arXiv subjects

Jiahui Chen

Publications and source records attributed to Jiahui Chen.

At least 73 records · Page 4Linked to original sources

arXiv2023

Persistent topological Laplacian analysis of SARS-CoV-2 variants

Topological data analysis (TDA) is an emerging field in mathematics and data science. Its central technique, persistent homology, has had tremendous success in many science and engineering disciplines. However, persistent homology has limitations, including its incapability of describing the homotopic shape evolution of data during filtration. Persistent topological Laplacians (PTLs), such as persistent Laplacian and persistent sheaf Laplacian, were proposed to overcome the drawback of persistent homology. In this work, we examine the modeling and analysis power of PTLs in the study of the protein structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike receptor binding domain (RBD) and its variants, i.e., Alpha, Beta, Gamma, BA.1, and BA.2. First, we employ PTLs to study how the RBD mutation-induced structural changes of RBD-angiotensin-converting enzyme 2 (ACE2) binding complexes are captured in the changes of spectra of the PTLs among SARS-CoV-2 variants. Additionally, we use PTLs to analyze the binding of RBD and ACE2-induced structural changes of various SARS-CoV-2 variants. Finally, we explore the impacts of computationally generated RBD structures on PTL-based machine learning, including deep learning, and predictions of deep mutational scanning datasets for the SARS-CoV-2 Omicron BA.2 variant. Our results indicate that PTLs have advantages over persistent homology in analyzing protein structural changes and provide a powerful new TDA tool for data science.

q-bio.QM↗

arXiv2023

Web3: The Next Internet Revolution

Since the first appearance of the World Wide Web, people more rely on the Web for their cyber social activities. The second phase of World Wide Web, named Web 2.0, has been extensively attracting worldwide people that participate in building and enjoying the virtual world. Nowadays, the next internet revolution: Web3 is going to open new opportunities for traditional social models. The decentralization property of Web3 is capable of breaking the monopoly of the internet companies. Moreover, Web3 will lead a paradigm shift from the Web as a publishing medium to a medium of interaction and participation. This change will deeply transform the relations among users and platforms, forces and relations of production, and the global economy. Therefore, it is necessary that we technically, practically, and more broadly take an overview of Web3. In this paper, we present a comprehensive survey of Web3, with a focus on current technologies, challenges, opportunities, and outlook. This article first introduces several major technologies of Web3. Then, we illustrate the type of Web3 applications in detail. Blockchain and smart contracts ensure that decentralized organizations will be less trusted and more truthful than that centralized organizations. Decentralized finance will be global, and open with financial inclusiveness for unbanked people. This paper also discusses the relationship between the Metaverse and Web3, as well as the differences and similarities between Web 3.0 and Web3. Inspired by the Maslow's hierarchy of needs theory, we further conduct a novel hierarchy of needs theory within Web3. Finally, several worthwhile future research directions of Web3 are discussed.

cs.CY↗

arXiv2022

Metaverse in Education: Vision, Opportunities, and Challenges

Traditional education has been updated with the development of information technology in human history. Within big data and cyber-physical systems, the Metaverse has generated strong interest in various applications (e.g., entertainment, business, and cultural travel) over the last decade. As a novel social work idea, the Metaverse consists of many kinds of technologies, e.g., big data, interaction, artificial intelligence, game design, Internet computing, Internet of Things, and blockchain. It is foreseeable that the usage of Metaverse will contribute to educational development. However, the architectures of the Metaverse in education are not yet mature enough. There are many questions we should address for the Metaverse in education. To this end, this paper aims to provide a systematic literature review of Metaverse in education. This paper is a comprehensive survey of the Metaverse in education, with a focus on current technologies, challenges, opportunities, and future directions. First, we present a brief overview of the Metaverse in education, as well as the motivation behind its integration. Then, we survey some important characteristics for the Metaverse in education, including the personal teaching environment and the personal learning environment. Next, we envisage what variations of this combination will bring to education in the future and discuss their strengths and weaknesses. We also review the state-of-the-art case studies (including technical companies and educational institutions) for Metaverse in education. Finally, we point out several challenges and issues in this promising area.

