

Published
2024

8. Distal Histidine Conformational Flexibility in Dehaloperoxidase from Amphitrite Ornata

Author

Chen, Zuxu

Subjects
X-ray crystal structure, distal histidine, Dehaloperoxidase
Abstract

The enzyme dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a heme protein, which has a globin fold, but can function as both a hemoglobin and a peroxidase. As a peroxidase, DHP is capable of converting para-halogenated phenols to the corresponding quinones in the presence of hydrogen peroxide. As a hemoglobin, DHP cycles between the oxy and deoxy states as it reversibly binds oxygen for storage. Herein, we report that the distal histidine shows a large conformational flexibility in the deoxy form. Crystals of deoxy ferrous DHP were obtained by reducing the ferric wild-type DHP in sodium dithionite solution and the structure was determined at 100K to a resolution of 1.22Ã…. The heme iron in the deoxy ferrous DHP is five-coordinate and has an out-of-plane displacement of 0.23 Ã… for the heme iron relative to the oxy form. The distal histidine, H55 is observed in conformations, which are analogous to the open and closed forms of myoglobin. In the closed conformation, H55 is located inside the distal pocket, but does not penetrate as deeply into the distal pocket as in the metaquo ferric or oxy ferrous structures. This observation is consistent with the hypothesis that H55 interacts with heme iron ligands through hydrogen bonding in the closed conformation. There are two open or solvent-exposed conformations, in which H55 is more than 9.5 Ã… away from the heme. The comparison of the deoxy structure with the other structures provides new insight into the correlation between the heme iron ligation and the conformation of distal histidine in the DHP.

Published
2008

9. Distal histidine conformational flexibility in dehaloperoxidase from Amphitrite ornata.

Author

Chen Z, de Serrano V, Betts L, and Franzen S

Subjects
Animals, Crystallization, Crystallography, X-Ray, Heme Oxygenase (Decyclizing) metabolism, Hemoglobins metabolism, Histidine metabolism, Iodobenzenes chemistry, Iodobenzenes metabolism, Peroxidases metabolism, Protein Binding, Protein Conformation, Solvents, Heme Oxygenase (Decyclizing) chemistry, Hemoglobins chemistry, Histidine chemistry, Peroxidases chemistry, Polychaeta enzymology
Abstract

The enzyme dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a heme protein which has a globin fold but can function as both a hemoglobin and a peroxidase. As a peroxidase, DHP is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. As a hemoglobin, DHP cycles between the oxy and deoxy states as it reversibly binds oxygen for storage. Here, it is reported that the distal histidine, His55, exhibits conformational flexibility in the deoxy form and is consequently observed in two solvent-exposed conformations more than 9.5 A away from the heme. These conformations are analogous to the open conformation of sperm whale myoglobin. The heme iron in deoxy ferrous DHP is five-coordinate and has an out-of-plane displacement of 0.25 A from the heme plane. The observation of five-coordinate heme iron with His55 in a remote solvent-exposed conformation is consistent with the hypothesis that His55 interacts with heme iron ligands through hydrogen bonding in the closed conformation. Since His55 is also displaced by the binding of 4-iodophenol in an internal pocket, these results provide new insight into the correlation between heme iron ligation, molecular binding in the distal pocket and the conformation of the distal histidine in DHP.

Published
2009
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10. X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata.

Author

de Serrano V, Chen Z, Davis MF, and Franzen S

Subjects
Animals, Binding Sites, Cysteine chemistry, Escherichia coli metabolism, Hydrogen Bonding, Models, Chemical, Models, Molecular, Molecular Conformation, Protein Conformation, Serine chemistry, Crystallography, X-Ray methods, Heme chemistry, Hemoglobins chemistry, Peroxidases chemistry, Polychaeta metabolism, Recombinant Proteins chemistry
Abstract

The dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is an enzyme that converts para-halogenated phenols to the corresponding quinones in the presence of hydrogen peroxide. Its enzymatic activity is similar to that of heme peroxidases such as horseradish peroxidase, yet it has the structural characteristics of the globin family of proteins, the main functions of which are oxygen transport and storage. In order to investigate the dual function of this hemoglobin peroxidase, the enzyme was expressed in Escherichia coli as a recombinant protein in its wild-type form and as a mutant protein in which Cys73 was replaced by a serine residue (C73S). Both the wild-type and mutant proteins were crystallized and their structures were determined at 100 K to a resolution of 1.62 A. The structure of the wild-type protein demonstrated that it was in the metaquo form, with the heme iron in the ferric oxidation state and the bound water lying 2.2 A from the heme iron. The structure of the C73S mutant protein was shown to contain a ferrous heme iron with a bound oxygen molecule. The bent bonding geometry of the Fe-O(1)-O(2) adduct results in a hydrogen bond of length 2.8 A between the second O atom, O(2), of molecular oxygen and N(2) of the distal histidine residue (His55) in both subunits contained within the asymmetric unit. This hydrogen-bonding interaction between His55 and the bound diatomic oxygen molecule provides new insight into the catalytic activation of H(2)O(2), which is essential for peroxidase activity.

Published
2007
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