Federated Learning (FL) is to collaboratively train a global model among distributed clients by iteratively aggregating their local updates without sharing their raw data, whereby the global modal can approximately converge to the centralized training way over a global dataset that composed of all local datasets (i.e., union of all users’ local data). However, in real-world scenarios, the distributions of the data classes are often imbalanced not only locally, but also in the global dataset, which severely deteriorate the FL performance due to the conflicting knowledge aggregation. Existing solutions for FL class imbalance either focus on the local data to regulate the training process or purely aim at the global datasets, which often fail to alleviate the class imbalance problem if there is mismatch between the local and global imbalance. Considering these limitations, this paper proposes a Global-Local Joint Learning method, namely GLJL, which simultaneously harmonizes the global and local class imbalance issue by jointly embedding the local and the global factors into each client’s loss function. Through extensive experiments over popular datasets with various class imbalance settings, we show that the proposed method can significantly improve the model accuracy over minority classes without sacrificing the accuracy of other classes.

Estimating causal effects among different events is of great importance to critical fields such as drug development. Nevertheless, the data features associated with events may be distributed across various silos and remain private within respective parties, impeding direct information exchange between them. This, in turn, can result in biased estimations of local causal effects, which rely on the characteristics of only a subset of the covariates. To tackle this challenge, we introduce an innovative disentangle architecture designed to facilitate the seamless cross-silo transmission of model parameters, enriched with causal mechanisms, through a combination of shared and private branches. Besides, we introduce global constraints into the equation to effectively mitigate bias within the various missing domains, thereby elevating the accuracy of our causal effect estimation. Extensive experiments conducted on new semi-synthetic datasets show that our method outperforms state-of-the-art baselines.

The advent of single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity and complexity in biological tissues. However, the nature of large, sparse scRNA-seq datasets and privacy regulations present challenges for efficient cell identification. Federated learning provides a solution, allowing efficient and private data use. Here, we introduce scFed, a unified federated learning framework that allows for benchmarking of four classification algorithms without violating data privacy, including single-cell-specific and general-purpose classifiers. We evaluated scFed using eight publicly available scRNA-seq datasets with diverse sizes, species and technologies, assessing its performance via intra-dataset and inter-dataset experimental setups. We find that scFed performs well on a variety of datasets with competitive accuracy to centralized models. Though Transformer-based model excels in centralized training, its performance slightly lags behind single-cell-specific model within the scFed framework, coupled with a notable time complexity concern. Our study not only helps select suitable cell identification methods but also highlights federated learning's potential for privacy-preserving, collaborative biomedical research.

Genome-wide association studies (GWAS) have been widely used for identifying potential risk variants in various diseases. A statistically meaningful GWAS typically requires a large sample size to detect disease-associated single nucleotide polymorphisms (SNPs). However, a single institution usually only possesses a limited number of samples. Therefore, cross-institutional partnerships are required to increase sample size and statistical power. However, cross-institutional partnerships offer significant challenges, a major one being data privacy. For example, the privacy awareness of people, the impact of data privacy leakages and the privacy-related risks are becoming increasingly important, while there is no de-identification standard available to safeguard genomic data sharing. In this paper, we introduce a novel privacy-preserving federated GWAS framework (iPRIVATES). Equipped with privacy-preserving federated analysis, iPRIVATES enables multiple institutions to jointly perform GWAS analysis without leaking patient-level genotyping data. Only aggregated local statistics are exchanged within the study network. In addition, we evaluate the performance of iPRIVATES through both simulated data and a real-world application for identifying potential risk variants in ankylosing spondylitis (AS). The experimental results showed that the strongest signal of AS-associated SNPs reside mostly around the human leukocyte antigen (HLA) regions. The proposed iPRIVATES framework achieved equivalent results as traditional centralized implementation, demonstrating its great potential in driving collaborative genomic research for different diseases while preserving data privacy.

