Defense Against Model Extraction Attacks on Recommender Systems

The robustness of recommender systems has become a prominent topic within the research community. Numerous adversarial attacks have been proposed, but most of them rely on extensive prior knowledge, such as all the white-box attacks or most of the black-box attacks which assume that certain external knowledge is available. Among these attacks, the model extraction attack stands out as a promising and practical method, involving training a surrogate model by repeatedly querying the target model. However, there is a significant gap in the existing literature when it comes to defending against model extraction attacks on recommender systems. In this paper, we introduce Gradient-based Ranking Optimization (GRO), which is the first defense strategy designed to counter such attacks. We formalize the defense as an optimization problem, aiming to minimize the loss of the protected target model while maximizing the loss of the attacker's surrogate model. Since top-k ranking lists are non-differentiable, we transform them into swap matrices which are instead differentiable. These swap matrices serve as input to a student model that emulates the surrogate model's behavior. By back-propagating the loss of the student model, we obtain gradients for the swap matrices. These gradients are used to compute a swap loss, which maximizes the loss of the student model. We conducted experiments on three benchmark datasets to evaluate the performance of GRO, and the results demonstrate its superior effectiveness in defending against model extraction attacks

Winter hardiness of \u3ci\u3eMiscanthus\u3c/i\u3e (III): Genome‐wide association and genomic prediction for overwintering ability in \u3ci\u3eMiscanthus sinensis\u3c/i\u3e

Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar, M. ×giganteus (M×g) ‘1993–1780’, in regions where average annual minimum temperatures are −26.1°C (USDA hardiness zone 5) or lower poses a pressing need to develop new cultivars with superior cold tolerance. To facilitate breeding of Miscanthus, this study characterized phenotypic and genetic variation of overwintering ability in an M. sinensis germplasm panel consisting of 564 accessions, evaluated in field trials at three locations in North America and two in Asia. Genome‐wide association (GWA) and genomic prediction analyses were performed. The Korea/N China M. sinensis genetic group is a valuable gene pool for cold tolerance. The Yangtze‐Qinling, Southern Japan, and Northern Japan genetic groups were also potential sources of cold tolerance. A total of 73 marker–trait associations were detected for overwintering ability. Estimated breeding value for overwintering ability based on these 73 markers could explain 55% of the variation for first winter overwintering ability among M. sinensis. Average genomic prediction ability for overwintering ability across 50 fivefold cross‐validations was high (~0.73) after accounting for population structure. Common genomic regions for overwintering ability were detected by GWA analyses and a previous parallel QTL mapping study using three interconnected biparental F1 populations. One QTL on Miscanthus LG 8 encompassed five GWA hits and a known cold‐responsive gene, COR47. The other overwintering ability QTL on Miscanthus LG 11 contained two GWA hits and three known cold stress‐related genes, carboxylesterase 13 (CEX13), WRKY2 transcription factor, and cold shock domain (CSDP1). Miscanthus accessions collected from high latitude locations with cold winters had higher rates of overwintering, and more alleles for overwintering, than accessions collected from southern locations with mild winters

Molecular cloning and expression profile of β-ketoacyl-acp synthase gene from tung tree (Vernicia fordii Hemsl.)

Tung tree (Vernicia fordii) is an important woody oil tree. Tung tree seeds contain 50-60% oil with approximately 80 mole α-eleostearic acid (9 cis, 11 trans, 13 trans octadecatrienoic acid). Fatty acid synthesis is catalyzed by the concerted action of acetyl-CoA carboxylase and fatty acid synthase, a multienzyme complex including β-ketoacyl-acyl-carrier-protein synthase (KAS). Little is known about KAS in tung tree. The objective of this study was to clone KAS genes and analyze their expression profiles in tung tree. A full-length cDNA encoding KAS III and a partial cDNA encoding KAS II were isolated from tung tree by PCR cloning using degenerate primers and rapid amplification of cDNA ends system. The full-length cDNA of VfKAS III was 1881 bp in length with an open reading frame of 1212 bp. VfKAS III genomic DNA was also isolated and sequenced, which contained 8 exons in 5403 bp length. The deduced VfKAS III protein shared approximately 80% identity with homologous KAS IIIs from other plants. Quantitative PCR analysis revealed that KAS II and KAS III were expressed in all of the tissues and organs tested but exhibited different expression patterns in tung tree. The expression levels of KAS II in young tissues were much lower than those in mature tissues, whereas the highest expression levels of KAS III were observed in young stem and young leaf. These results should facilitate further studies on the regulation of tung oil biosynthesis by KAS in tung tree

Identification, Classification and Differential Expression of Oleosin Genes in Tung Tree (<i>Vernicia fordii</i>)

