31 research outputs found
Fairly Adaptive Negative Sampling for Recommendations
Pairwise learning strategies are prevalent for optimizing recommendation
models on implicit feedback data, which usually learns user preference by
discriminating between positive (i.e., clicked by a user) and negative items
(i.e., obtained by negative sampling). However, the size of different item
groups (specified by item attribute) is usually unevenly distributed. We
empirically find that the commonly used uniform negative sampling strategy for
pairwise algorithms (e.g., BPR) can inherit such data bias and oversample the
majority item group as negative instances, severely countering group fairness
on the item side. In this paper, we propose a Fairly adaptive Negative sampling
approach (FairNeg), which improves item group fairness via adaptively adjusting
the group-level negative sampling distribution in the training process. In
particular, it first perceives the model's unfairness status at each step and
then adjusts the group-wise sampling distribution with an adaptive momentum
update strategy for better facilitating fairness optimization. Moreover, a
negative sampling distribution Mixup mechanism is proposed, which gracefully
incorporates existing importance-aware sampling techniques intended for mining
informative negative samples, thus allowing for achieving multiple optimization
purposes. Extensive experiments on four public datasets show our proposed
method's superiority in group fairness enhancement and fairness-utility
tradeoff.Comment: Accepted by TheWebConf202
RNA-seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish
BACKGROUND: Zebrafish (Danio rerio) is a prominent vertebrate model of human development and pathogenic disease and has recently been utilized to study teleost immune responses to infectious agents threatening the aquaculture industry. In this work, to clarify the host immune mechanisms underlying the protective effects of a putative vaccine and improve its immunogenicity in the future efforts, high-throughput RNA sequencing technology was used to investigate the immunization-related gene expression patterns of zebrafish immunized with Edwardsiella tarda live attenuated vaccine. RESULTS: Average reads of 18.13 million and 14.27 million were obtained from livers of zebrafish immunized with phosphate buffered saline (mock) and E. tarda vaccine (WED), respectively. The reads were annotated with the Ensembl zebrafish database before differential expressed genes sequencing (DESeq) comparative analysis, which identified 4565 significantly differentially expressed genes (2186 up-regulated and 2379 down-regulated in WED; p<0.05). Among those, functional classifications were found in the Gene Ontology database for 3891 and in the Kyoto Encyclopedia of Genes and Genomes database for 3467. Several pathways involved in acute phase response, complement activation, immune/defense response, and antigen processing and presentation were remarkably affected at the early stage of WED immunization. Further qPCR analysis confirmed that the genes encoding the factors involved in major histocompatibility complex (MHC)-I processing pathway were up-regulated, while those involved in MHC-II pathway were down-regulated. CONCLUSION: These data provided insights into the molecular mechanisms underlying zebrafish immune response to WED immunization and might aid future studies to develop a highly immunogenic vaccine against gram-negative bacteria in teleosts
DiffusePast: Diffusion-based Generative Replay for Class Incremental Semantic Segmentation
The Class Incremental Semantic Segmentation (CISS) extends the traditional
segmentation task by incrementally learning newly added classes. Previous work
has introduced generative replay, which involves replaying old class samples
generated from a pre-trained GAN, to address the issues of catastrophic
forgetting and privacy concerns. However, the generated images lack semantic
precision and exhibit out-of-distribution characteristics, resulting in
inaccurate masks that further degrade the segmentation performance. To tackle
these challenges, we propose DiffusePast, a novel framework featuring a
diffusion-based generative replay module that generates semantically accurate
images with more reliable masks guided by different instructions (e.g., text
prompts or edge maps). Specifically, DiffusePast introduces a dual-generator
paradigm, which focuses on generating old class images that align with the
distribution of downstream datasets while preserving the structure and layout
of the original images, enabling more precise masks. To adapt to the novel
visual concepts of newly added classes continuously, we incorporate class-wise
token embedding when updating the dual-generator. Moreover, we assign adequate
pseudo-labels of old classes to the background pixels in the new step images,
further mitigating the forgetting of previously learned knowledge. Through
comprehensive experiments, our method demonstrates competitive performance
across mainstream benchmarks, striking a better balance between the performance
of old and novel classes.Comment: e.g.: 13 pages, 7 figure
High-Resolution Boundary Detection for Medical Image Segmentation with Piece-Wise Two-Sample T-Test Augmented Loss
Deep learning methods have contributed substantially to the rapid advancement
of medical image segmentation, the quality of which relies on the suitable
design of loss functions. Popular loss functions, including the cross-entropy
and dice losses, often fall short of boundary detection, thereby limiting
high-resolution downstream applications such as automated diagnoses and
procedures. We developed a novel loss function that is tailored to reflect the
boundary information to enhance the boundary detection. As the contrast between
segmentation and background regions along the classification boundary naturally
induces heterogeneity over the pixels, we propose the piece-wise two-sample
t-test augmented (PTA) loss that is infused with the statistical test for such
heterogeneity. We demonstrate the improved boundary detection power of the PTA
loss compared to benchmark losses without a t-test component
Genome Sequence of the Versatile Fish Pathogen Edwardsiella tarda Provides Insights into its Adaptation to Broad Host Ranges and Intracellular Niches