MOTIVATION: The generalized linear mixed model (GLMM) is an extension of the generalized linear model (GLM) in which the linear predictor takes random effects into account. Given its power of precisely modeling the mixed effects from multiple sources of random variations, the method has been widely used in biomedical computation, for instance in the genome-wide association studies (GWASs) that aim to detect genetic variance significantly associated with phenotypes such as human diseases. Collaborative GWAS on large cohorts of patients across multiple institutions is often impeded by the privacy concerns of sharing personal genomic and other health data. To address such concerns, we present in this paper a privacy-preserving Expectation-Maximization (EM) algorithm to build GLMM collaboratively when input data are distributed to multiple participating parties and cannot be transferred to a central server. We assume that the data are horizontally partitioned among participating parties: i.e. each party holds a subset of records (including observational values of fixed effect variables and their corresponding outcome), and for all records, the outcome is regulated by the same set of known fixed effects and random effects. RESULTS: Our collaborative EM algorithm is mathematically equivalent to the original EM algorithm commonly used in GLMM construction. The algorithm also runs efficiently when tested on simulated and real human genomic data, and thus can be practically used for privacy-preserving GLMM construction. We implemented the algorithm for collaborative GLMM (cGLMM) construction in R. The data communication was implemented using the rsocket package. AVAILABILITY AND IMPLEMENTATION: The software is released in open source at https://github.com/huthvincent/cGLMM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Genomic data hold salient information about the characteristics of a living organism. Throughout the past decade, pinnacle developments have given us more accurate and inexpensive methods to retrieve genome sequences of humans. However, with the advancement of genomic research, there is a growing privacy concern regarding the collection, storage and analysis of such sensitive human data. Recent results show that given some background information, it is possible for an adversary to reidentify an individual from a specific genomic data set. This can reveal the current association or future susceptibility of some diseases for that individual (and sometimes the kinship between individuals) resulting in a privacy violation. Regardless of these risks, our genomic data hold much importance in analyzing the well-being of us and the future generation. Thus, in this article, we discuss the different privacy and security-related problems revolving around human genomic data. In addition, we will explore some of the cardinal cryptographic concepts, which can bring efficacy in secure and private genomic data computation. This article will relate the gaps between these two research areas-Cryptography and Genomics.

Machine learning applications are intensively utilized in various science fields, and increasingly the biomedical and healthcare sector. Applying predictive modeling to biomedical data introduces privacy and security concerns requiring additional protection to prevent accidental disclosure or leakage of sensitive patient information. Significant advancements in secure computing methods have emerged in recent years, however, many of which require substantial computational and/or communication overheads, which might hinder their adoption in biomedical applications. In this work, we propose SecureLR, a novel framework allowing researchers to leverage both the computational and storage capacity of Public Cloud Servers to conduct learning and predictions on biomedical data without compromising data security or efficiency. Our model builds upon homomorphic encryption methodologies with hardware-based security reinforcement through Software Guard Extensions (SGX), and our implementation demonstrates a practical hybrid cryptographic solution to address important concerns in conducting machine learning with public clouds.

Recent studies demonstrate that effective healthcare can benefit from using the human genomic information. Consequently, many institutions are using statistical analysis of genomic data, which are mostly based on genome-wide association studies (GWAS). GWAS analyze genome sequence variations in order to identify genetic risk factors for diseases. These studies often require pooling data from different sources together in order to unravel statistical patterns, and relationships between genetic variants and diseases. Here, the primary challenge is to fulfill one major objective: accessing multiple genomic data repositories for collaborative research in a privacy-preserving manner. Due to the privacy concerns regarding the genomic data, multi-jurisdictional laws and policies of cross-border genomic data sharing are enforced among different countries. In this article, we present SAFETY, a hybrid framework, which can securely perform GWAS on federated genomic datasets using homomorphic encryption and recently introduced secure hardware component of Intel Software Guard Extensions to ensure high efficiency and privacy at the same time. Different experimental settings show the efficacy and applicability of such hybrid framework in secure conduction of GWAS. To the best of our knowledge, this hybrid use of homomorphic encryption along with Intel SGX is not proposed to this date. SAFETY is up to 4.82 times faster than the best existing secure computation technique.

