arXiv subjects

Jiahui Chen

Publications and source records attributed to Jiahui Chen.

At least 91 records · Page 5Linked to original sources

arXiv2021

FUIM: Fuzzy Utility Itemset Mining

Because of usefulness and comprehensibility, fuzzy data mining has been extensively studied and is an emerging topic in recent years. Compared with utility-driven itemset mining technologies, fuzzy utility mining not only takes utilities (e.g., profits) into account, but also considers quantities of items in each transaction for discovering high fuzzy utility itemsets (HFUIs). Thus, fuzziness can be regard as a key criterion to select high-utility itemsets, while the exiting algorithms are not efficient enough. In this paper, an efficient one-phase algorithm named Fuzzy-driven Utility Itemset Miner (FUIM) is proposed to find out a complete set of HFUIs effectively. In addition, a novel compact data structure named fuzzy-list keeps the key information from quantitative transaction databases. Using fuzzy-list, FUIM can discover HFUIs from transaction databases efficiently and effectively. Both completeness and correctness of the FUIM algorithm are proved by five theorems. At last, substantial experiments test three terms (runtime cost, memory consumption, and scalability) to confirm that FUIM considerably outperforms the state-of-the-art algorithms.

cs.DB↗

arXiv2021

TargetUM: Targeted High-Utility Itemset Querying

Traditional high-utility itemset mining (HUIM) aims to determine all high-utility itemsets (HUIs) that satisfy the minimum utility threshold (\textit{minUtil}) in transaction databases. However, in most applications, not all HUIs are interesting because only specific parts are required. Thus, targeted mining based on user preferences is more important than traditional mining tasks. This paper is the first to propose a target-based HUIM problem and to provide a clear formulation of the targeted utility mining task in a quantitative transaction database. A tree-based algorithm known as Target-based high-Utility iteMset querying using (TargetUM) is proposed. The algorithm uses a lexicographic querying tree and three effective pruning strategies to improve the mining efficiency. We implemented experimental validation on several real and synthetic databases, and the results demonstrate that the performance of \textbf{TargetUM} is satisfactory, complete, and correct. Finally, owing to the lexicographic querying tree, the database no longer needs to be scanned repeatedly for multiple queries.

cs.DB↗

arXiv2021

A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver

The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in developing a Galerkin boundary integral method for solving the Poisson-Boltzmann (PB) equation. The solver has combined advantages in accuracy, efficiency, and memory usage as it applies a well-posed boundary integral formulation to circumvent many numerical difficulties associated with the PB equation and uses an O(N) Cartesian Fast Multipole Method (FMM) to accelerate the GMRES iteration. In addition, special numerical treatments such as adaptive FMM order, block diagonal preconditioners, Galerkin discretization, and Duffy's transformation are combined to improve the performance of the solver, which is validated on benchmark Kirkwood's sphere and a series of testing proteins.

physics.comp-ph↗

arXiv2021

The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America

The importance of understanding SARS-CoV-2 evolution cannot be overemphasized. Recent studies confirm that natural selection is the dominating mechanism of SARS-CoV-2 evolution, which favors mutations that strengthen viral infectivity. We demonstrate that vaccine-breakthrough or antibody-resistant mutations provide a new mechanism of viral evolution. Specifically, vaccine-resistant mutation Y449S in the spike (S) protein receptor-bonding domain (RBD), which occurred in co-mutation [Y449S, N501Y], has reduced infectivity compared to the original SARS-CoV-2 but can disrupt existing antibodies that neutralize the virus. By tracing the evolutionary trajectories of vaccine-resistant mutations in over 1.9 million SARS-CoV-2 genomes, we reveal that the occurrence and frequency of vaccine-resistant mutations correlate strongly with the vaccination rates in Europe and America. We anticipate that as a complementary transmission pathway, vaccine-resistant mutations will become a dominating mechanism of SARS-CoV-2 evolution when most of the world's population is vaccinated. Our study sheds light on SARS-CoV-2 evolution and transmission and enables the design of the next-generation mutation-proof vaccines and antibody drugs.

q-bio.PE↗

arXiv2021

Graph-Enhanced Multi-Task Learning of Multi-Level Transition Dynamics for Session-based Recommendation