<div><p>Triacylglycerols (TAG) are the major molecules of energy storage in eukaryotes. TAG are packed in subcellular structures called oil bodies or lipid droplets. Oleosins (OLE) are the major proteins in plant oil bodies. Multiple isoforms of OLE are present in plants such as tung tree (<i>Vernicia fordii</i>), whose seeds are rich in novel TAG with a wide range of industrial applications. The objectives of this study were to identify OLE genes, classify OLE proteins and analyze OLE gene expression in tung trees. We identified five tung tree OLE genes coding for small hydrophobic proteins. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that the five tung OLE genes represented the five OLE subfamilies and all contained the “proline knot” motif (PX5SPX3P) shared among 65 OLE from 19 tree species, including the sequenced genomes of <i>Prunus persica</i> (peach), <i>Populus trichocarpa</i> (poplar), <i>Ricinus communis</i> (castor bean), <i>Theobroma cacao</i> (cacao) and <i>Vitis vinifera</i> (grapevine). Tung OLE1, OLE2 and OLE3 belong to the S type and OLE4 and OLE5 belong to the SM type of <i>Arabidopsis</i> OLE. TaqMan and SYBR Green qPCR methods were used to study the differential expression of OLE genes in tung tree tissues. Expression results demonstrated that 1) All five OLE genes were expressed in developing tung seeds, leaves and flowers; 2) OLE mRNA levels were much higher in seeds than leaves or flowers; 3) OLE1, OLE2 and OLE3 genes were expressed in tung seeds at much higher levels than OLE4 and OLE5 genes; 4) OLE mRNA levels rapidly increased during seed development; and 5) OLE gene expression was well-coordinated with tung oil accumulation in the seeds. These results suggest that tung OLE genes 1–3 probably play major roles in tung oil accumulation and/or oil body development. Therefore, they might be preferred targets for tung oil engineering in transgenic plants.</p></div

Relative levels of OLE gene expression in developing tung seeds, leaves and flowers.

<p>(A) TaqMan qPCR. The qPCR reaction mixtures contained 25 ng of RNA-equivalent cDNA from tung seeds and 200 nM of each primer and probe. (B) SYBR Green qPCR. The qPCR reaction mixtures contained 5 ng of RNA-equivalent cDNA from various stages of tung seed, leaves and flowers and 200 nM of each primer. The means of mRNA expression levels calculated from two qPCR assays in each seed stage using Rpl19b as the reference mRNA is presented. The results using Gapdh and Ubl as the reference mRNA are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088409#pone.0088409.s005" target="_blank">Figure S5</a> (TaqMan qPCR assay) and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088409#pone.0088409.s006" target="_blank">Figure S6</a> (SYBR Green qPCR assay).</p

Phylogenetic analysis of 65 OLE from 19 tree species and 23 reference OLE from <i>Arabidopsis</i>.

<p>(A) Phylogenetic analysis of OLE from tung tree and other tree species. (B) Phylogenetic analysis of OLE from tung tree and <i>Arabidopsis</i>. Tung OLE are highlighted in red. The names of 17 subfamilies from 23 <i>Arabidopsis</i> OLE are highlighted in green. S, seed-specific OLE, SM, seed-microspore-specific OLE, T, tapetum-specific OLE. The abbreviations of the organisms are: Ath, <i>Arabidopsis thaliana</i>; Car, <i>Coffea arabica</i> (coffee); Cca, <i>Coffea canephora</i> (coffee); Cav, <i>Corylus avellana</i> (hazelnut); Col, <i>Camellia oleifera</i> (tea oil); Csi, <i>Citrus sinensis</i> (orange); Egu, <i>Elaeis guineensis</i> (oil palm); Fpu, <i>Ficus pumila</i> (climbing fig); Jcu, <i>Jatropha curcas</i> (barbados nut); Jre, <i>Juglans regia</i> (walnut); Oeu, <i>Olea europaea</i> (olive); Pam, <i>Persea Americana</i> (avocado); Pdu, <i>Prunus dulcis</i> (almond); Ppe, <i>Prunus persica</i> (peach); Pta, <i>Pinus taeda</i> (loblolly pine); Ptr, <i>Populus trichocarpa</i> (poplar); Rco, <i>Ricinus communis</i> (castor bean); Tca, <i>Theobroma cacao</i> (cacao); Vfo, <i>Vernicia fordii</i> (tung tree); Vvi, <i>Vitis vinifera</i> (grapevine).</p

Ole gene expression profiles analyzed by qPCR and the nucleotide sequences of real-time PCR primers and TaqMan probes.

<p>Ole gene expression profiles analyzed by qPCR and the nucleotide sequences of real-time PCR primers and TaqMan probes.</p

Variation of Ole gene expression among tung trees.

<p>TaqMan qPCR reaction mixtures (25 µl) contained 25 ng of RNA-equivalent cDNA from various stages of tung seeds, the optimized concentrations of each primer and probe (200 nM) and QPCR Mix. The expression levels under each tree represent the means and standard deviations of the expression fold calculated using three reference mRNA (Rpl19b, Gapdh and Ubl) from 11 stages of seeds with 2–4 assays for each stage. Ole gene expression in tree 1 seeds was used as the calibrator for the calculation of Ole gene expression in tree 2 and tree 3 seeds.</p

Amino acid sequence alignment of the five tung tree OLE proteins.

<p>Multiple sequence alignment was performed using the ClustalW algorithm of the AlignX program of the Vector NTI software. OLE name is on the left of alignment followed by the start of the amino acid sequence of each OLE protein. The numbers at the top of the alignment are the positions of the multiple sequence alignment. The letters at the bottom of the alignment are the consensus amino acid residues. Residues in red on yellow represent those conserved in all five OLE sequences at a given position, whereas those in black on blue represent residues conserved in majority of the sequences at a given position.</p