Gaining knowledge and actionable insights from complex, high-dimensional and heterogeneous biomedical data remains a key challenge in transforming health care. Various types of data have been emerging in modern biomedical research, including electronic health records, imaging, -omics, sensor data and text, which are complex, heterogeneous, poorly annotated and generally unstructured. Traditional data mining and statistical learning approaches typically need to first perform feature engineering to obtain effective and more robust features from those data, and then build prediction or clustering models on top of them. There are lots of challenges on both steps in a scenario of complicated data and lacking of sufficient domain knowledge. The latest advances in deep learning technologies provide new effective paradigms to obtain end-to-end learning models from complex data. In this article, we review the recent literature on applying deep learning technologies to advance the health care domain. Based on the analyzed work, we suggest that deep learning approaches could be the vehicle for translating big biomedical data into improved human health. However, we also note limitations and needs for improved methods development and applications, especially in terms of ease-of-understanding for domain experts and citizen scientists. We discuss such challenges and suggest developing holistic and meaningful interpretable architectures to bridge deep learning models and human interpretability.

Privacy concern in data sharing especially for health data gains particularly increasing attention nowadays. Now some patients agree to open their information for research use, which gives rise to a new question of how to effectively use the public information to better understand the private dataset without breaching privacy. In this paper, we specialize this question as selecting an optimal subset of the public dataset for M-estimators in the framework of differential privacy (DP) in [1]. From a perspective of non-interactive learning, we first construct the weighted private density estimation from the hybrid datasets under DP. Along the same line as [2], we analyze the accuracy of the DP M-estimators based on the hybrid datasets. Our main contributions are (i) we find that the bias-variance tradeoff in the performance of our M-estimators can be characterized in the sample size of the released dataset; (2) based on this finding, we develop an algorithm to select the optimal subset of the public dataset to release under DP. Our simulation studies and application to the real datasets confirm our findings and set a guideline in the real application.

In the age of big data, information sharing paradigm has been fundamentally changed: Data collection and consumption are increasingly decentralized (partly due to the advent of personal computing devices), and sharing personal data over the Internet becomes a prominent paradigm for new applications. One of these applications is Health Information Exchange (or HIE) where a patient's electronic medical record (EMR) was produced at one hospital, and is consumed by a physician in another hospital.

Motivation: We introduce PRINCESS, a privacy-preserving international collaboration framework for analyzing rare disease genetic data that are distributed across different continents. PRINCESS leverages Software Guard Extensions (SGX) and hardware for trustworthy computation. Unlike a traditional international collaboration model, where individual-level patient DNA are physically centralized at a single site, PRINCESS performs a secure and distributed computation over encrypted data, fulfilling institutional policies and regulations for protected health information. Results: To demonstrate PRINCESS' performance and feasibility, we conducted a family-based allelic association study for Kawasaki Disease, with data hosted in three different continents. The experimental results show that PRINCESS provides secure and accurate analyses much faster than alternative solutions, such as homomorphic encryption and garbled circuits (over 40 000× faster). Availability and Implementation: https://github.com/achenfengb/PRINCESS_opensource. Contact: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.

