arXiv subjects

Yan Fu

Publications and source records attributed to Yan Fu.

36 records · Page 2Linked to original sources

arXiv2020

The MUIR Framework: Cross-Linking MOOC Resources to Enhance Discussion Forums

New learning resources are created and minted in Massive Open Online Courses every week -- new videos, quizzes, assessments and discussion threads are deployed and interacted with -- in the era of on-demand online learning. However, these resources are often artificially siloed between platforms and artificial web application models. Facilitating the linking between such resources facilitates learning and multimodal understanding, bettering learners' experience. We create a framework for MOOC Uniform Identifier for Resources (MUIR). MUIR enables applications to refer and link to such resources in a cross-platform way, allowing the easy minting of identifiers to MOOC resources, akin to #hashtags. We demonstrate the feasibility of this approach to the automatic identification, linking and resolution -- a task known as Wikification -- of learning resources mentioned on MOOC discussion forums, from a harvested collection of 100K+ resources. Our Wikification system achieves a high initial rate of 54.6% successful resolutions on key resource mentions found in discussion forums, demonstrating the utility of the MUIR framework. Our analysis on this new problem shows that context is a key factor in determining the correct resolution of such mentions.

cs.IR↗

arXiv2020

Enhancing Answer Boundary Detection for Multilingual Machine Reading Comprehension

Multilingual pre-trained models could leverage the training data from a rich source language (such as English) to improve performance on low resource languages. However, the transfer quality for multilingual Machine Reading Comprehension (MRC) is significantly worse than sentence classification tasks mainly due to the requirement of MRC to detect the word level answer boundary. In this paper, we propose two auxiliary tasks in the fine-tuning stage to create additional phrase boundary supervision: (1) A mixed MRC task, which translates the question or passage to other languages and builds cross-lingual question-passage pairs; (2) A language-agnostic knowledge masking task by leveraging knowledge phrases mined from web. Besides, extensive experiments on two cross-lingual MRC datasets show the effectiveness of our proposed approach.

cs.CL↗

arXiv2019

Multimodal Cross-registration and Quantification of Metric Distortions in Whole Brain Histology of Marmoset using Diffeomorphic Mappings

Whole brain neuroanatomy using tera-voxel light-microscopic data sets is of much current interest. A fundamental problem in this field is the mapping of individual brain data sets to a reference space. Previous work has not rigorously quantified the distortions in brain geometry from in-vivo to ex-vivo brains due to the tissue processing, which will be important when computing properties such as local cell and process densities at the voxel level in creating reference brain maps. Further, existing approaches focus on registering uni-modal volumetric data; however, given the increasing interest in the marmoset model for neuroscience research, it is necessary to cross-register multi-modal data sets including MRIs and multiple histological series that can help address individual variations in brain architecture. Here we present a computational approach for same-subject multimodal MRI guided reconstruction of a histological series, jointly with diffeomorphic mapping to a reference atlas. We quantify the scale change during the different stages of histological processing of the brains using the Jacobian determinant of the diffeomorphic transformations involved. There are two major steps in the histology process with associated scale distortions (a) brain perfusion (b) histological sectioning and reassembly. By mapping the final image stacks to the ex-vivo post fixation MRI, we show that tape-transfer histology can be reassembled accurately into 3D volumes with a local scale change of 2.0 $\pm$ 0.4% per axis dimension. In contrast, the perfusion step, as assessed by mapping the in-vivo MRIs to the ex-vivo post fixation MRIs, shows a larger local scale change of 6.9 $\pm$ 2.1% per axis dimension. This is the first systematic quantification of the local metric distortions associated with whole-brain histological processing, and we expect that the results will generalize to other species.

q-bio.NC↗

arXiv2018

Resource Mention Extraction for MOOC Discussion Forums

In discussions hosted on discussion forums for MOOCs, references to online learning resources are often of central importance. They contextualize the discussion, anchoring the discussion participants' presentation of the issues and their understanding. However they are usually mentioned in free text, without appropriate hyperlinking to their associated resource. Automated learning resource mention hyperlinking and categorization will facilitate discussion and searching within MOOC forums, and also benefit the contextualization of such resources across disparate views. We propose the novel problem of learning resource mention identification in MOOC forums. As this is a novel task with no publicly available data, we first contribute a large-scale labeled dataset, dubbed the Forum Resource Mention (FoRM) dataset, to facilitate our current research and future research on this task. We then formulate this task as a sequence tagging problem and investigate solution architectures to address the problem. Importantly, we identify two major challenges that hinder the application of sequence tagging models to the task: (1) the diversity of resource mention expression, and (2) long-range contextual dependencies. We address these challenges by incorporating character-level and thread context information into a LSTM-CRF model. First, we incorporate a character encoder to address the out-of-vocabulary problem caused by the diversity of mention expressions. Second, to address the context dependency challenge, we encode thread contexts using an RNN-based context encoder, and apply the attention mechanism to selectively leverage useful context information during sequence tagging. Experiments on FoRM show that the proposed method improves the baseline deep sequence tagging models notably, significantly bettering performance on instances that exemplify the two challenges.

