With the rapid development of blockchain and its applications, the amount of data stored on decentralized storage networks (DSNs) has grown exponentially. DSNs bring together affordable storage resources from around the world to provide robust, decentralized storage services for tens of thousands of decentralized applications (dApps). However, existing DSNs do not offer verifiability when implementing erasure coding for redundant storage, making them vulnerable to Byzantine encoders. Additionally, there is a lack of Byzantine fault-tolerant consensus for optimal resilience in DSNs. This paper introduces BFT-DSN, a Byzantine fault-tolerant decentralized storage network designed to address these challenges. BFT-DSN combines storage-weighted BFT consensus with erasure coding and incorporates homomorphic fingerprints and weighted threshold signatures for decentralized verification. The implementation of BFT-DSN demonstrates its comparable performance in terms of storage cost and latency as well as superior performance in Byzantine resilience when compared to existing industrial decentralized storage networks.

Overprivilege Attack, a widely reported phenomenon in IoT that accesses unauthorized or excessive resources, is notoriously hard to prevent, trace and mitigate. In this paper, we propose TBAC, a Tokoin-Based Access Control model enabled by blockchain and Trusted Execution Environment (TEE) technologies, to offer fine-grained access control and strong auditability for IoT. TBAC materializes the virtual access power into a definite-amount, secure and accountable cryptographic coin, termed “tokoin” (token+coin), and manages it using atomic and accountable state-transition functions in a blockchain. A tokoin carries a fine-grained policy defined by the resource owner to specify the requirements to be satisfied before an access is granted, and the behavioral constraints that describe the correct procedure to follow during access. The strong-auditability is achieved with blockchain and a TEE-enabled trusted access control object (TACO) to ensure that all access activities are securely monitored and auditable. We prototype TBAC by implementing all its functions with well-studied cryptographic primitives over different blockchain platforms, building a TACO on top of the ARM Cortex-M33 TEE microcontroller, and constructing a user-friendly APP for regular users. A case study is finally presented to demonstrate how TBAC is employed to enable autonomous and secure in-home cargo delivery.

Decentralized Storage Networks (DSNs) can gather storage resources from mutually untrusted providers and form worldwide decentralized file systems. Compared to traditional storage networks, DSNs are built on top of blockchains, which can incentivize service providers and ensure strong security. However, existing DSNs face two major challenges. First, deduplication can only be achieved at the directory-level. Missing file-level deduplication leads to unavoidable extra storage and bandwidth cost. Second, current DSNs realize file indexing by storing extra metadata while blockchain ledgers are not fully exploited. To overcome these problems, we propose FileDAG, a DSN built on DAG-based blockchain to support file-level deduplication in storing multi-versioned files. When updating files, we adopt an increment generation method to calculate and store only the increments instead of the entire updated files. Besides, we introduce a two-layer DAG-based blockchain ledger, by which FileDAG can provide flexible and storage-saving file indexing by directly using the blockchain database without incurring extra storage overhead. We implement FileDAG and evaluate its performance with extensive experiments. The results demonstrate that FileDAG outperforms the state-of-the-art industrial DSNs considering storage cost and latency.

Known as a distributed ledger technology (DLT), blockchain has attracted much attention due to its properties such as decentralization, security, immutability and transparency, and its potential of servicing as an infrastructure for various applications. Blockchain can empower wireless networks with identity management, data integrity, access control, and high-level security. However, previous studies on blockchain-enabled wireless networks mostly focus on proposing architectures or building systems with popular blockchain protocols. Nevertheless, such existing protocols have obvious shortcomings when adopted in wireless networks where nodes may have limited physical resources, may fall short of well-established reliable channels, or may suffer from variable bandwidths impacted by environments or jamming attacks. In this paper, we propose a novel consensus protocol named Proof-of-Channel (PoC) leveraging the natural properties of wireless communications, and develop a permissioned BLOWN protocol (BLOckchain protocol for Wireless Networks) for single-hop wireless networks under an adversarial SINR model. We formalize BLOWN with the universal composition framework and prove its security properties, namely persistence and liveness, as well as its strengths in countering against adversarial jamming, double-spending, and Sybil attacks, which are also demonstrated by extensive simulation studies.