MOTIVATION: Inappropriate disclosure of human genomes may put the privacy of study subjects and of their family members at risk. Existing privacy-preserving mechanisms for Genome-Wide Association Studies (GWAS) mainly focus on protecting individual information in case-control studies. Protecting privacy in family-based studies is more difficult. The transmission disequilibrium test (TDT) is a powerful family-based association test employed in many rare disease studies. It gathers information about families (most frequently involving parents, affected children and their siblings). It is important to develop privacy-preserving approaches to disclose TDT statistics with a guarantee that the risk of family 're-identification' stays below a pre-specified risk threshold. 'Re-identification' in this context means that an attacker can infer that the presence of a family in a study. METHODS: In the context of protecting family-level privacy, we developed and evaluated a suite of differentially private (DP) mechanisms for TDT. They include Laplace mechanisms based on the TDT test statistic, P-values, projected P-values and exponential mechanisms based on the TDT test statistic and the shortest Hamming distance (SHD) score. RESULTS: Using simulation studies with a small cohort and a large one, we showed that that the exponential mechanism based on the SHD score preserves the highest utility and privacy among all proposed DP methods. We provide a guideline on applying our DP TDT in a real dataset in analyzing Kawasaki disease with 187 families and 906 SNPs. There are some limitations, including: (1) the performance of our implementation is slow for real-time results generation and (2) handling missing data is still challenging. AVAILABILITY AND IMPLEMENTATION: The software dpTDT is available in https://github.com/mwgrassgreen/dpTDT. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The Global Alliance for Genomics and Health (GA4GH) created the Beacon Project as a means of testing the willingness of data holders to share genetic data in the simplest technical context-a query for the presence of a specified nucleotide at a given position within a chromosome. Each participating site (or "beacon") is responsible for assuring that genomic data are exposed through the Beacon service only with the permission of the individual to whom the data pertains and in accordance with the GA4GH policy and standards.While recognizing the inference risks associated with large-scale data aggregation, and the fact that some beacons contain sensitive phenotypic associations that increase privacy risk, the GA4GH adjudged the risk of re-identification based on the binary yes/no allele-presence query responses as acceptable. However, recent work demonstrated that, given a beacon with specific characteristics (including relatively small sample size and an adversary who possesses an individual's whole genome sequence), the individual's membership in a beacon can be inferred through repeated queries for variants present in the individual's genome.In this paper, we propose three practical strategies for reducing re-identification risks in beacons. The first two strategies manipulate the beacon such that the presence of rare alleles is obscured; the third strategy budgets the number of accesses per user for each individual genome. Using a beacon containing data from the 1000 Genomes Project, we demonstrate that the proposed strategies can effectively reduce re-identification risk in beacon-like datasets.

We present an efficient approach to text localization. We restrict our attention to the text localization and refer to our method as 'text search'. In particular, we pre-trained a text detection ConvNet which skip the region proposal process, and integrates bounding boxes and text confidence score into the output layer. Our approach achieved similar high precision with [1], and acceptable level of recall.

MOTIVATION: Genome-wide association studies (GWAS) have been widely used in discovering the association between genotypes and phenotypes. Human genome data contain valuable but highly sensitive information. Unprotected disclosure of such information might put individual's privacy at risk. It is important to protect human genome data. Exact logistic regression is a bias-reduction method based on a penalized likelihood to discover rare variants that are associated with disease susceptibility. We propose the HEALER framework to facilitate secure rare variants analysis with a small sample size. RESULTS: We target at the algorithm design aiming at reducing the computational and storage costs to learn a homomorphic exact logistic regression model (i.e. evaluate P-values of coefficients), where the circuit depth is proportional to the logarithmic scale of data size. We evaluate the algorithm performance using rare Kawasaki Disease datasets. AVAILABILITY AND IMPLEMENTATION: Download HEALER at http://research.ucsd-dbmi.org/HEALER/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

