arXiv subjects

Jun Pang

Publications and source records attributed to Jun Pang.

At least 55 records · Page 3Linked to original sources

arXiv2020

Semantic and Relational Spaces in Science of Science: Deep Learning Models for Article Vectorisation

Over the last century, we observe a steady and exponentially growth of scientific publications globally. The overwhelming amount of available literature makes a holistic analysis of the research within a field and between fields based on manual inspection impossible. Automatic techniques to support the process of literature review are required to find the epistemic and social patterns that are embedded in scientific publications. In computer sciences, new tools have been developed to deal with large volumes of data. In particular, deep learning techniques open the possibility of automated end-to-end models to project observations to a new, low-dimensional space where the most relevant information of each observation is highlighted. Using deep learning to build new representations of scientific publications is a growing but still emerging field of research. The aim of this paper is to discuss the potential and limits of deep learning for gathering insights about scientific research articles. We focus on document-level embeddings based on the semantic and relational aspects of articles, using Natural Language Processing (NLP) and Graph Neural Networks (GNNs). We explore the different outcomes generated by those techniques. Our results show that using NLP we can encode a semantic space of articles, while with GNN we are able to build a relational space where the social practices of a research community are also encoded.

cs.SI↗

arXiv2020

A Dynamics-based Approach for the Target Control of Boolean Networks

We study the target control problem of asynchronous Boolean networks, to identify a set of nodes, the perturbation of which can drive the dynamics of the network from any initial state to the desired steady state (or attractor). We are particularly interested in temporary perturbations, which are applied for sufficient time and then released to retrieve the original dynamics. Temporary perturbations have the apparent advantage of averting unforeseen consequences, which might be induced by permanent perturbations. Despite the infamous state-space explosion problem, in this work, we develop an efficient method to compute the temporary target control for a given target attractor of a Boolean network. We apply our method to a number of real-life biological networks and compare its performance with the stable motif-based control method to demonstrate its efficacy and efficiency.

eess.SY↗

arXiv2020

Sequential Control of Boolean Networks with Temporary and Permanent Perturbations

Direct cell reprogramming makes it feasible to reprogram abundant somatic cells into desired cells. It has great potential for regenerative medicine and tissue engineering. In this work, we study the control of biological networks, modelled as Boolean networks, to identify control paths driving the dynamics of the network from a source attractor (undesired cells) to the target attractor (desired cells). Instead of achieving control in one step, we develop attractor-based sequential temporary and permanent control methods (AST and ASP) to identify a sequence of interventions that can alter the dynamics in a stepwise manner. To improve their feasibility, both AST and ASP only use biologically observable attractors as intermediates. They can find the shortest sequential paths and guarantee 100% reachability of the target attractor. We apply the two methods to several real-life biological networks and compare their performance with the attractor-based sequential instantaneous control (ASI). The results demonstrate that AST and ASP have the ability to identify a richer set of control paths with fewer perturbations than ASI, which will greatly facilitate practical applications.

eess.SY↗

arXiv2020

Synthesis and temperature-dependent photoluminescence of high density GeSe triangular nanoplate arrays on Si substrates

We have grown germanium selenide (GeSe) triangular nanoplate arrays (TNAs) with a high density (3.82E+6 / mm2) on the Si (111) substrate using a simple thermal evaporation method. The thickness and trilateral lengths of a single triangular nanoplate were statistically estimated by atomic force microscopy (AFM) as 44 nm, 365 nm, 458 nm and 605 nm, respectively. Transmission electron microscopy (TEM) images and X-ray diffraction (XRD) patterns show that the TNAs were composed of single crystalline GeSe phase. The Se-related defects in the lattice were also revealed by TEM images and Raman vibration modes. Unlike previously reported GeSe compounds, the GeSe TNAs exhibited temperature-dependent photoluminescence (PL). In addition, not previously reported PL peak (1.25 eV) of the 44 nm thick TNAs at 5 K was in the gaps between those of GeSe monolayers (1.5 nm) and thin films (400 nm), revealing a close relationship between the PL peak and the thickness of GeSe. The high-density structure and temperature-dependent PL of the TNAs on the Si substrate may be useful for temperature controllable semiconductor nanodevices.

