Federated Learning Attacks and Defenses: A Survey

In terms of artificial intelligence, there are several security and privacy deficiencies in the traditional centralized training methods of machine learning models by a server. To address this limitation, federated learning (FL) has been proposed and is known for breaking down ``data silos" and protecting the privacy of users. However, FL has not yet gained popularity in the industry, mainly due to its security, privacy, and high cost of communication. For the purpose of advancing the research in this field, building a robust FL system, and realizing the wide application of FL, this paper sorts out the possible attacks and corresponding defenses of the current FL system systematically. Firstly, this paper briefly introduces the basic workflow of FL and related knowledge of attacks and defenses. It reviews a great deal of research about privacy theft and malicious attacks that have been studied in recent years. Most importantly, in view of the current three classification criteria, namely the three stages of machine learning, the three different roles in federated learning, and the CIA (Confidentiality, Integrity, and Availability) guidelines on privacy protection, we divide attack approaches into two categories according to the training stage and the prediction stage in machine learning. Furthermore, we also identify the CIA property violated for each attack method and potential attack role. Various defense mechanisms are then analyzed separately from the level of privacy and security. Finally, we summarize the possible challenges in the application of FL from the aspect of attacks and defenses and discuss the future development direction of FL systems. In this way, the designed FL system has the ability to resist different attacks and is more secure and stable.Comment: IEEE BigData. 10 pages, 2 figures, 2 table

Selection and mutation on microRNA target sequences during rice evolution

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) posttranscriptionally down-regulate gene expression by binding target mRNAs. Analysis of the evolution of miRNA binding sites is helpful in understanding the co-evolution between miRNAs and their targets. To understand this process in plants a comparative analysis of miRNA-targeted duplicated gene pairs derived from a well-documented whole genome duplication (WGD) event in combination with a population genetics study of six experimentally validated miRNA binding sites in rice (<it>O. sativa</it>) was carried out.</p> <p>Results</p> <p>Of the 1,331 pairs of duplicate genes from the WGD, 41 genes (29 pairs) were computationally predicted to be miRNA targets. Sequence substitution analysis indicated that the synonymous substitution rate was significantly lower in the miRNA binding sites than their 5' and 3' flanking regions. Of the 29 duplicated gene pairs, 17 have only one paralog been targeted by a miRNA. This could be due to either gain of a miRNA binding site after the WGD or because one of the duplicated genes has escaped from being a miRNA target after the WGD (loss of miRNA binding site). These possibilities were distinguished by separating miRNAs conserved in both dicots and monocot plants from rice-specific miRNAs and by phylogenetic analysis of miRNA target gene families. The gain/loss rate of miRNA binding sites was estimated to be 3.0 × 10^-9gain/loss per year. Most (70.6%) of the gains/losses were due to nucleotide mutation. By analysis of cultivated (<it>O. sativa</it>; <it>n </it>= 30) and wild (<it>O. rufipogon</it>; <it>n </it>= 15) rice populations, no segregating site was observed in six miRNA binding sites whereas 0.12–0.20 SNPs per 21-nt or 1.53–1.80 × 10^-3of the average pairwise nucleotide diversity (π) were found in their flanking regions.</p> <p>Conclusion</p> <p>Both molecular evolution and population genetics support the hypothesis that conservation of miRNA binding sites is maintained by purifying selection through elimination of deleterious alleles. Nucleotide mutations play a major role in the gain/loss of miRNA binding sites during evolution.</p

Identification of wounding and topping responsive small RNAs in tobacco (Nicotiana tabacum)

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are two major classes of small RNAs. They play important regulatory roles in plants and animals by regulating transcription, stability and/or translation of target genes in a sequence-complementary dependent manner. Over 4,000 miRNAs and several classes of siRNAs have been identified in plants, but in tobacco only computational prediction has been performed and no tobacco-specific miRNA has been experimentally identified. Wounding is believed to induce defensive response in tobacco, but the mechanism responsible for this response is yet to be uncovered.</p> <p>Results</p> <p>To get insight into the role of small RNAs in damage-induced responses, we sequenced and analysed small RNA populations in roots and leaves from wounding or topping treated tobacco plants. In addition to confirmation of expression of 27 known miRNA families, we identified 59 novel tobacco-specific miRNA members of 38 families and a large number of loci generating phased 21- or 24-nt small RNAs (including ta-siRNAs). A number of miRNAs and phased small RNAs were found to be responsive to wounding or topping treatment. Targets of small RNAs were further surveyed by degradome sequencing.</p> <p>Conclusions</p> <p>The expression changes of miRNAs and phased small RNAs responsive to wounding or topping and identification of defense related targets for these small RNAs suggest that the inducible defense response in tobacco might be controlled by pathways involving small RNAs.</p