cs.CL↗

arXiv2018

Diffusion-like recommendation with enhanced similarity of objects

In last decades, diversity and accuracy have been regarded as two important measures in evaluating a recommendation model. However, a clear concern is that a model focusing excessively on one measure will put the other one at risk, thus it is not easy to greatly improve diversity and accuracy simultaneously. In this paper, we propose to enhance the Resource-Allocation (RA) similarity in resource transfer equations of diffusion-like models, by giving a tunable exponent to the RA similarity, and traversing the value of the exponent to achieve the optimal recommendation results. In this way, we can increase the recommendation scores (allocated resource) of many unpopular objects. Experiments on three benchmark data sets, MovieLens, Netflix, and RateYourMusic show that the modified models can yield remarkable performance improvement compared with the original ones.

cs.IR↗

arXiv2015

A theoretical foundation of the target-decoy search strategy for false discovery rate control in proteomics

Motivation: Target-decoy search (TDS) is currently the most popular strategy for estimating and controlling the false discovery rate (FDR) of peptide identifications in mass spectrometry-based shotgun proteomics. While this strategy is very useful in practice and has been intensively studied empirically, its theoretical foundation has not yet been well established. Result: In this work, we systematically analyze the TDS strategy in a rigorous statistical sense. We prove that the commonly used concatenated TDS provides a conservative estimate of the FDR for any given score threshold, but it cannot rigorously control the FDR. We prove that with a slight modification to the commonly used formula for FDR estimation, the peptide-level FDR can be rigorously controlled based on the concatenated TDS. We show that the spectrum-level FDR control is difficult. We verify the theoretical conclusions with real mass spectrometry data.

stat.AP↗

arXiv2014

Local degree blocking model for link prediction in complex networks

Recovering and reconstructing networks by accurately identifying missing and unreliable links is a vital task in the domain of network analysis and mining. In this article, by studying a specific local structure, namely a degree block having a node and its all immediate neighbors, we find it contains important statistical features of link formation for complex networks. We therefore propose a parameter-free local blocking (LB) predictor to quantitatively detect link formation in given networks via local link density calculations. The promising experimental results performed on six real-world networks suggest that the new index can outperform other traditional local similarity-based methods on most of tested networks. After further analyzing the scores' correlations between LB and two other methods, we find that the features of LB index are analogous to those of both PA index and short-path-based index, which empirically verify that large degree principle and short path principle simultaneously captured by the LB index are jointly driving link formation in complex networks.

cs.SI↗

arXiv2014

Information Filtering on Coupled Social Networks

In this paper, based on the coupled social networks (CSN), we propose a hybrid algorithm to nonlinearly integrate both social and behavior information of online users. Filtering algorithm based on the coupled social networks, which considers the effects of both social influence and personalized preference. Experimental results on two real datasets, \emph{Epinions} and \emph{Friendfeed}, show that hybrid pattern can not only provide more accurate recommendations, but also can enlarge the recommendation coverage while adopting global metric. Further empirical analyses demonstrate that the mutual reinforcement and rich-club phenomenon can also be found in coupled social networks where the identical individuals occupy the core position of the online system. This work may shed some light on the in-depth understanding structure and function of coupled social networks.

cs.SI↗

arXiv2014

Information Filtering via Balanced Diffusion on Bipartite Networks

Recent decade has witnessed the increasing popularity of recommender systems, which help users acquire relevant commodities and services from overwhelming resources on Internet. Some simple physical diffusion processes have been used to design effective recommendation algorithms for user-object bipartite networks, typically mass diffusion (MD) and heat conduction (HC) algorithms which have different advantages respectively on accuracy and diversity. In this paper, we investigate the effect of weight assignment in the hybrid of MD and HC, and find that a new hybrid algorithm of MD and HC with balanced weights will achieve the optimal recommendation results, we name it balanced diffusion (BD) algorithm. Numerical experiments on three benchmark data sets, MovieLens, Netflix and RateYourMusic (RYM), show that the performance of BD algorithm outperforms the existing diffusion-based methods on the three important recommendation metrics, accuracy, diversity and novelty. Specifically, it can not only provide accurately recommendation results, but also yield higher diversity and novelty in recommendations by accurately recommending unpopular objects.

cs.IR↗

arXiv2014

Efficient allocation of heterogeneous response times in information spreading process