cs.CY↗

arXiv2022

D$^3$ETR: Decoder Distillation for Detection Transformer

While various knowledge distillation (KD) methods in CNN-based detectors show their effectiveness in improving small students, the baselines and recipes for DETR-based detectors are yet to be built. In this paper, we focus on the transformer decoder of DETR-based detectors and explore KD methods for them. The outputs of the transformer decoder lie in random order, which gives no direct correspondence between the predictions of the teacher and the student, thus posing a challenge for knowledge distillation. To this end, we propose MixMatcher to align the decoder outputs of DETR-based teachers and students, which mixes two teacher-student matching strategies, i.e., Adaptive Matching and Fixed Matching. Specifically, Adaptive Matching applies bipartite matching to adaptively match the outputs of the teacher and the student in each decoder layer, while Fixed Matching fixes the correspondence between the outputs of the teacher and the student with the same object queries, with the teacher's fixed object queries fed to the decoder of the student as an auxiliary group. Based on MixMatcher, we build \textbf{D}ecoder \textbf{D}istillation for \textbf{DE}tection \textbf{TR}ansformer (D$^3$ETR), which distills knowledge in decoder predictions and attention maps from the teachers to students. D$^3$ETR shows superior performance on various DETR-based detectors with different backbones. For example, D$^3$ETR improves Conditional DETR-R50-C5 by $\textbf{7.8}/\textbf{2.4}$ mAP under $12/50$ epochs training settings with Conditional DETR-R101-C5 as the teacher.

cs.CV↗

arXiv2022

CAE v2: Context Autoencoder with CLIP Target

Masked image modeling (MIM) learns visual representation by masking and reconstructing image patches. Applying the reconstruction supervision on the CLIP representation has been proven effective for MIM. However, it is still under-explored how CLIP supervision in MIM influences performance. To investigate strategies for refining the CLIP-targeted MIM, we study two critical elements in MIM, i.e., the supervision position and the mask ratio, and reveal two interesting perspectives, relying on our developed simple pipeline, context autodecoder with CLIP target (CAE v2). Firstly, we observe that the supervision on visible patches achieves remarkable performance, even better than that on masked patches, where the latter is the standard format in the existing MIM methods. Secondly, the optimal mask ratio positively correlates to the model size. That is to say, the smaller the model, the lower the mask ratio needs to be. Driven by these two discoveries, our simple and concise approach CAE v2 achieves superior performance on a series of downstream tasks. For example, a vanilla ViT-Large model achieves 81.7% and 86.7% top-1 accuracy on linear probing and fine-tuning on ImageNet-1K, and 55.9% mIoU on semantic segmentation on ADE20K with the pre-training for 300 epochs. We hope our findings can be helpful guidelines for the pre-training in the MIM area, especially for the small-scale models.

cs.CV↗

arXiv2022

Group DETR v2: Strong Object Detector with Encoder-Decoder Pretraining

We present a strong object detector with encoder-decoder pretraining and finetuning. Our method, called Group DETR v2, is built upon a vision transformer encoder ViT-Huge~\cite{dosovitskiy2020image}, a DETR variant DINO~\cite{zhang2022dino}, and an efficient DETR training method Group DETR~\cite{chen2022group}. The training process consists of self-supervised pretraining and finetuning a ViT-Huge encoder on ImageNet-1K, pretraining the detector on Object365, and finally finetuning it on COCO. Group DETR v2 achieves $\textbf{64.5}$ mAP on COCO test-dev, and establishes a new SoTA on the COCO leaderboard https://paperswithcode.com/sota/object-detection-on-coco

cs.CV↗

arXiv2022

Emerging dominant SARS-CoV-2 variants

Accurate and reliable forecasting of emerging dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants enables policymakers and vaccine makers to get prepared for future waves of infections. The last three waves of SARS-CoV-2 infections caused by dominant variants Omicron (BA.1), BA.2, and BA.4/BA.5 were accurately foretold by our artificial intelligence (AI) models built with biophysics, genotyping of viral genomes, experimental data, algebraic topology, and deep learning. Based on newly available experimental data, we analyzed the impacts of all possible viral spike (S) protein receptor-binding domain (RBD) mutations on the SARS-CoV-2 infectivity. Our analysis sheds light on viral evolutionary mechanisms, i.e., natural selection through infectivity strengthening and antibody resistance. We forecast that BA.2.10.4, BA.2.75, BQ.1.1, and particularly, BA.2.75+R346T, have high potential to become new dominant variants to drive the next surge.