OBJECTIVE: To develop an accurate logistic regression (LR) algorithm to support federated data analysis of vertically partitioned distributed data sets. MATERIAL AND METHODS: We propose a novel technique that solves the binary LR problem by dual optimization to obtain a global solution for vertically partitioned data. We evaluated this new method, VERTIcal Grid lOgistic regression (VERTIGO), in artificial and real-world medical classification problems in terms of the area under the receiver operating characteristic curve, calibration, and computational complexity. We assumed that the institutions could "align" patient records (through patient identifiers or hashed "privacy-protecting" identifiers), and also that they both had access to the values for the dependent variable in the LR model (eg, that if the model predicts death, both institutions would have the same information about death). RESULTS: The solution derived by VERTIGO has the same estimated parameters as the solution derived by applying classical LR. The same is true for discrimination and calibration over both simulated and real data sets. In addition, the computational cost of VERTIGO is not prohibitive in practice. DISCUSSION: There is a technical challenge in scaling up federated LR for vertically partitioned data. When the number of patients m is large, our algorithm has to invert a large Hessian matrix. This is an expensive operation of time complexity O(m(3)) that may require large amounts of memory for storage and exchange of information. The algorithm may also not work well when the number of observations in each class is highly imbalanced. CONCLUSION: The proposed VERTIGO algorithm can generate accurate global models to support federated data analysis of vertically partitioned data.

Biomedical Informatics is a growing interdisciplinary field in which research topics and citation trends have been evolving rapidly in recent years. To analyze these data in a fast, reproducible manner, automation of certain processes is needed. JAMIA is a "generalist" journal for biomedical informatics. Its articles reflect the wide range of topics in informatics. In this study, we retrieved Medical Subject Headings (MeSH) terms and citations of JAMIA articles published between 2009 and 2014. We use tensors (i.e., multidimensional arrays) to represent the interaction among topics, time and citations, and applied tensor decomposition to automate the analysis. The trends represented by tensors were then carefully interpreted and the results were compared with previous findings based on manual topic analysis. A list of most cited JAMIA articles, their topics, and publication trends over recent years is presented. The analyses confirmed previous studies and showed that, from 2012 to 2014, the number of articles related to MeSH terms Methods, Organization & Administration, and Algorithms increased significantly both in number of publications and citations. Citation trends varied widely by topic, with Natural Language Processing having a large number of citations in particular years, and Medical Record Systems, Computerized remaining a very popular topic in all years.

OBJECTIVE: The Cox proportional hazards model is a widely used method for analyzing survival data. To achieve sufficient statistical power in a survival analysis, it usually requires a large amount of data. Data sharing across institutions could be a potential workaround for providing this added power. METHODS AND MATERIALS: The authors develop a web service for distributed Cox model learning (WebDISCO), which focuses on the proof-of-concept and algorithm development for federated survival analysis. The sensitive patient-level data can be processed locally and only the less-sensitive intermediate statistics are exchanged to build a global Cox model. Mathematical derivation shows that the proposed distributed algorithm is identical to the centralized Cox model. RESULTS: The authors evaluated the proposed framework at the University of California, San Diego (UCSD), Emory, and Duke. The experimental results show that both distributed and centralized models result in near-identical model coefficients with differences in the range [Formula: see text] to [Formula: see text]. The results confirm the mathematical derivation and show that the implementation of the distributed model can achieve the same results as the centralized implementation. LIMITATION: The proposed method serves as a proof of concept, in which a publicly available dataset was used to evaluate the performance. The authors do not intend to suggest that this method can resolve policy and engineering issues related to the federated use of institutional data, but they should serve as evidence of the technical feasibility of the proposed approach.Conclusions WebDISCO (Web-based Distributed Cox Regression Model; https://webdisco.ucsd-dbmi.org:8443/cox/) provides a proof-of-concept web service that implements a distributed algorithm to conduct distributed survival analysis without sharing patient level data.

SUMMARY: MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours->600% end-to-end performance improvement over state of the art. MAGI's salient features are (i) transfer of large input files in native FASTA with Qualities (FASTQ) format through drag-and-drop operations, (ii) rapid prediction of microRNA target genes leveraging parallel computing with GPU devices, (iii) all-in-one analytics with novel feature extraction, statistical test for differential expression and diagnostic plot generation for quality control and (iv) interactive visualization and exploration of results in web reports that are readily available for publication. AVAILABILITY AND IMPLEMENTATION: MAGI relies on the Node.js JavaScript framework, along with NVIDIA CUDA C, PHP: Hypertext Preprocessor (PHP), Perl and R. It is freely available at http://magi.ucsd.edu.