Recently, the impacts of spatiotemporal heterogeneities of human activities on spreading dynamics have attracted extensive attention. In this paper, to study heterogeneous response times on information spreading, we focus on the susceptible-infected spreading dynamics with adjustable power-law response time distribution based on uncorrelated scale-free networks. We find that the stronger the heterogeneity of response times is, the faster the information spreading is in the early and middle stages. Following a given heterogeneity, the procedure of reducing the correlation between the response times and degrees of individuals can also accelerate the spreading dynamics in the early and middle stages. However, the dynamics in the late stage is slightly more complicated, and there is an optimal value of the full prevalence time changing with the heterogeneity of response times and the response time-degree correlation, respectively. The optimal phenomena results from the efficient allocation of heterogeneous response times.

physics.soc-ph↗

arXiv2013

Discovery of Proteomics based on Machine learning

The ultimate target of proteomics identification is to identify and quantify the protein in the organism. Mass spectrometry (MS) based on label-free protein quantitation has mainly focused on analysis of peptide spectral counts and ion peak heights. Using several observed peptides (proteotypic) can identify the origin protein. However, each peptide's possibility to be detected was severely influenced by the peptide physicochemical properties, which confounded the results of MS accounting. Using about a million peptide identification generated by four different kinds of proteomic platforms, we successfully identified >16,000 proteotypic peptides. We used machine learning classification to derive peptide detection probabilities that are used to predict the number of trypic peptides to be observed, which can serve to estimate the absolutely abundance of protein with highly accuracy. We used the data of peptides (provides by CAS lab) to derive the best model from different kinds of methods. We first employed SVM and Random Forest classifier to identify the proteotypic and unobserved peptides, and then searched the best parameter for better prediction results. Considering the excellent performance of our model, we can calculate the absolutely estimation of protein abundance.

q-bio.QM↗

arXiv2013

Privacy Preserving Social Network Publication Against Mutual Friend Attacks

Publishing social network data for research purposes has raised serious concerns for individual privacy. There exist many privacy-preserving works that can deal with different attack models. In this paper, we introduce a novel privacy attack model and refer it as a mutual friend attack. In this model, the adversary can re-identify a pair of friends by using their number of mutual friends. To address this issue, we propose a new anonymity concept, called k-NMF anonymity, i.e., k-anonymity on the number of mutual friends, which ensures that there exist at least k-1 other friend pairs in the graph that share the same number of mutual friends. We devise algorithms to achieve the k-NMF anonymity while preserving the original vertex set in the sense that we allow the occasional addition but no deletion of vertices. Further we give an algorithm to ensure the k-degree anonymity in addition to the k-NMF anonymity. The experimental results on real-word datasets demonstrate that our approach can preserve the privacy and utility of social networks effectively against mutual friend attacks.

cs.DB↗

arXiv2013

Scaling behavior of online human activity

The rapid development of Internet technology enables human explore the web and record the traces of online activities. From the analysis of these large-scale data sets (i.e. traces), we can get insights about dynamic behavior of human activity. In this letter, the scaling behavior and complexity of human activity in the e-commerce, such as music, book, and movie rating, are comprehensively investigated by using detrended fluctuation analysis technique and multiscale entropy method. Firstly, the interevent time series of rating behaviors of these three type medias show the similar scaling property with exponents ranging from 0.53 to 0.58, which implies that the collective behaviors of rating media follow a process embodying self-similarity and long-range correlation. Meanwhile, by dividing the users into three groups based their activities (i.e., rating per unit time), we find that the scaling exponents of interevent time series in three groups are different. Hence, these results suggest the stronger long-range correlations exist in these collective behaviors. Furthermore, their information complexities vary from three groups. To explain the differences of the collective behaviors restricted to three groups, we study the dynamic behavior of human activity at individual level, and find that the dynamic behaviors of a few users have extremely small scaling exponents associating with long-range anticorrelations. By comparing with the interevent time distributions of four representative users, we can find that the bimodal distributions may bring the extraordinary scaling behaviors. These results of analyzing the online human activity in the e-commerce may not only provide insights to understand its dynamic behaviors but also be applied to acquire the potential economic interest.

physics.soc-ph↗

arXiv2012

Emergence of scale-free close-knit friendship structure in online social networks