q-bio.PE↗

arXiv2022

A Generic Algorithm for Top-K On-Shelf Utility Mining

On-shelf utility mining (OSUM) is an emerging research direction in data mining. It aims to discover itemsets that have high relative utility in their selling time period. Compared with traditional utility mining, OSUM can find more practical and meaningful patterns in real-life applications. However, there is a major drawback to traditional OSUM. For normal users, it is hard to define a minimum threshold minutil for mining the right amount of on-shelf high utility itemsets. On one hand, if the threshold is set too high, the number of patterns would not be enough. On the other hand, if the threshold is set too low, too many patterns will be discovered and cause an unnecessary waste of time and memory consumption. To address this issue, the user usually directly specifies a parameter k, where only the top-k high relative utility itemsets would be considered. Therefore, in this paper, we propose a generic algorithm named TOIT for mining Top-k On-shelf hIgh-utility paTterns to solve this problem. TOIT applies a novel strategy to raise the minutil based on the on-shelf datasets. Besides, two novel upper-bound strategies named subtree utility and local utility are applied to prune the search space. By adopting the strategies mentioned above, the TOIT algorithm can narrow the search space as early as possible, improve the mining efficiency, and reduce the memory consumption, so it can obtain better performance than other algorithms. A series of experiments have been conducted on real datasets with different styles to compare the effects with the state-of-the-art KOSHU algorithm. The experimental results showed that TOIT outperforms KOSHU in both running time and memory consumption.

cs.DB↗

arXiv2022

Temporal Fuzzy Utility Maximization with Remaining Measure

High utility itemset mining approaches discover hidden patterns from large amounts of temporal data. However, an inescapable problem of high utility itemset mining is that its discovered results hide the quantities of patterns, which causes poor interpretability. The results only reflect the shopping trends of customers, which cannot help decision makers quantify collected information. In linguistic terms, computers use mathematical or programming languages that are precisely formalized, but the language used by humans is always ambiguous. In this paper, we propose a novel one-phase temporal fuzzy utility itemset mining approach called TFUM. It revises temporal fuzzy-lists to maintain less but major information about potential high temporal fuzzy utility itemsets in memory, and then discovers a complete set of real interesting patterns in a short time. In particular, the remaining measure is the first adopted in the temporal fuzzy utility itemset mining domain in this paper. The remaining maximal temporal fuzzy utility is a tighter and stronger upper bound than that of previous studies adopted. Hence, it plays an important role in pruning the search space in TFUM. Finally, we also evaluate the efficiency and effectiveness of TFUM on various datasets. Extensive experimental results indicate that TFUM outperforms the state-of-the-art algorithms in terms of runtime cost, memory usage, and scalability. In addition, experiments prove that the remaining measure can significantly prune unnecessary candidates during mining.

cs.DB↗

arXiv2022

Itemset Utility Maximization with Correlation Measure

As an important data mining technology, high utility itemset mining (HUIM) is used to find out interesting but hidden information (e.g., profit and risk). HUIM has been widely applied in many application scenarios, such as market analysis, medical detection, and web click stream analysis. However, most previous HUIM approaches often ignore the relationship between items in an itemset. Therefore, many irrelevant combinations (e.g., \{gold, apple\} and \{notebook, book\}) are discovered in HUIM. To address this limitation, many algorithms have been proposed to mine correlated high utility itemsets (CoHUIs). In this paper, we propose a novel algorithm called the Itemset Utility Maximization with Correlation Measure (CoIUM), which considers both a strong correlation and the profitable values of the items. Besides, the novel algorithm adopts a database projection mechanism to reduce the cost of database scanning. Moreover, two upper bounds and four pruning strategies are utilized to effectively prune the search space. And a concise array-based structure named utility-bin is used to calculate and store the adopted upper bounds in linear time and space. Finally, extensive experimental results on dense and sparse datasets demonstrate that CoIUM significantly outperforms the state-of-the-art algorithms in terms of runtime and memory consumption.

cs.AI↗

arXiv2022

In situ X-ray area detector gain correction at an operating photon energy

Gain calibration of x-ray area detectors is a challenge due to the inability to generate an x-ray flat field at the selected photon energy that the beamline operates at, which has a strong influence on the detector's gain behavior. A method is presented in which a gain map is calculated without flat field measurements. Rather, a series of quick scattering measurements from an amorphous scatterer is used to calculate a gain map. The ability to rapidly obtain a gain map allows for a recalibration of an x-ray detector as needed without significant expenditure of either time or effort. Area detectors on the beamlines used, such as the Pilatus 2M CdTe or Varex XRD 4343CT, were found to have gains which drift slightly over timescales of several weeks or after exposure to high photon flux, suggesting the need to more frequently recalibrate for detector gain.