Session-based recommendation plays a central role in a wide spectrum of online applications, ranging from e-commerce to online advertising services. However, the majority of existing session-based recommendation techniques (e.g., attention-based recurrent network or graph neural network) are not well-designed for capturing the complex transition dynamics exhibited with temporally-ordered and multi-level inter-dependent relation structures. These methods largely overlook the relation hierarchy of item transitional patterns. In this paper, we propose a multi-task learning framework with Multi-level Transition Dynamics (MTD), which enables the jointly learning of intra- and inter-session item transition dynamics in automatic and hierarchical manner. Towards this end, we first develop a position-aware attention mechanism to learn item transitional regularities within individual session. Then, a graph-structured hierarchical relation encoder is proposed to explicitly capture the cross-session item transitions in the form of high-order connectivities by performing embedding propagation with the global graph context. The learning process of intra- and inter-session transition dynamics are integrated, to preserve the underlying low- and high-level item relationships in a common latent space. Extensive experiments on three real-world datasets demonstrate the superiority of MTD as compared to state-of-the-art baselines.

cs.IR↗

arXiv2021

MLIMC: Machine learning-based implicit-solvent Monte Carlo

Monte Carlo (MC) methods are important computational tools for molecular structure optimizations and predictions. When solvent effects are explicitly considered, MC methods become very expensive due to the large degree of freedom associated with the water molecules and mobile ions. Alternatively implicit-solvent MC can largely reduce the computational cost by applying a mean field approximation to solvent effects and meanwhile maintains the atomic detail of the target molecule. The two most popular implicit-solvent models are the Poisson-Boltzmann (PB) model and the Generalized Born (GB) model in a way such that the GB model is an approximation to the PB model but is much faster in simulation time. In this work, we develop a machine learning-based implicit-solvent Monte Carlo (MLIMC) method by combining the advantages of both implicit solvent models in accuracy and efficiency. Specifically, the MLIMC method uses a fast and accurate PB-based machine learning (PBML) scheme to compute the electrostatic solvation free energy at each step. We validate our MLIMC method by using a benzene-water system and a protein-water system. We show that the proposed MLIMC method has great advantages in speed and accuracy for molecular structure optimization and prediction.

q-bio.BM↗

arXiv2021

Review of the mechanisms of SARS-CoV-2 evolution and transmission

The mechanism of SARS-CoV-2 evolution and transmission is elusive and its understanding, a prerequisite to forecast emerging variants, is of paramount importance. SARS-CoV-2 evolution is driven by the mechanisms at molecular and organism scales and regulated by the transmission pathways at the population scale. In this review, we show that infectivity-based natural selection was discovered as the mechanism for SARS-CoV-2 evolution and transmission in July 2020. In April 2021, we proved beyond all doubt that such a natural selection via infectivity-based transmission pathway remained the sole mechanism for SARS-CoV-2 evolution. However, we reveal that antibody-disruptive co-mutations [Y449S, N501Y] debuted as a new vaccine-resistant transmission pathway of viral evolution in highly vaccinated populations a few months ago. Over one year ago, we foresaw that mutations spike protein RBD residues, 452 and 501, would "have high chances to mutate into significantly more infectious COVID-19 strains". Mutations on these residues underpin prevailing SARS-CoV-2 variants Alpha, Beta, Gamma, Delta, Epsilon, Theta, Kappa, Lambda, and Mu at present and are expected to be vital to emerging variants. We anticipate that viral evolution will combine RBD co-mutations at these two sites, creating future variants that are tens of times more infectious than the original SARS-CoV-2. Additionally, two complementary transmission pathways of viral evolution: infectivity and vaccine-resistant, will prolong our battle with COVID-19 for years. We predict that RBD co-mutation [A411S, L452R, T478K], [L452R, T478K, N501Y], [L452R, T478K, E484K, N501Y], [K417N, L452R, T478K], and [P384L, K417N, E484K, N501Y] will have high chances to grow into dominating variants due to their high infectivity and/or strong ability to break through current vaccines, calling for the development of new vaccines and antibody therapies.