Despite the structural properties of online social networks have attracted much attention, the properties of the close-knit friendship structures remain an important question. Here, we mainly focus on how these mesoscale structures are affected by the local and global structural properties. Analyzing the data of four large-scale online social networks reveals several common structural properties. It is found that not only the local structures given by the indegree, outdegree, and reciprocal degree distributions follow a similar scaling behavior, the mesoscale structures represented by the distributions of close-knit friendship structures also exhibit a similar scaling law. The degree correlation is very weak over a wide range of the degrees. We propose a simple directed network model that captures the observed properties. The model incorporates two mechanisms: reciprocation and preferential attachment. Through rate equation analysis of our model, the local-scale and mesoscale structural properties are derived. In the local-scale, the same scaling behavior of indegree and outdegree distributions stems from indegree and outdegree of nodes both growing as the same function of the introduction time, and the reciprocal degree distribution also shows the same power-law due to the linear relationship between the reciprocal degree and in/outdegree of nodes. In the mesoscale, the distributions of four closed triples representing close-knit friendship structures are found to exhibit identical power-laws, a behavior attributed to the negligible degree correlations. Intriguingly, all the power-law exponents of the distributions in the local-scale and mesoscale depend only on one global parameter -- the mean in/outdegree, while both the mean in/outdegree and the reciprocity together determine the ratio of the reciprocal degree of a node to its in/outdegree.

physics.soc-ph↗

arXiv2012

Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells

The innate immune system, acting as the first line of host defense, senses and adapts to foreign challenges through complex intracellular and intercellular signaling networks. Endotoxin tolerance and priming elicited by macrophages are classic examples of the complex adaptation of innate immune cells. Upon repetitive exposures to different doses of bacterial endotoxin (lipopolysaccharide) or other stimulants, macrophages show either suppressed or augmented inflammatory responses compared to a single exposure to the stimulant. Endotoxin tolerance and priming are critically involved in both immune homeostasis and the pathogenesis of diverse inflammatory diseases. However, the underlying molecular mechanisms are not well understood. By means of a computational search through the parameter space of a coarse-grained three-node network with a two-stage Metropolis sampling approach, we enumerated all the network topologies that can generate priming or tolerance. We discovered three major mechanisms for priming (pathway synergy, suppressor deactivation, activator induction) and one for tolerance (inhibitor persistence). These results not only explain existing experimental observations, but also reveal intriguing test scenarios for future experimental studies to clarify mechanisms of endotoxin priming and tolerance.

q-bio.MN↗

arXiv2012

Slow dynamics of Zero Range Process in the Framework of Traps Model

The relaxation dynamics of zero range process (ZRP) has always been an interesting problem. In this study, we set up the relationship between ZRP and traps model, and investigate the slow dynamics of ZRP in the framework of traps model. Through statistical quantities such as the average rest time, the particle distribution, the two-time correlation function and the average escape time, we find that the particle interaction, especially the resulted condensation, can significantly influence the dynamics. In the stationary state, both the average rest time and the average escape time caused by the attraction among particles are obtained analytically. In the transient state, a hierarchical nature of the aging dynamics is revealed by both simulations and scaling analysis. Moreover, by comparing the particle diffusion in both the transient state and the stationary state, we find that the closer ZRP systems approach the stationary state, the more slowly particles diffuse.

cond-mat.stat-mech↗

arXiv2011

Hamiltonian Connectivity of Twisted Hypercube-Like Networks under the Large Fault Model

Twisted hypercube-like networks (THLNs) are an important class of interconnection networks for parallel computing systems, which include most popular variants of the hypercubes, such as crossed cubes, Möbius cubes, twisted cubes and locally twisted cubes. This paper deals with the fault-tolerant hamiltonian connectivity of THLNs under the large fault model. Let $G$ be an $n$-dimensional THLN and $F \subseteq V(G)\bigcup E(G)$, where $n \geq 7$ and $|F| \leq 2n - 10$. We prove that for any two nodes $u,v \in V(G - F)$ satisfying a simple necessary condition on neighbors of $u$ and $v$, there exists a hamiltonian or near-hamiltonian path between $u$ and $v$ in $G-F$. The result extends further the fault-tolerant graph embedding capability of THLNs.

cs.DC↗

arXiv2010

Resonant activation: a strategy against bacterial persistence

A bacterial colony may develop a small number of cells genetically identical to, but phenotypically different from other normally growing bacteria. These so-called persister cells keep themselves in a dormant state and thus are insensitive to antibiotic treatment, resulting in serious problems of drug resistance. In this paper, we proposed a novel strategy to "kill" persister cells by triggering them to switch, in a fast and synchronized way, into normally growing cells that are susceptible to antibiotics. The strategy is based on resonant activation (RA), a well-studied phenomenon in physics where the internal noise of a system can constructively facilitate fast and synchronized barrier crossings. Through stochastic Gilliespie simulation with a generic toggle switch model, we demonstrated that RA exists in the phenotypic switching of a single bacterium. Further, by coupling single cell level and population level simulations, we showed that with RA, one can greatly reduce the time and total amount of antibiotics needed to sterilize a bacterial population. We suggest that resonant activation is a general phenomenon in phenotypic transition, and can find other applications such as cancer therapy.

q-bio.MN↗