Post-Domestication Selection in the Maize Starch Pathway

Modern crops have usually experienced domestication selection and subsequent genetic improvement (post-domestication selection). Chinese waxy maize, which originated from non-glutinous domesticated maize (Zea mays ssp. mays), provides a unique model for investigating the post-domestication selection of maize. In this study, the genetic diversity of six key genes in the starch pathway was investigated in a glutinous population that included 55 Chinese waxy accessions, and a selective bottleneck that resulted in apparent reductions in diversity in Chinese waxy maize was observed. Significant positive selection in waxy (wx) but not amylose extender1 (ae1) was detected in the glutinous population, in complete contrast to the findings in non-glutinous maize, which indicated a shift in the selection target from ae1 to wx during the improvement of Chinese waxy maize. Our results suggest that an agronomic trait can be quickly improved into a target trait with changes in the selection target among genes in a crop pathway

Mapping epistasis and environment × QTX interaction based on four -omics genotypes for the detected QTX loci controlling complex traits in tobacco

Using newly developed methods and software, association mapping was conducted for chromium content and total sugar in tobacco leaf, based on four -omics datasets. Our objective was to collect data on genotype and phenotype for 60 leaf samples at four developmental stages, from three plant architectural positions and for three cultivars that were grown in two locations. Association mapping was conducted to detect genetic variants at quantitative trait SNP (QTS) loci, quantitative trait transcript (QTT) differences, quantitative trait protein (QTP) variability, and quantitative trait metabolite (QTM) changes, which can be summarized as QTX locus variation. The total heritabilities of the four -omics loci for both traits tested were 23.60% for epistasis and 15.26% for treatment interaction. Epistasis and environment × treatment interaction had important impacts on complex traits at all -omics levels. For decreasing chromium content and increasing total sugar in tobacco leaf, six methylated loci can be directly used for marker-assisted selection, and expression of ten QTTs, seven QTPs and six QTMs can be modified by selection or cultivation

Bulked Segregant Analysis Coupled with Whole-Genome Sequencing (BSA-Seq) Mapping Identifies a Novel pi21 Haplotype Conferring Basal Resistance to Rice Blast Disease

Basal or partial resistance has been considered race-non-specific and broad-spectrum. Therefore, the identification of genes or quantitative trait loci (QTLs) conferring basal resistance and germplasm containing them is of significance in breeding crops with durable resistance. In this study, we performed a bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) to identify QTLs controlling basal resistance to blast disease in an F2 population derived from two rice varieties, 02428 and LiXinGeng (LXG), which differ significantly in basal resistance to rice blast. Four candidate QTLs, qBBR-4, qBBR-7, qBBR-8, and qBBR-11, were mapped on chromosomes 4, 7, 8, and 11, respectively. Allelic and genotypic association analyses identified a novel haplotype of the durable blast resistance gene pi21 carrying double deletions of 30 bp and 33 bp in 02428 (pi21-2428) as a candidate gene of qBBR-4. We further assessed haplotypes of Pi21 in 325 rice accessions, and identified 11 haplotypes among the accessions, of which eight were novel types. While the resistant pi21 gene was found only in japonica before, three Chinese indica varieties, ShuHui881, Yong4, and ZhengDa4Hao, were detected carrying the resistant pi21-2428 allele. The pi21-2428 allele and pi21-2428-containing rice germplasm, thus, provide valuable resources for breeding rice varieties, especially indica rice varieties, with durable resistance to blast disease. Our results also lay the foundation for further identification and functional characterization of the other three QTLs to better understand the molecular mechanisms underlying rice basal resistance to blast disease

A host plant genome (Zizania latifolia) after a century-long endophyte infection

Despite the importance of host-microbe interactions in natural ecosystems, agriculture and medicine, the impact of long-term (especially decades or longer) microbial colonization on the dynamics of host genomes is not well understood. The vegetable crop Jiaobai' with enlarged edible stems was domesticated from wild Zizania latifolia (Oryzeae) approximately 2000years ago as a result of persistent infection by a fungal endophyte, Ustilago esculenta. Asexual propagation via infected rhizomes is the only means of Jiaobai production, and the Z.latifolia-endophyte complex has been maintained continuously for two centuries. Here, genomic analysis revealed that cultivated Z.latifolia has a significantly smaller repertoire of immune receptors compared with wild Z.latifolia. There are widespread gene losses/mutations and expression changes in the plant-pathogen interaction pathway in Jiaobai. These results show that continuous long-standing endophyte association can have a major effect on the evolution of the structural and transcriptomic components of the host genome. Significance Statement This study reports the genome of Jiaobai, a unique crop species domesticated from wild Zizania latifolia (Oryzeae) as a consequence of persistent infection by a fungal endophyte. Cultivated Z.latifolia (Jiaobai') has a significantly smaller repertoire of immune receptors compared with wild Z.latifolia, showing that continuous long-standing endophyte association can have a major effect on the evolution of the host genome