Blockchain creates a secure environment on top of strict cryptographic assumptions and rigorous security proofs. It permits on-chain interactions to achieve trustworthy properties such as traceability, transparency, and accountability. However, current blockchain trustworthiness is only confined to on-chain, creating a “trust gap” to the physical, off-chain environment. This is due to the lack of a scheme that can truthfully reflect the physical world in a real-time and consistent manner. Such an absence hinders further blockchain applications in the physical world, especially for the security-sensitive ones. In this paper, we propose a framework to extend blockchain trust from on-chain to off-chain, and take trustworthy vaccine tracing as an example scheme. Our scheme consists of 1) a Trusted Execution Environment (TEE)-enabled trusted environment monitoring system built with the Arm Cortex-M33 microcontroller that continuously senses the inside of a vaccine box through trusted sensors and generates anti-forgery data; and 2) a consistency protocol to upload the environment status data from the TEE system to blockchain in a truthful, real-time consistent, continuous and fault-tolerant fashion. Our security analysis indicates that no adversary can tamper with the vaccine in any way without being captured. We carry out an experiment to record the internal status of a vaccine shipping box during transportation, and the results indicate that the proposed system incurs an average latency of 84 ms in local sensing and processing followed by an average latency of 130 ms to have the sensed data transmitted to and been available in the blockchain.

This paper presents$\mathit {wChain}$, a blockchain protocol specifically designed for multihop wireless networks that deeply integrates wireless communication properties and blockchain technologies under the realistic SINR model. We adopt a hierarchical spanner as the communication backbone to address medium contention and achieve fast data aggregation within$O(\log N\log \Gamma)$slots where$N$is the network size and$\Gamma $refers to the ratio of the maximum distance to the minimum distance between any two nodes. Besides,$\mathit {wChain}$employs data aggregation and reaggregation as well as node recovery mechanisms to ensure efficiency, fault tolerance, persistence, and liveness. The worst-case runtime of$\mathit {wChain}$is upper bounded by$O(f\log N\log \Gamma)$, where$f=\lfloor \frac {N}{2} \rfloor $is the upper bound of the number of faulty nodes. To validate our design, we conduct both theoretical analysis and simulation studies. The results not only demonstrate the nice properties of$\mathit {wChain}$, but also point to a large new space for the exploration of blockchain protocols in wireless networks.

Smart home systems have become more and more prevailent in recent years. On the one hand, they make our everyday life more convenient; on the other hand, they suffer from the two notorious security problems, namely, the open-port problem and the overprivilege problem, making their security situations extremely worrying and uncheerful. In this article, we proposed HomeShield, a novel credential-less authentication framework to shield smart home systems by effectively defending against the attacks resulted from these two security problems without the need for sensitive credentials. We further detailed an implementation of HomeShield based on the side channels that are publicly available in Android smartphones serving as controllers of smart home systems and presented its workflow in protecting against various attacks caused by the open-port and overprivilege problems. Finally, we tested our HomeShield implementation on a real-world smart home system and considered four threat models that cover basically all practical attacks, including Mirai and its variants. We also considered the effectiveness of our HomeShield implementation on the SmartApps of the Samsung SmartThings platform, which also suffers from the open-port and overprivilege problems, even though its overprivilege issue has been extensively studied by the recently proposed works, such as ContexIoT and SmartAuth. The evaluation results indicate that our HomeShield realization can successfully defend against over 90% attack trials with an average latency of less than 1 s.

MOTIVATION: In recent years, several experimental studies have revealed that the microRNAs (miRNAs) in serum, plasma, exosome and whole blood are dysregulated in various types of diseases, indicating that the circulating miRNAs may serve as potential noninvasive biomarkers for disease diagnosis and prognosis. However, no database has been constructed to integrate the large-scale circulating miRNA profiles, explore the functional pathways involved and predict the potential biomarkers using feature selection between the disease conditions. Although there have been several studies attempting to generate a circulating miRNA database, they have not yet integrated the large-scale circulating miRNA profiles or provided the biomarker-selection function using machine learning methods. RESULTS: To fill this gap, we constructed the Circulating MicroRNA Expression Profiling (CMEP) database for integrating, analyzing and visualizing the large-scale expression profiles of phenotype-specific circulating miRNAs. The CMEP database contains massive datasets that were manually curated from NCBI GEO and the exRNA Atlas, including 66 datasets, 228 subsets and 10 419 samples. The CMEP provides the differential expression circulating miRNAs analysis and the KEGG functional pathway enrichment analysis. Furthermore, to provide the function of noninvasive biomarker discovery, we implemented several feature-selection methods, including ridge regression, lasso regression, support vector machine and random forests. Finally, we implemented a user-friendly web interface to improve the user experience and to visualize the data and results of CMEP. AVAILABILITY AND IMPLEMENTATION: CMEP is accessible at http://syslab5.nchu.edu.tw/CMEP.