cond-mat.mes-hall↗

arXiv2019

Characterising Probabilistic Alternating Simulation for Concurrent Games

Probabilistic game structures combine both nondeterminism and stochasticity, where players repeatedly take actions simultaneously to move to the next state of the concurrent game. Probabilistic alternating simulation is an important tool to compare the behaviour of different probabilistic game structures. In this paper, we present a sound and complete modal characterisation of this simulation relation by proposing a new logic based on probabilistic distributions. The logic enables a player to enforce a property in the next state or distribution. Its extension with fixpoints, which also characterises the simulation relation, can express a lot of interesting properties in practical applications.

cs.LO↗

arXiv2018

Formal Analysis of an E-Health Protocol

Given the sensitive nature of health data, security and privacy in e-health systems is of prime importance. It is crucial that an e-health system must ensure that users remain private - even if they are bribed or coerced to reveal themselves, or others: a pharmaceutical company could, for example, bribe a pharmacist to reveal information which breaks a doctor's privacy. In this paper, we first identify and formalise several new but important privacy properties on enforcing doctor privacy. Then we analyse the security and privacy of a complicated and practical e-health protocol (DLV08). Our analysis uncovers ambiguities in the protocol, and shows to what extent these new privacy properties as well as other security properties (such as secrecy and authentication) and privacy properties (such as anonymity and untraceability) are satisfied by the protocol. Finally, we address the found ambiguities which result in both security and privacy flaws, and propose suggestions for fixing them.

cs.CR↗

arXiv2018

Towards the Existential Control of Boolean Networks: A Preliminary Report (Extended Abstract)

Given a Boolean network BN and a subset A of attractors of BN, we study the problem of identifying a minimal subset C of vertices of BN, such that the dynamics of BN can reach from a state s in any attractor As in A to any attractor At in A by controlling or toggling a subset of vertices in C in a single time step. We describe a method based on the decomposition of the network structure into strongly connected components called blocks. The control subset can be locally computed for each such block and the results then merged to derive the global control subset C. This potentially improves the efficiency for many real-life networks that are large but modular and well-structured. We are currently in the process of implementing our method in software.

eess.SY↗

arXiv2018

A Decomposition-based Approach towards the Control of Boolean Networks (Technical Report)

We study the problem of computing a minimal subset of nodes of a given asynchronous Boolean network that need to be controlled to drive its dynamics from an initial steady state (or attractor) to a target steady state. Due to the phenomenon of state-space explosion, a simple global approach that performs computations on the entire network, may not scale well for large networks. We believe that efficient algorithms for such networks must exploit the structure of the networks together with their dynamics. Taking such an approach, we derive a decomposition-based solution to the minimal control problem which can be significantly faster than the existing approaches on large networks. We apply our solution to both real-life biological networks and randomly generated networks, demonstrating promising results.

eess.SY↗

arXiv2018

Tagvisor: A Privacy Advisor for Sharing Hashtags

Hashtag has emerged as a widely used concept of popular culture and campaigns, but its implications on people's privacy have not been investigated so far. In this paper, we present the first systematic analysis of privacy issues induced by hashtags. We concentrate in particular on location, which is recognized as one of the key privacy concerns in the Internet era. By relying on a random forest model, we show that we can infer a user's precise location from hashtags with accuracy of 70\% to 76\%, depending on the city. To remedy this situation, we introduce a system called Tagvisor that systematically suggests alternative hashtags if the user-selected ones constitute a threat to location privacy. Tagvisor realizes this by means of three conceptually different obfuscation techniques and a semantics-based metric for measuring the consequent utility loss. Our findings show that obfuscating as little as two hashtags already provides a near-optimal trade-off between privacy and utility in our dataset. This in particular renders Tagvisor highly time-efficient, and thus, practical in real-world settings.

