In this paper, we study the co-embedding problem of how to map different types of patterns into one common low-dimensional space, given only the associations (relation values) between samples. We conduct a generic analysis to discover the commonalities between existing co-embedding algorithms and indirectly related approaches and investigate possible factors controlling the shapes and distributions of the co-embeddings. The primary contribution of this work is a novel method for computing co-embeddings, termed the automatic co-embedding with adaptive shaping (ACAS) algorithm, based on an efficient transformation of the co-embedding problem. Its advantages include flexible model adaptation to the given data, an economical set of model variables leading to a parametric co-embedding formulation, and a robust model fitting criterion for model optimization based on a quantization procedure. The secondary contribution of this work is the introduction of a set of generic schemes for the qualitative analysis and quantitative assessment of the output of co-embedding algorithms, using existing labeled benchmark datasets. Experiments with synthetic and real-world datasets show that the proposed algorithm is very competitive compared to existing ones.
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http://dx.doi.org/10.1109/TPAMI.2013.66 | DOI Listing |
Phys Med Biol
January 2025
Department of Radiation Oncology, Division of Medical Physics and Engineering , UT Southwestern Medical Center, 2280 Inwood Road, Dallas, Texas, 75390-9096, UNITED STATES.
One bottleneck of MRI-guided Online Adaptive Radiotherapy (MRoART) is the time-consuming daily online replanning process. The current leaf sequencing method takes up to 10 minutes, with potential dosimetric degradation and small segment openings that increase delivery time. This work aims to replace this process with a fast deep learning-based method to provide deliverable MLC sequences almost instantaneously, potentially accelerating and enhancing online adaption.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
February 2025
Molecular Ecology and Evolution Group, School of Environmental and Natural Sciences, Bangor University, Bangor LL57 2UW, United Kingdom.
Phenotypic plasticity may pave the way for rapid adaptation to newly encountered environments. Although it is often contested, there is growing evidence that initial plastic responses of ancestral populations to new environmental cues may promote subsequent adaptation. However, we do not know whether plasticity to cues present in the ancestral habitat (past-cue plasticity) can facilitate adaptation to novel cues.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
February 2025
Museum of Natural History, University of Colorado-Boulder, Boulder, CO 80309.
Amid global challenges like climate change, extinctions, and disease epidemics, science and society require nuanced, international solutions that are grounded in robust, interdisciplinary perspectives and datasets that span deep time. Natural history collections, from modern biological specimens to the archaeological and fossil records, are crucial tools for understanding cultural and biological processes that shape our modern world. At the same time, natural history collections in low and middle-income countries are at-risk and underresourced, imperiling efforts to build the infrastructure and scientific capacity necessary to tackle critical challenges.
View Article and Find Full Text PDFPlant Dis
January 2025
Tamil Nadu Agricultural University, Department of Plant Pathology, Coimbatore, Tamil Nadu, India;
Ashwagandha (Withania somnifera), enriched in alkaloids, steroidal lactones and saponins, is a valuable herb in Indian Ayurvedic medicine. During December 2023, Va-1 (Vallabh Ashwagandha-1) plants at ICAR -Central Tobacco Research Institute, Vedasandur, Tamil Nadu (10.53717ºN, 77.
View Article and Find Full Text PDFMol Biol Evol
January 2025
UMR 8222 LECOB CNRS-Sorbonne Université, Observatoire Océanologique de Banyuls, Avenue du Fontaulé, 66650, Banyuls-sur-mer, France.
How the interplay of biotic and abiotic factors shapes current genetic diversity at the community level remains an open question, particularly in the deep sea. Comparative phylogeography of multiple species can reveal the influence of past climatic events, geographic barriers, and species life history traits on spatial patterns of genetic structure across lineages. To shed light on the factors that shape community-level genetic variation and to improve our understanding of deep-sea biogeographic patterns, we conducted a comparative population genomics study on seven hydrothermal vent species co-distributed in the Back-Arc Basins (BABs) of the Southwest Pacific region.
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