Internet of Things (IoT)-based E-commerce is a new business model that relies on autonomous transaction management on IoT-devices. The management system toward IoT-based E-commerce demands autonomy, lightweight, and legitimacy. As blockchain is an innovative technology that is competent in governing the decentralized network, we adopt it to design the autonomous transaction management system on IoT E-commerce. However, current blockchain solutions, most namely cryptocurrencies, have fatal drawbacks of nonsupervisability and huge computational overhead, and hence cannot be directly applied on IoT-based E-commerce. In this paper, we propose NormaChain, a blockchain-based normalized autonomous transaction settlement system for IoT-based E-commerce. By designing a special three-layer sharding blockchain network, we can significantly increase transaction efficiency and system scalability. Additionally, by designing an innovative decentralized public key searchable encryption scheme (decentralized public key encryption with keyword search (PEKS) scheme), we can uncover illegal and criminal transactions and achieve crime traceability. Our new decentralized PEKS scheme cryptographically eliminates the dependence of a trusted central authority in the original PEKS scheme and instead expands it to a fully decentralized governance, which distributes the supervision power equally among all parties. More importantly, by proving NormaChain is secure against chosen ciphertext attacks and against the stealing of the secret key, we show that NormaChain prevents a legitimate user’s privacy from being violated by banks, supervisors or malicious adversaries. Finally, we deliver the NormaChain system with design details and full implementations. Experiments show that the average transaction-per-second on IoT devices is around 113, and the supervision accuracy is 100% when proper target illegal keywords are provided.

The rapid developments of the Internet of Things (IoT) and smart mobile devices in recent years have been dramatically incentivizing the advancement of edge computing. On the one hand, edge computing has provided a great assistance for lightweight devices to accomplish complicated tasks in an efficient way; on the other hand, its hasty development leads to the neglection of security threats to a large extent in edge computing platforms and their enabled applications. In this paper, we provide a comprehensive survey on the most influential and basic attacks as well as the corresponding defense mechanisms that have edge computing specific characteristics and can be practically applied to real-world edge computing systems. More specifically, we focus on the following four types of attacks that account for 82% of the edge computing attacks recently reported by Statista: distributed denial of service attacks, side-channel attacks, malware injection attacks, and authentication and authorization attacks. We also analyze the root causes of these attacks, present the status quo and grand challenges in edge computing security, and propose future research directions.

Crowdsourcing applications are vulnerable to malicious behaviors, posing serious threats to their adoption and large deployment. Based on the notion that the requestor (i.e., the crowdsourcer) can block malicious behaviors via leveraging the market power through task allocation and pricing, we propose two novel frameworks based on the mechanism design game theory (i.e., the reverse game theory). To the best of our knowledge, we are the first to exploit the market power and to apply the mechanism design game theory in thwarting malicious behaviors in crowdsourcing. The first proposed framework is built on a requestor-dominant mechanism design game (Rd-MDG), where the game rule is determined solely by the requestor. The second proposed framework is based on the worker-assisted mechanism design game (WaMDG), where the worker (i.e., the contributor) can assist the requestor to determine the game rules by offering advices. These two frameworks have the following salient features: i) neither of them requires the workers to reveal their private information; ii) the game rules of each framework are designed to be able to force the workers to calculate their best strategies based on their actual private information; iii) our theoretical analysis shows that equilibriums exist for both frameworks; and iv) our extensive simulation results demonstrate that these two frameworks can thwart malicious behaviors by driving the workers with a higher attack intent into obtaining lower utilities.

MOTIVATION: Eukaryotic gene expression (GE) is subjected to precisely coordinated multi-layer controls, across the levels of epigenetic, transcriptional and post-transcriptional regulations. Recently, the emerging multi-dimensional genomic dataset has provided unprecedented opportunities to study the cross-layer regulatory interplay. In these datasets, the same set of samples is profiled on several layers of genomic activities, e.g. copy number variation (CNV), DNA methylation (DM), GE and microRNA expression (ME). However, suitable analysis methods for such data are currently sparse. RESULTS: In this article, we introduced a sparse Multi-Block Partial Least Squares (sMBPLS) regression method to identify multi-dimensional regulatory modules from this new type of data. A multi-dimensional regulatory module contains sets of regulatory factors from different layers that are likely to jointly contribute to a local 'gene expression factory'. We demonstrated the performance of our method on the simulated data as well as on The Cancer Genomic Atlas Ovarian Cancer datasets including the CNV, DM, ME and GE data measured on 230 samples. We showed that majority of identified modules have significant functional and transcriptional enrichment, higher than that observed in modules identified using only a single type of genomic data. Our network analysis of the modules revealed that the CNV, DM and microRNA can have coupled impact on expression of important oncogenes and tumor suppressor genes. AVAILABILITY AND IMPLEMENTATION: The source code implemented by MATLAB is freely available at: http://zhoulab.usc.edu/sMBPLS/. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary material are available at Bioinformatics online.

