Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries. Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States

Evidence of Vocal Tract Articulation in Self-Supervised Learning of Speech

Recent self-supervised learning (SSL) models have proven to learn rich representations of speech, which can readily be utilized by diverse downstream tasks. To understand such utilities, various analyses have been done for speech SSL models to reveal which and how information is encoded in the learned representations. Although the scope of previous analyses is extensive in acoustic, phonetic, and semantic perspectives, the physical grounding by speech production has not yet received full attention. To bridge this gap, we conduct a comprehensive analysis to link speech representations to articulatory trajectories measured by electromagnetic articulography (EMA). Our analysis is based on a linear probing approach where we measure articulatory score as an average correlation of linear mapping to EMA. We analyze a set of SSL models selected from the leaderboard of the SUPERB benchmark and perform further layer-wise analyses on two most successful models, Wav2Vec 2.0 and HuBERT. Surprisingly, representations from the recent speech SSL models are highly correlated with EMA traces (best: r = 0.81), and only 5 minutes are sufficient to train a linear model with high performance (r = 0.77). Our findings suggest that SSL models learn to align closely with continuous articulations, and provide a novel insight into speech SSL

Generation and collective interaction of giant magnetic dipoles in laser cluster plasma

Interaction of circularly polarized laser pulses with spherical nano-droplets generates nanometer-size magnets with lifetime on the order of hundreds of femtoseconds. Such magnetic dipoles are close enough in a cluster target and magnetic interaction takes place. We investigate such system of several magnetic dipoles and describe their rotation in the framework of Lagrangian formalism. The semi-analytical results are compared to particle-in-cell simulations, which confirm the theoretically obtained terrahertz frequency of the dipole oscillation

D3Former: Debiased Dual Distilled Transformer for Incremental Learning

In class incremental learning (CIL) setting, groups of classes are introduced to a model in each learning phase. The goal is to learn a unified model performant on all the classes observed so far. Given the recent popularity of Vision Transformers (ViTs) in conventional classification settings, an interesting question is to study their continual learning behaviour. In this work, we develop a Debiased Dual Distilled Transformer for CIL dubbed $\textrm{D}^3\textrm{Former}$. The proposed model leverages a hybrid nested ViT design to ensure data efficiency and scalability to small as well as large datasets. In contrast to a recent ViT based CIL approach, our $\textrm{D}^3\textrm{Former}$ does not dynamically expand its architecture when new tasks are learned and remains suitable for a large number of incremental tasks. The improved CIL behaviour of $\textrm{D}^3\textrm{Former}$ owes to two fundamental changes to the ViT design. First, we treat the incremental learning as a long-tail classification problem where the majority samples from new classes vastly outnumber the limited exemplars available for old classes. To avoid the bias against the minority old classes, we propose to dynamically adjust logits to emphasize on retaining the representations relevant to old tasks. Second, we propose to preserve the configuration of spatial attention maps as the learning progresses across tasks. This helps in reducing catastrophic forgetting by constraining the model to retain the attention on the most discriminative regions. $\textrm{D}^3\textrm{Former}$ obtains favorable results on incremental versions of CIFAR-100, MNIST, SVHN, and ImageNet datasets. Code is available at https://tinyurl.com/d3formerComment: Accepted to CLVision at CVPR 202