q-bio.PE↗

arXiv2021

Emerging vaccine-breakthrough SARS-CoV-2 variants

The recent global surge in COVID-19 infections has been fueled by new SARS-CoV-2 variants, namely Alpha, Beta, Gamma, Delta, etc. The molecular mechanism underlying such surge is elusive due to 4,653 non-degenerate mutations on the spike protein, which is the target of most COVID-19 vaccines. The understanding of the molecular mechanism of transmission and evolution is a prerequisite to foresee the trend of emerging vaccine-breakthrough variants and the design of mutation-proof vaccines and monoclonal antibodies. We integrate the genotyping of 1,489,884 SARS-CoV-2 genomes isolates, 130 human antibodies, tens of thousands of mutational data points, topological data analysis, and deep learning to reveal SARS-CoV-2 evolution mechanism and forecast emerging vaccine-escape variants. We show that infectivity-strengthening and antibody-disruptive co-mutations on the S protein RBD can quantitatively explain the infectivity and virulence of all prevailing variants. We demonstrate that Lambda is as infectious as Delta but is more vaccine-resistant. We analyze emerging vaccine-breakthrough co-mutations in 20 countries, including the United Kingdom, the United States, Denmark, Brazil, and Germany, etc. We envision that natural selection through infectivity will continue to be the main mechanism for viral evolution among unvaccinated populations, while antibody disruptive co-mutations will fuel the future growth of vaccine-breakthrough variants among fully vaccinated populations. Finally, we have identified the co-mutations that have the great likelihood of becoming dominant: [A411S, L452R, T478K], [L452R, T478K, N501Y], [V401L, L452R, T478K], [K417N, L452R, T478K], [L452R, T478K, E484K, N501Y], and [P384L, K417N, E484K, N501Y]. We predict they, particularly the last four, will break through existing vaccines. We foresee an urgent need to develop new vaccines that target these co-mutations.

q-bio.BM↗

arXiv2021

Practical and Configurable Network Traffic Classification Using Probabilistic Machine Learning

Network traffic classification that is widely applicable and highly accurate is valuable for many network security and management tasks. A flexible and easily configurable classification framework is ideal, as it can be customized for use in a wide variety of networks. In this paper, we propose a highly configurable and flexible machine learning traffic classification method that relies only on statistics of sequences of packets to distinguish known, or approved, traffic from unknown traffic. Our method is based on likelihood estimation, provides a measure of certainty for classification decisions, and can classify traffic at adjustable certainty levels. Our classification method can also be applied in different classification scenarios, each prioritizing a different classification goal. We demonstrate how our classification scheme and all its configurations perform well on real-world traffic from a high performance computing network environment.

cs.LG↗

arXiv2021

Coded Caching for Broadcast Networks with User Cooperation

In this paper, we investigate the transmission delay of cache-aided broadcast networks with user cooperation. Novel coded caching schemes are proposed for both centralized and decentralized caching settings, by efficiently exploiting time and cache resources and creating parallel data delivery at the server and users. We derive a lower bound on the transmission delay and show that the proposed centralized coded caching scheme is \emph{order-optimal} in the sense that it achieves a constant multiplicative gap within the lower bound. Our decentralized coded caching scheme is also order-optimal when each user's cache size is larger than the threshold $N(1-\sqrt[{K-1}]{ {1}/{(K+1)}})$ (approaching 0 as $K\to \infty$), where $K$ is the total number of users and $N$ is the size of file library. Moreover, for both the centralized and decentralized caching settings, our schemes obtain an additional \emph{cooperation gain} offered by user cooperation and an additional \emph{parallel gain} offered by the parallel transmission among the server and users. It is shown that in order to reduce the transmission delay, the number of users parallelly sending signals should be appropriately chosen according to user's cache size, and alway letting more users parallelly send information could cause high transmission delay.

cs.IT↗

arXiv2021

TOPIC: Top-k High-Utility Itemset Discovering

Utility-driven itemset mining is widely applied in many real-world scenarios. However, most algorithms do not work for itemsets with negative utilities. Several efficient algorithms for high-utility itemset (HUI) mining with negative utilities have been proposed. These algorithms can find complete HUIs with or without negative utilities. However, the major problem with these algorithms is how to select an appropriate minimum utility (minUtil) threshold. To address this issue, some efficient algorithms for extracting top-k HUIs have been proposed, where parameter k is the quantity of HUIs to be discovered. However, all of these algorithms can solve only one part of the above problem. In this paper, we present a method for TOP-k high-utility Itemset disCovering (TOPIC) with positive and negative utility values, which utilizes the advantages of the above algorithms. TOPIC adopts transaction merging and database projection techniques to reduce the database scanning cost, and utilizes minUtil threshold raising strategies. It also uses an array-based utility technique, which calculates the utility of itemsets and upper bounds in linear time. We conducted extensive experiments on several real and synthetic datasets, and the results showed that TOPIC outperforms state-of-the-art algorithm in terms of runtime, memory costs, and scalability.