BACKGROUND:Edwardsiella tarda is the etiologic agent of edwardsiellosis, a devastating fish disease prevailing in worldwide aquaculture industries. Here we describe the complete genome of E. tarda, EIB202, a highly virulent and multi-drug resistant isolate in China. METHODOLOGY/PRINCIPAL FINDINGS:E. tarda EIB202 possesses a single chromosome of 3,760,463 base pairs containing 3,486 predicted protein coding sequences, 8 ribosomal rRNA operons, and 95 tRNA genes, and a 43,703 bp conjugative plasmid harboring multi-drug resistant determinants and encoding type IV A secretion system components. We identified a full spectrum of genetic properties related to its genome plasticity such as repeated sequences, insertion sequences, phage-like proteins, integrases, recombinases and genomic islands. In addition, analysis also indicated that a substantial proportion of the E. tarda genome might be devoted to the growth and survival under diverse conditions including intracellular niches, with a large number of aerobic or anaerobic respiration-associated proteins, signal transduction proteins as well as proteins involved in various stress adaptations. A pool of genes for secretion systems, pili formation, nonfimbrial adhesions, invasions and hemagglutinins, chondroitinases, hemolysins, iron scavenging systems as well as the incomplete flagellar biogenesis might feature its surface structures and pathogenesis in a fish body. CONCLUSION/SIGNIFICANCE:Genomic analysis of the bacterium offered insights into the phylogeny, metabolism, drug-resistance, stress adaptation, and virulence characteristics of this versatile pathogen, which constitutes an important first step in understanding the pathogenesis of E. tarda to facilitate construction of a practical effective vaccine used for combating fish edwardsiellosis
Edwardsiella Comparative Phylogenomics Reveal the New Intra/Inter-Species Taxonomic Relationships, Virulence Evolution and Niche Adaptation Mechanisms
Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC). Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII) based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA) of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS) as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and niche adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen
RNA-seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish
Abstract Background Zebrafish (Danio rerio) is a prominent vertebrate model of human development and pathogenic disease and has recently been utilized to study teleost immune responses to infectious agents threatening the aquaculture industry. In this work, to clarify the host immune mechanisms underlying the protective effects of a putative vaccine and improve its immunogenicity in the future efforts, high-throughput RNA sequencing technology was used to investigate the immunization-related gene expression patterns of zebrafish immunized with Edwardsiella tarda live attenuated vaccine. Results Average reads of 18.13 million and 14.27 million were obtained from livers of zebrafish immunized with phosphate buffered saline (mock) and E. tarda vaccine (WED), respectively. The reads were annotated with the Ensembl zebrafish database before differential expressed genes sequencing (DESeq) comparative analysis, which identified 4565 significantly differentially expressed genes (2186 up-regulated and 2379 down-regulated in WED; p Conclusion These data provided insights into the molecular mechanisms underlying zebrafish immune response to WED immunization and might aid future studies to develop a highly immunogenic vaccine against gram-negative bacteria in teleosts.</p
A quorum sensing-based in vivo expression system and its application in multivalent bacterial vaccine
Adaptive Ridge Point Refinement for Seeds Detection in X-Ray Coronary Angiogram
Seed point is prerequired condition for tracking based method for extracting centerline or vascular structures from the angiogram. In this paper, a novel seed point detection method for coronary artery segmentation is proposed. Vessels on the image are first enhanced according to the distribution of Hessian eigenvalue in multiscale space; consequently, centerlines of tubular vessels are also enhanced. Ridge point is extracted as candidate seed point, which is then refined according to its mathematical definition. The theoretical feasibility of this method is also proven. Finally, all the detected ridge points are checked using a self-adaptive threshold to improve the robustness of results. Clinical angiograms are used to evaluate the performance of the proposed algorithm, and the results show that the proposed algorithm can detect a large set of true seed points located on most branches of vessels. Compared with traditional seed point detection algorithms, the proposed method can detect a larger number of seed points with higher precision. Considering that the proposed method can achieve accurate seed detection without any human interaction, it can be utilized for several clinical applications, such as vessel segmentation, centerline extraction, and topological identification
Transposon insertion sequencing reveals T4SS as the major genetic trait for conjugation transfer of multi-drug resistance pEIB202 from Edwardsiella
Abstract Background Conjugation is a major type of horizontal transmission of genes that involves transfer of a plasmid into a recipient using specific conjugation machinery, which results in an extended spectrum of bacterial antibiotics resistance. However, there is inadequate knowledge about the regulator and mechanisms that control the conjugation processes, especially in an aquaculture environment where a cocktail of antibiotics may be present. Here, we investigated these with pEIB202, a typical multi-drug resistant IncP plasmid encoding tetracycline, streptomycin, sulfonamide and chloramphenicol resistance in fish pathogen Edwardsiella piscicida strain EIB202. Results We used transposon insertion sequencing (TIS) to identify genes that are responsible for conjugation transfer of pEIB202. All ten of the plasmid-borne type IV secretion system (T4SS) genes and a putative lipoprotein p007 were identified to play an important role in pEIB202 horizontal transfer. Antibiotics appear to modulate conjugation frequencies by repressing T4SS gene expression. In addition, we identified topA gene, which encodes topoisomerase I, as an inhibitor of pEIB202 transfer. Furthermore, the RNA-seq analysis of the response regulator EsrB encoded on the chromosome also revealed its essential role in facilitating the conjugation by upregulating the T4SS genes. Conclusions Collectively, our screens unraveled the genetic basis of the conjugation transfer of pEIB202 and the influence of horizontally acquired EsrB on this process. Our results will improve the understanding of the mechanism of plasmid conjugation processes that facilitate dissemination of antibiotic resistance especially in aquaculture industries