The rapid accumulation of biological networks poses new challenges and calls for powerful integrative analysis tools. Most existing methods capable of simultaneously analyzing a large number of networks were primarily designed for unweighted networks, and cannot easily be extended to weighted networks. However, it is known that transforming weighted into unweighted networks by dichotomizing the edges of weighted networks with a threshold generally leads to information loss. We have developed a novel, tensor-based computational framework for mining recurrent heavy subgraphs in a large set of massive weighted networks. Specifically, we formulate the recurrent heavy subgraph identification problem as a heavy 3D subtensor discovery problem with sparse constraints. We describe an effective approach to solving this problem by designing a multi-stage, convex relaxation protocol, and a non-uniform edge sampling technique. We applied our method to 130 co-expression networks, and identified 11,394 recurrent heavy subgraphs, grouped into 2,810 families. We demonstrated that the identified subgraphs represent meaningful biological modules by validating against a large set of compiled biological knowledge bases. We also showed that the likelihood for a heavy subgraph to be meaningful increases significantly with its recurrence in multiple networks, highlighting the importance of the integrative approach to biological network analysis. Moreover, our approach based on weighted graphs detects many patterns that would be overlooked using unweighted graphs. In addition, we identified a large number of modules that occur predominately under specific phenotypes. This analysis resulted in a genome-wide mapping of gene network modules onto the phenome. Finally, by comparing module activities across many datasets, we discovered high-order dynamic cooperativeness in protein complex networks and transcriptional regulatory networks.

BACKGROUND: Disease classification has been an important application of microarray technology. However, most microarray-based classifiers can only handle data generated within the same study, since microarray data generated by different laboratories or with different platforms can not be compared directly due to systematic variations. This issue has severely limited the practical use of microarray-based disease classification. RESULTS: In this study, we tested the feasibility of disease classification by integrating the large amount of heterogeneous microarray datasets from the public microarray repositories. Cross-platform data compatibility is created by deriving expression log-rank ratios within datasets. One may then compare vectors of log-rank ratios across datasets. In addition, we systematically map textual annotations of datasets to concepts in Unified Medical Language System (UMLS), permitting quantitative analysis of the phenotype "distance" between datasets and automated construction of disease classes. We design a new classification approach named ManiSVM, which integrates Manifold data transformation with SVM learning to exploit the data properties. Using the leave one dataset out cross validation, ManiSVM achieved the overall accuracy of 70.7% (68.6% precision and 76.9% recall) with many disease classes achieving the accuracy higher than 80%. CONCLUSION: Our results not only demonstrated the feasibility of the integrated disease classification approach, but also showed that the classification accuracy increases with the number of homogenous training datasets. Thus, the power of the integrative approach will increase with the continuous accumulation of microarray data in public repositories. Our study shows that automated disease diagnosis can be an important and promising application of the enormous amount of costly to generate, yet freely available, public microarray data.

BACKGROUND: Genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN) is a machine learning technique that can effectively process complex and high noise data. Here, ANNs are applied to process the unique subsequence distribution for prediction of specific oligos. RESULTS: We present a novel and efficient algorithm, named the integration of ANN and BLAST (IAB) algorithm, to identify specific oligos. We establish the unique marker database for human and rat gene index databases using the hash table algorithm. We then create the input vectors, via the unique marker database, to train and test the ANN. The trained ANN predicted the specific oligos with high efficiency, and these oligos were subsequently verified by BLAST. To improve the prediction performance, the ANN over-fitting issue was avoided by early stopping with the best observed error and a k-fold validation was also applied. The performance of the IAB algorithm was about 5.2, 7.1, and 6.7 times faster than the BLAST search without ANN for experimental results of 70-mer, 50-mer, and 25-mer specific oligos, respectively. In addition, the results of polymerase chain reactions showed that the primers predicted by the IAB algorithm could specifically amplify the corresponding genes. The IAB algorithm has been integrated into a previously published comprehensive web server to support microarray analysis and genome-wide iterative enrichment analysis, through which users can identify a group of desired genes and then discover the specific oligos of these genes. CONCLUSION: The IAB algorithm has been developed to construct SpecificDB, a web server that provides a specific and valid oligo database of the probe, siRNA, and primer design for the human genome. We also demonstrate the ability of the IAB algorithm to predict specific oligos through polymerase chain reaction experiments. SpecificDB provides comprehensive information and a user-friendly interface.