BACKGROUND AND OBJECTIVE: Short-read sequencing is becoming the standard of practice for the study of structural variants associated with disease. However, with the growth of sequence data largely surpassing reasonable storage capability, the biomedical community is challenged with the management, transfer, archiving, and storage of sequence data. METHODS: We developed Hierarchical mUlti-reference Genome cOmpression (HUGO), a novel compression algorithm for aligned reads in the sorted Sequence Alignment/Map (SAM) format. We first aligned short reads against a reference genome and stored exactly mapped reads for compression. For the inexact mapped or unmapped reads, we realigned them against different reference genomes using an adaptive scheme by gradually shortening the read length. Regarding the base quality value, we offer lossy and lossless compression mechanisms. The lossy compression mechanism for the base quality values uses k-means clustering, where a user can adjust the balance between decompression quality and compression rate. The lossless compression can be produced by setting k (the number of clusters) to the number of different quality values. RESULTS: The proposed method produced a compression ratio in the range 0.5-0.65, which corresponds to 35-50% storage savings based on experimental datasets. The proposed approach achieved 15% more storage savings over CRAM and comparable compression ratio with Samcomp (CRAM and Samcomp are two of the state-of-the-art genome compression algorithms). The software is freely available at https://sourceforge.net/projects/hierachicaldnac/with a General Public License (GPL) license. LIMITATION: Our method requires having different reference genomes and prolongs the execution time for additional alignments. CONCLUSIONS: The proposed multi-reference-based compression algorithm for aligned reads outperforms existing single-reference based algorithms.

Summary form only given. Distributed Source Coding (DSC) is rapidly gaining popularity, and has many good applications. However, some important correlations are sometimes omitted, such as temporal correlation. In this paper, we consider the correlations of the source data both in spatial and temporal domains for DSC decoding. And this is equally to integrate a Kalman filter in our algorithm. We tested our algorithm on the practical temperature network, and the results turn out it achieved better performance than the algorithm without temporal correlation.

In this paper, we develop a novel genome compression framework based on distributed source coding (DSC)[3], which is specially tailored to the need of miniaturized devices. At the encoder side, subsequences with adaptive code length can be compressed flexibly through either low complexity DSC based syndrome coding or hash coding with the decision determined by the existence of variations between source and reference known from the decoder feedback. Moreover, to tackle the variations between source and reference at the decoder, we carefully designed a factor graph based low-density parity-check (LDPC) decoder, which automatically detects insertion, deletion and substitution.

UNLABELLED: WebGLORE is a free web service that enables privacy-preserving construction of a global logistic regression model from distributed datasets that are sensitive. It only transfers aggregated local statistics (from participants) through Hypertext Transfer Protocol Secure to a trusted server, where the global model is synthesized. WebGLORE seamlessly integrates AJAX, JAVA Applet/Servlet and PHP technologies to provide an easy-to-use web service for biomedical researchers to break down policy barriers during information exchange. AVAILABILITY AND IMPLEMENTATION: http://dbmi-engine.ucsd.edu/webglore3/. WebGLORE can be used under the terms of GNU general public license as published by the Free Software Foundation.

Estimating accurately channel noise has significant impact on the performance of channel coding. In this paper, we present a low complexity online estimator at the decoder side for low-density parity check (LDPC) codes over additive white Gaussian noise (AWGN) channels with a time-varying noise. The proposed algorithm is obtained by modeling the channel statistic as a Bayesian inference problem on a factor graph. Since BP algorithm cannot adapt efficiently to the statistical change of SNR in an AWGN channel, we apply the Laplace propagation (LP) algorithm on the proposed algorithm. Through simulations, we show that the proposed algorithm can simultaneously decode LDPC codes and estimate the time-varying SNR at the bit-level, which enhance the BP decoding performance. Moreover, the proposed LP estimator shows a very low computational complexity.