cs.CR↗

arXiv2017

walk2friends: Inferring Social Links from Mobility Profiles

The development of positioning technologies has resulted in an increasing amount of mobility data being available. While bringing a lot of convenience to people's life, such availability also raises serious concerns about privacy. In this paper, we concentrate on one of the most sensitive information that can be inferred from mobility data, namely social relationships. We propose a novel social relation inference attack that relies on an advanced feature learning technique to automatically summarize users' mobility features. Compared to existing approaches, our attack is able to predict any two individuals' social relation, and it does not require the adversary to have any prior knowledge on existing social relations. These advantages significantly increase the applicability of our attack and the scope of the privacy assessment. Extensive experiments conducted on a large dataset demonstrate that our inference attack is effective, and achieves between 13% to 20% improvement over the best state-of-the-art scheme. We propose three defense mechanisms -- hiding, replacement and generalization -- and evaluate their effectiveness for mitigating the social link privacy risks stemming from mobility data sharing. Our experimental results show that both hiding and replacement mechanisms outperform generalization. Moreover, hiding and replacement achieve a comparable trade-off between utility and privacy, the former preserving better utility and the latter providing better privacy.

cs.CR↗

arXiv2017

Quantifying Location Sociality

The emergence of location-based social networks provides an unprecedented chance to study the interaction between human mobility and social relations. This work is a step towards quantifying whether a location is suitable for conducting social activities, and the notion is named location sociality. Being able to quantify location sociality creates practical opportunities such as urban planning and location recommendation. To quantify a location's sociality, we propose a mixture model of HITS and PageRank on a heterogeneous network linking users and locations. By exploiting millions of check-in data generated by Instagram users in New York and Los Angeles, we investigate the relation between location sociality and several location properties, including location categories, rating and popularity. We further perform two case studies, i.e., friendship prediction and location recommendation, experimental results demonstrate the usefulness of our quantification.

cs.SI↗

arXiv2017

Taming Asynchrony for Attractor Detection in Large Boolean Networks (Technical Report)

Boolean networks is a well-established formalism for modelling biological systems. A vital challenge for analysing a Boolean network is to identify all the attractors. This becomes more challenging for large asynchronous Boolean networks, due to the asynchronous updating scheme. Existing methods are prohibited due to the well-known state-space explosion problem in large Boolean networks. In this paper, we tackle this challenge by proposing a SCC-based decomposition method. We prove the correctness of our proposed method and demonstrate its efficiency with two real-life biological networks.

q-bio.MN↗

arXiv2017

Should We Learn Probabilistic Models for Model Checking? A New Approach and An Empirical Study

Many automated system analysis techniques (e.g., model checking, model-based testing) rely on first obtaining a model of the system under analysis. System modeling is often done manually, which is often considered as a hindrance to adopt model-based system analysis and development techniques. To overcome this problem, researchers have proposed to automatically "learn" models based on sample system executions and shown that the learned models can be useful sometimes. There are however many questions to be answered. For instance, how much shall we generalize from the observed samples and how fast would learning converge? Or, would the analysis result based on the learned model be more accurate than the estimation we could have obtained by sampling many system executions within the same amount of time? In this work, we investigate existing algorithms for learning probabilistic models for model checking, propose an evolution-based approach for better controlling the degree of generalization and conduct an empirical study in order to answer the questions. One of our findings is that the effectiveness of learning may sometimes be limited.

cs.SE↗

arXiv2016

Reviving the Two-state Markov Chain Approach (Technical Report)