cs.DB↗

arXiv2021

THUE: Discovering Top-K High Utility Episodes

Episode discovery from an event is a popular framework for data mining tasks and has many real-world applications. An episode is a partially ordered set of objects (e.g., item, node), and each object is associated with an event type. This episode can also be considered as a complex event sub-sequence. High-utility episode mining is an interesting utility-driven mining task in the real world. Traditional episode mining algorithms, by setting a threshold, usually return a huge episode that is neither intuitive nor saves time. In general, finding a suitable threshold in a pattern-mining algorithm is a trivial and time-consuming task. In this paper, we propose a novel algorithm, called Top-K High Utility Episode (THUE) mining within the complex event sequence, which redefines the previous mining task by obtaining the K highest episodes. We introduce several threshold-raising strategies and optimize the episode-weighted utilization upper bounds to speed up the mining process and effectively reduce the memory cost. Finally, the experimental results on both real-life and synthetic datasets reveal that the THUE algorithm can offer six to eight orders of magnitude running time performance improvement over the state-of-the-art algorithm and has low memory consumption.

cs.DB↗

arXiv2021

Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, South Africa, and other COVID-19-devastated countries

Recently, the SARS-CoV-2 variants from the United Kingdom (UK), South Africa, and Brazil have received much attention for their increased infectivity, potentially high virulence, and possible threats to existing vaccines and antibody therapies. The question remains if there are other more infectious variants transmitted around the world. We carry out a large-scale study of 252,874 SARS-CoV-2 genome isolates from patients to identify many other rapidly growing mutations on the spike (S) protein receptor-binding domain (RDB). We reveal that 88 out of 95 significant mutations that were observed more than 10 times strengthen the binding between the RBD and the host angiotensin-converting enzyme 2 (ACE2), indicating the virus evolves toward more infectious variants. In particular, we discover new fast-growing RBD mutations N439K, L452R, S477N, S477R, and N501T that also enhance the RBD and ACE2 binding. We further unveil that mutation N501Y involved in United Kingdom (UK), South Africa, and Brazil variants may moderately weaken the binding between the RBD and many known antibodies, while mutations E484K and K417N found in South Africa and Brazilian variants can potentially disrupt the binding between the RDB and many known antibodies. Among three newly identified fast-growing RBD mutations, L452R, which is now known as part of the California variant B.1.427, and N501T are able to effectively weaken the binding of many known antibodies with the RBD. Finally, we hypothesize that RBD mutations that can simultaneously make SARS-CoV-2 more infectious and disrupt the existing antibodies, called vaccine escape mutations, will pose an imminent threat to the current crop of vaccines. A list of most likely vaccine escape mutations is given, including N501Y, L452R, E484K, N501T, S494P, and K417N.

q-bio.PE↗

arXiv2021

Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies

Antibody therapeutics and vaccines are among our last resort to end the raging COVID-19 pandemic. They, however, are prone to over 5,000 mutations on the spike (S) protein uncovered by a Mutation Tracker based on over 200,000 genome isolates. It is imperative to understand how mutations would impact vaccines and antibodies in the development. In this work, we study the mechanism, frequency, and ratio of mutations on the S protein. Additionally, we use 56 antibody structures and analyze their 2D and 3D characteristics. Moreover, we predict the mutation-induced binding free energy (BFE) changes for the complexes of S protein and antibodies or ACE2. By integrating genetics, biophysics, deep learning, and algebraic topology, we reveal that most of 462 mutations on the receptor-binding domain (RBD) will weaken the binding of S protein and antibodies and disrupt the efficacy and reliability of antibody therapies and vaccines. A list of 31 vaccine escape mutants is identified, while many other disruptive mutations are detailed as well. We also unveil that about 65\% existing RBD mutations, including those variants recently found in the United Kingdom (UK) and South Africa, are binding-strengthen mutations, resulting in more infectious COVID-19 variants. We discover the disparity between the extreme values of RBD mutation-induced BFE strengthening and weakening of the bindings with antibodies and ACE2, suggesting that SARS-CoV-2 is at an advanced stage of evolution for human infection, while the human immune system is able to produce optimized antibodies. This discovery implies the vulnerability of current vaccines and antibody drugs to new mutations. Our predictions were validated by comparison with more than 1,400 deep mutations on the S protein RBD. Our results show the urgent need to develop new mutation-resistant vaccines and antibodies and to prepare for seasonal vaccinations.

q-bio.BM↗

arXiv2021

Methodology-centered review of molecular modeling, simulation, and prediction of SARS-CoV-2