In order to estimate the amount of energy that will be generated by a wind farm and provide efficient power distribution planning, it is necessary to deliver information of wind speed at all wind turbines. This paper proposes a scheme for compressing wind speed measurements exploiting both temporal and spatial correlation between the turbine readings via distributed source coding. The proposed scheme relies on a correlation model based on true measurements. A compression scheme proposed is of low encoding complexity and uses a particle-filtering based belief propagation decoder that adaptively estimates the nonstationary noise of the correlation model. Simulation results using realistic models show significant performance improvements compared to the scheme that does not dynamically refine correlation.

Distributed video coding (DVC) is rapidly gaining popularity as a low cost, robust video coding solution, that reduces video encoding complexity. DVC is built on distributed source coding (DSC) principles where correlation between sources to be compressed is exploited at the decoder side. In the case of DVC, a current frame available only at the encoder is estimated at the decoder with side information generated from other frames available at the decoder. One of the main challenges in DVC design is that correlation among the source and side information needs to be estimated online and as accurately as possible. Since correlation dynamically changes with the scene, in order to exploit the robustness of DSC code designs, we integrate particle filtering (PF) with standard belief propagation (BP) decoding for inference on one joint factor graph to estimate correlation among source and side information. Correlation estimation is performed online as it is carried out jointly with decoding of the graph-based DSC code. Moreover, we demonstrate our joint bit-plane decoding with adaptive correlation estimation schemes within state-of-the-art DVC systems, which are transform-domain based with a feedback channel for rate adaptation. Experimental results show that our proposed system gives a significant performance improvement compared to the benchmark state-of-the-art DISCOVER codec (including correlation estimation) and the case without dynamic PF tracking, due to improved knowledge of timely correlation statistics via the combination of joint bit-plane decoding and particle-based BP (PBP) tracking.

We propose an adaptive distributed compression solution using particle filtering that tracks correlation, as well as performing disparity estimation, at the decoder side. The proposed algorithm is tested on the stereo solar images captured by the twin satellites system of NASA's Solar TErrestrial RElations Observatory (STEREO) project. Our experimental results show improved compression performance w.r.t. to a benchmark compression scheme, accurate correlation estimation by our proposed particle-based belief propagation algorithm, and significant peak signal-to-noise ratio improvement over traditional separate bit-plane decoding without dynamic correlation and disparity estimation.

In this paper, we propose a system using video cameras to perform vehicle identification. We tackle this problem by reconstructing an input by using multiple linear regression models and compressed sensing, which provide new ways to deal with three crucial issues in vehicle identification, namely, feature extraction, online vehicle identification database buildup , and robustness to occlusions and misalignment. The results show the capability of the proposed approach.

Belief propagation (BP) is a powerful algorithm to decode low- density parity check (LDPC) codes over additive white Gaussian noise (AWGN) channels. However, the traditional BP algorithm cannot adapt efficiently to the statistical change of SNR in an AWGN channel. This paper proposes an adaptive scheme that incorporates expectation propagation (EP) into the BP based LDPC decoding process. The proposed scheme is able to perform online estimation of both stationary and time-varying SNR at the bit-level, and enhance the BP decoding performance simultaneously. Moreover, the proposed EP estimator shows a very fast convergence speed, and the additional computational overhead of the proposed decoder is less than 10% of the standard BP decoder.

In this paper, we propose an adaptive Distributed Video Coding (DVC) scheme that dynamically estimates correlation statistics of the scene in a video sequence to enhance belief-propagation (BP) Slepian-Wolf (SW) decoding. In order to exploit the robustness of distributed source coding (DSC) designs, we integrate particle filtering with standard BP decoding in one factor graph to estimate online correlation among source and side information. Our proposed system boasts improved performance over classical DVC without correlation estimation, due to improved knowledge of correlation statistics via the combination of bit-plane coding and particle-based BP tracking in each frame, as shown by our results.