Probabilistic Boolean networks (PBNs) is a well-established computational framework for modelling biological systems. The steady-state dynamics of PBNs is of crucial importance in the study of such systems. However, for large PBNs, which often arise in systems biology, obtaining the steady-state distribution poses a significant challenge. In fact, statistical methods for steady-state approximation are the only viable means when dealing with large networks. In this paper, we revive the two-state Markov chain approach presented in the literature. We first identify a problem of generating biased results, due to the size of the initial sample with which the approach needs to start and we propose a few heuristics to avoid such a pitfall. Second, we conduct an extensive experimental comparison of the two-state Markov chain approach and another approach based on the Skart method and we show that statistically the two-state Markov chain has a better performance. Finally, we apply this approach to a large PBN model of apoptosis in hepatocytes.

cs.CE↗

arXiv2016

DeepCity: A Feature Learning Framework for Mining Location Check-ins

Online social networks being extended to geographical space has resulted in large amount of user check-in data. Understanding check-ins can help to build appealing applications, such as location recommendation. In this paper, we propose DeepCity, a feature learning framework based on deep learning, to profile users and locations, with respect to user demographic and location category prediction. Both of the predictions are essential for social network companies to increase user engagement. The key contribution of DeepCity is the proposal of task-specific random walk which uses the location and user properties to guide the feature learning to be specific to each prediction task. Experiments conducted on 42M check-ins in three cities collected from Instagram have shown that DeepCity achieves a superior performance and outperforms other baseline models significantly.

cs.SI↗

arXiv2016

Fast Simulation of Probabilistic Boolean Networks (Technical Report)

Probabilistic Boolean networks (PBNs) is an important mathematical framework widely used for modelling and analysing biological systems. PBNs are suited for modelling large biological systems, which more and more often arise in systems biology. However, the large system size poses a~significant challenge to the analysis of PBNs, in particular, to the crucial analysis of their steady-state behaviour. Numerical methods for performing steady-state analyses suffer from the state-space explosion problem, which makes the utilisation of statistical methods the only viable approach. However, such methods require long simulations of PBNs, rendering the simulation speed a crucial efficiency factor. For large PBNs and high estimation precision requirements, a slow simulation speed becomes an obstacle. In this paper, we propose a structure-based method for fast simulation of PBNs. This method first performs a network reduction operation and then divides nodes into groups for parallel simulation. Experimental results show that our method can lead to an approximately 10 times speedup for computing steady-state probabilities of a real-life biological network.

cs.CE↗

arXiv2016

A New Access Control Scheme for Facebook-style Social Networks

The popularity of online social networks (OSNs) makes the protection of users' private information an important but scientifically challenging problem. In the literature, relationship-based access control schemes have been proposed to address this problem. However, with the dynamic developments of OSNs, we identify new access control requirements which cannot be fully captured by the current schemes. In this paper, we focus on public information in OSNs and treat it as a new dimension which users can use to regulate access to their resources. We define a new OSN model containing users and their relationships as well as public information. Based on this model, we introduce a variant of hybrid logic for formulating access control policies. We exploit a type of category information and relationship hierarchy to further extend our logic for its usage in practice. In the end, we propose a few solutions to address the problem of information reliability in OSNs, and formally model collaborative access control in our access control scheme.

cs.CR↗

arXiv2016

Location Prediction: Communities Speak Louder than Friends

Humans are social animals, they interact with different communities of friends to conduct different activities. The literature shows that human mobility is constrained by their social relations. In this paper, we investigate the social impact of a person's communities on his mobility, instead of all friends from his online social networks. This study can be particularly useful, as certain social behaviors are influenced by specific communities but not all friends. To achieve our goal, we first develop a measure to characterize a person's social diversity, which we term `community entropy'. Through analysis of two real-life datasets, we demonstrate that a person's mobility is influenced only by a small fraction of his communities and the influence depends on the social contexts of the communities. We then exploit machine learning techniques to predict users' future movement based on their communities' information. Extensive experiments demonstrate the prediction's effectiveness.

cs.SI↗