physics.ins-det↗

arXiv2022

Optimal and robust experiment design for quantum state tomography of star-topology register

While quantum state tomography plays a vital role in the verification and benchmarking of quantum systems, it is an intractable task if the controllability and measurement of quantum registers are constrained. In this paper, we study the quantum state tomography of star-topology registers, in which the individual addressability of peripheral spins is infeasible. Based on the star-symmetry, we decompose the Hilbert space to alleviate the complexity of tomography and design a compact strategy with minimum number of measurements. By optimizing the parameterized quantum circuit for information transfer, the robustness against measurement errors is also improved. Furthermore, we apply this method to a 10-spin star-topology register and demonstrate its ability to characterize large-scale systems. Our results can help future investigations of quantum systems with constrained ability of quantum control and measurement.

quant-ph↗

arXiv2022

Smart System: Joint Utility and Frequency for Pattern Classification

Nowadays, the environments of smart systems for Industry 4.0 and Internet of Things (IoT) are experiencing fast industrial upgrading. Big data technologies such as design making, event detection, and classification are developed to help manufacturing organizations to achieve smart systems. By applying data analysis, the potential values of rich data can be maximized and thus help manufacturing organizations to finish another round of upgrading. In this paper, we propose two new algorithms with respect to big data analysis, namely UFC$_{gen}$ and UFC$_{fast}$. Both algorithms are designed to collect three types of patterns to help people determine the market positions for different product combinations. We compare these algorithms on various types of datasets, both real and synthetic. The experimental results show that both algorithms can successfully achieve pattern classification by utilizing three different types of interesting patterns from all candidate patterns based on user-specified thresholds of utility and frequency. Furthermore, the list-based UFC$_{fast}$ algorithm outperforms the level-wise-based UFC$_{gen}$ algorithm in terms of both execution time and memory consumption.

cs.AI↗

arXiv2022

Persistent Laplacian projected Omicron BA.4 and BA.5 to become new dominating variants

Due to its high transmissibility, Omicron BA.1 ousted the Delta variant to become a dominating variant in late 2021 and was replaced by more transmissible Omicron BA.2 in March 2022. An important question is which new variants will dominate in the future. Topology-based deep learning models have had tremendous success in forecasting emerging variants in the past. However, topology is insensitive to homotopic shape variations in virus-human protein-protein binding, which are crucial to viral evolution and transmission. This challenge is tackled with persistent Laplacian, which is able to capture both the topology and shape of data. Persistent Laplacian-based deep learning models are developed to systematically evaluate variant infectivity. Our comparative analysis of Alpha, Beta, Gamma, Delta, Lambda, Mu, and Omicron BA.1, BA.1.1, BA.2, BA.2.11, BA.2.12.1, BA.3, BA.4, and BA.5 unveils that Omicron BA.2.11, BA.2.12.1, BA.3, BA.4, and BA.5 are more contagious than BA.2. In particular, BA.4 and BA.5 are about 36\% more infectious than BA.2 and are projected to become new dominating variants by natural selection. Moreover, the proposed models outperform the state-of-the-art methods on three major benchmark datasets for mutation-induced protein-protein binding free energy changes.

q-bio.BM↗

arXiv2022

Mathematical artificial intelligence design of mutation-proof COVID-19 monoclonal antibodies

Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have compromised existing vaccines and posed a grand challenge to coronavirus disease 2019 (COVID-19) prevention, control, and global economic recovery. For COVID-19 patients, one of the most effective COVID-19 medications is monoclonal antibody (mAb) therapies. The United States Food and Drug Administration (U.S. FDA) has given the emergency use authorization (EUA) to a few mAbs, including those from Regeneron, Eli Elly, etc. However, they are also undermined by SARS-CoV-2 mutations. It is imperative to develop effective mutation-proof mAbs for treating COVID-19 patients infected by all emerging variants and/or the original SARS-CoV-2. We carry out a deep mutational scanning to present the blueprint of such mAbs using algebraic topology and artificial intelligence (AI). To reduce the risk of clinical trial-related failure, we select five mAbs either with FDA EUA or in clinical trials as our starting point. We demonstrate that topological AI-designed mAbs are effective to variants of concerns and variants of interest designated by the World Health Organization (WHO), as well as the original SARS-CoV-2. Our topological AI methodologies have been validated by tens of thousands of deep mutational data and their predictions have been confirmed by results from tens of experimental laboratories and population-level statistics of genome isolates from hundreds of thousands of patients.