The deadly coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gone out of control globally. Despite much effort by scientists, medical experts, and society in general, the slow progress on drug discovery and antibody therapeutic development, the unknown possible side effects of the existing vaccines, and the high transmission rate of the SARS-CoV-2, remind us of the sad reality that our current understanding of the transmission, infectivity, and evolution of SARS-CoV-2 is unfortunately very limited. The major limitation is the lack of mechanistic understanding of viral-host cell interactions, the viral regulation, protein-protein interactions, including antibody-antigen binding, protein-drug binding, host immune response, etc. This limitation will likely haunt the scientific community for a long time and have a devastating consequence in combating COVID-19 and other pathogens. Notably, compared to the long-cycle, highly cost, and safety-demanding molecular-level experiments, the theoretical and computational studies are economical, speedy, and easy to perform. There exists a tsunami of the literature on molecular modeling, simulation, and prediction of SARS-CoV-2 that has become impossible to fully be covered in a review. To provide the reader a quick update about the status of molecular modeling, simulation, and prediction of SARS-CoV-2, we present a comprehensive and systematic methodology-centered narrative in the nick of time. Aspects such as molecular modeling, Monte Carlo (MC) methods, structural bioinformatics, machine learning, deep learning, and mathematical approaches are included in this review. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are assessing the current status in the field.

q-bio.BM↗

arXiv2020

On the Construction of a Post-Quantum Blockchain for Smart City

Owing to some special characteristics and features, blockchain is a very useful technique that can securely organize diverse devices in a smart city. It finds wide applications, especially in distributed environments, where entities such as wireless sensors need to be certain of the authenticity of the server. As contemporary blockchain techniques that address post-quantum concerns have not been designed, in this study, we investigate a blockchain in the post-quantum setting and seek to discover how it can resist attacks from quantum computing. In addition, traditional proof of work (PoW)-based consensus protocols such as Bitcoin cannot supply memory mining, and the transaction capacity of each block in a blockchain is limited and needs to be expanded. Thus, a new post-quantum proof of work (post-quantum PoW) consensus algorithm for security and privacy of smart city applications is proposed. It can be used to not only protect a blockchain under a quantum computing attack compared to existing classical hash-based PoW algorithms but also to supply memory mining. Meanwhile, an identity-based post-quantum signature is embedded into a transaction process to construct lightweight transactions. Subsequently, we provide a detailed description on the execution of the post-quantum lightweight transaction in a blockchain. Overall, this work can help enrich the research on future post-quantum blockchain and support the construction or architecture of emerging blockchain-based smart cities.

cs.CR↗

arXiv2020

HERMES: Persistent spectral graph software

Persistent homology (PH) is one of the most popular tools in topological data analysis (TDA), while graph theory has had a significant impact on data science. Our earlier work introduced the persistent spectral graph (PSG) theory as a unified multiscale paradigm to encompass TDA and geometric analysis. In PSG theory, families of persistent Laplacians (PLs) corresponding to various topological dimensions are constructed via a filtration to sample a given dataset at multiple scales. The harmonic spectra from the null spaces of PLs offer the same topological invariants, namely persistent Betti numbers, at various dimensions as those provided by PH, while the non-harmonic spectra of PLs give rise to additional geometric analysis of the shape of the data. In this work, we develop an open-source software package, called highly efficient robust multidimensional evolutionary spectra (HERMES), to enable broad applications of PSGs in science, engineering, and technology. To ensure the reliability and robustness of HERMES, we have validated the software with simple geometric shapes and complex datasets from three-dimensional (3D) protein structures. We found that the smallest non-zero eigenvalues are very sensitive to data abnormality.

math.AT↗

arXiv2020

Reduce Transmission Delay for Cache-Aided Two-Layer Network

In this paper, we consider a cache-aided relay network, where a single server consisting of a library of N files connects with K1 relays through a shared noiseless link, and each relay connects with K2 users through a shared noiseless link. Each relay and user are equipped with a cache memory of M1 and M2 files, respectively. We propose a centralized and a decentralized coded caching scheme that exploit the spared transmission time resource by allowing concurrent transmission between the two layers. It is shown that both caching schemes are approximately optimal, and greatly reduce the transmission delay compared to the previously known caching schemes. Surprisingly, we show that when the relay's caching size is equal to a threshold that is strictly smaller than N (e.g. M1=0.382N under the decentralized setup and (K1-1)N/K1 under the centralized setup, when K1=2), our schemes achieve the same delay as if each relay had access to the full library. To our best knowledge, this is the first result showing that even the caching size is strictly smaller than the library's size, increasing the caching size is wasteful in reducing the transmission latency.

cs.IT↗