Acquiring and processing astronomical images is becoming increasingly important for accurate space weather prediction and expanding our understanding about the Sun and the Universe. These images are often rich in content, large in size and dynamic range. Efficient, low-complexity compression solutions are essential to reduce onboard storage, processing, and communication resources. Distributed compression is a promising technique for onboard coding of solar images by exploiting correlation between successively acquired images. In this paper we propose an adaptive distributed compression solution using particle filtering that tracks correlation, as well as performing disparity estimation, at the decoder side. The proposed algorithm is tested on the stereo solar images captured by the twin satellites system of NASA's STEREO project. Our experimental results show the significant PSNR improvement over traditional separate bit-plane decoding without dynamic correlation and disparity estimation.

A major difficulty that plagues the practical use of Slepian-Wolf (SW) coding (and distributed source coding in general) is that the precise correlation among sources needs to be known a priori. To resolve this problem, we propose an adaptive asymmetric SW decoding scheme using particle based belief propagation (PBP). We explain the adaptive scheme for asymmetric setup in detail and then further extend it to the non-asymmetric setup based on the code partitioning approach. Moreover, we introduce a Metropolis-Hastings (MH) algorithm in the resampling step, which efficiently decreases the number of simulation iterations. We show through experiments that the proposed algorithm can simultaneously reconstruct the compressed sources and estimate the joint correlation among sources. Further, comparing to the conventional SW decoder based on standard belief propagation, the proposed approach can achieve higher compression under varying correlation statistics.

Belief propagation (BP) is a powerful algorithm to decode low-density parity check (LDPC) codes over additive white Gaussian noise (AWGN) channels. However, the traditional BP algorithm cannot adapt efficiently to the statistical change of SNR in an AWGN channel. This paper proposes an adaptive scheme that incorporates a particle filtering (PF) algorithm into the BP based LDPC decoding process. The proposed scheme is capable to perform online estimation of time-varying SNR at the bit-level and enhance the BP decoding performance simultaneously.

This paper addresses the problem of distributed source coding (DSC) of binary sources with unknown varying correlation statistics over erasure channels. We propose an adaptive asymmetric Slepian-Wolf (SW) decoding scheme using particle-based belief propagation (BP) based on Raptor codes. We show through the experiments that the proposed algorithm can simultaneously reconstruct the compressed sources and estimate the correlation between source and side information. Moreover, compared to the conventional Raptor decoder, the proposed approach can achieve a higher compression ratio and provide stronger erasure protection under unknown varying correlation statistics. The ability to estimate the statistical correlation in the code structure makes our approach very useful for real applications.

In this paper we propose an adaptive Wyner-Ziv (WZ) coding scheme for non-binary correlated sources with side information at the decoder. At the encoder, a low density parity check (LDPC) code is employed to implement Slepian-Wolf (SW) coding for each bit-plane independently. The joint "source-channel" decoder, which combines SW decoding and dequantizing in a single step, preserves the symbol-domain correlation and decreases the distortion. Moreover, the incorporation of particle-based belief propagation (BP) in the decoder can extend the scheme to perform an online estimation of the correlation and enhance the BP decoding performance simultaneously. Our proposed framework is universal and can be applied to any parametric correlation model.

A major difficulty that plagues the practical use of Slepian-Wolf coding (and distributed source coding in general) is that the precise correlation among sources need to be known a priori. To resolve this problem, we have proposed an adaptive asymmetric Slepian-Wolf decoding scheme using particle filtering based belief propagation in our recent work. In this paper, we extend the adaptive scheme to the non-asymmetric setup based on the code partitioning approach. We show through experiments that the proposed algorithm can simultaneously reconstruct the compressed sources and estimate the joint correlation among sources. Further, comparing to the conventional Slepian-Wolf decoder based on standard belief propagation, the proposed approach can achieve higher compression under varying correlation statistics.