q-bio.BM↗

arXiv2022

Omicron BA.2 (B.1.1.529.2): high potential to becoming the next dominating variant

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly replaced the Delta variant as a dominating SARS-CoV-2 variant because of natural selection, which favors the variant with higher infectivity and stronger vaccine breakthrough ability. Omicron has three lineages or subvariants, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3). Among them, BA.1 is the currently prevailing subvariant. BA.2 shares 32 mutations with BA.1 but has 28 distinct ones. BA.3 shares most of its mutations with BA.1 and BA.2 except for one. BA.2 is found to be able to alarmingly reinfect patients originally infected by Omicron BA.1. An important question is whether BA.2 or BA.3 will become a new dominating "variant of concern". Currently, no experimental data has been reported about BA.2 and BA.3. We construct a novel algebraic topology-based deep learning model trained with tens of thousands of mutational and deep mutational data to systematically evaluate BA.2's and BA.3's infectivity, vaccine breakthrough capability, and antibody resistance. Our comparative analysis of all main variants namely, Alpha, Beta, Gamma, Delta, Lambda, Mu, BA.1, BA.2, and BA.3, unveils that BA.2 is about 1.5 and 4.2 times as contagious as BA.1 and Delta, respectively. It is also 30% and 17-fold more capable than BA.1 and Delta, respectively, to escape current vaccines. Therefore, we project that Omicron BA.2 is on its path to becoming the next dominating variant. We forecast that like Omicron BA.1, BA.2 will also seriously compromise most existing mAbs, except for sotrovimab developed by GlaxoSmithKline.

q-bio.PE↗

arXiv2021

Omicron (B.1.1.529): Infectivity, vaccine breakthrough, and antibody resistance

The latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has ushered panic responses around the world due to its contagious and vaccine escape mutations. The essential infectivity and antibody resistance of the SARS-CoV-2 variant are determined by its mutations on the spike (S) protein receptor-binding domain (RBD). However, a complete experimental evaluation of Omicron might take weeks or even months. Here, we present a comprehensive quantitative analysis of Omicron's infectivity, vaccine-breakthrough, and antibody resistance. An artificial intelligence (AI) model, which has been trained with tens of thousands of experimental data points and extensively validated by experimental data on SARS-CoV-2, reveals that Omicron may be over ten times more contagious than the original virus or about twice as infectious as the Delta variant. Based on 132 three-dimensional (3D) structures of antibody-RBD complexes, we unveil that Omicron may be twice more likely to escape current vaccines than the Delta variant. The Food and Drug Administration (FDA)-approved monoclonal antibodies (mAbs) from Eli Lilly may be seriously compromised. Omicron may also diminish the efficacy of mAbs from Celltrion and Rockefeller University. However, its impact on Regeneron mAb cocktail appears to be mild.

q-bio.QM↗

arXiv2021

Anomaly Rule Detection in Sequence Data

Analyzing sequence data usually leads to the discovery of interesting patterns and then anomaly detection. In recent years, numerous frameworks and methods have been proposed to discover interesting patterns in sequence data as well as detect anomalous behavior. However, existing algorithms mainly focus on frequency-driven analytic, and they are challenging to be applied in real-world settings. In this work, we present a new anomaly detection framework called DUOS that enables Discovery of Utility-aware Outlier Sequential rules from a set of sequences. In this pattern-based anomaly detection algorithm, we incorporate both the anomalousness and utility of a group, and then introduce the concept of utility-aware outlier sequential rule (UOSR). We show that this is a more meaningful way for detecting anomalies. Besides, we propose some efficient pruning strategies w.r.t. upper bounds for mining UOSR, as well as the outlier detection. An extensive experimental study conducted on several real-world datasets shows that the proposed DUOS algorithm has a better effectiveness and efficiency. Finally, DUOS outperforms the baseline algorithm and has a suitable scalability.

cs.DB↗