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Related Concept Videos

Language01:16

Language

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Language is a unique communication system that uses words and systematic rules to organize and transmit information. Unlike other forms of communication, which may involve postures, movements, odors, or vocalizations, language relies on symbols and grammar. This makes human communication distinct from that of other species, who also communicate but do not use language in the same way humans do.
Corballis and Suddendorf (2007) and Tomasello and Rakoczy (2003) highlight the role of language in...
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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Language, whether spoken, signed, or written, consists of specific components: lexicon and grammar. The lexicon is the vocabulary of a language, comprising its words. Grammar is the set of rules used to convey meaning through the lexicon. For example, English grammar adds “-ed” to most verbs to indicate past tense. Words are formed by combining phonemes, which are the basic sound units of a language. Different languages have different sets of phonemes (e.g., “ah” vs.
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Language Development01:22

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Children master language quickly and with relative ease, supported by both biological predisposition and reinforcement. B. F. Skinner (1957) proposed that language is learned through reinforcement, while Noam Chomsky (1965) argued that language acquisition mechanisms are biologically determined.
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Language serves as a bridge between ideas and communication, influencing how individuals perceive and interact with the world. Psychologists have long debated whether language shapes thought or vice versa. This discussion gained grip with Edward Sapir and Benjamin Lee Whorf in the 1940s, who proposed that language determines thought, a concept known as linguistic determinism. They suggested that the vocabulary and structure of a language influence how its speakers think and perceive reality.
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Inertial Frames of Reference01:03

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Newton’s first law is usually considered to be a statement about reference frames. It provides a method for identifying a special type of reference frame: the inertial reference frame. In principle, we can make the net force on a body zero. If its velocity relative to a given frame is constant, then that frame is said to be inertial. So, by definition, an inertial reference frame is a reference frame where Newton's first law holds valid. Newton's first law applies to objects with...
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Related Experiment Video

Updated: Feb 5, 2026

Mining Spatial Transcriptomics Datasets using DeepSpaceDB
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Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 2025

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spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language

Tianyu Liu1,2, Tinglin Huang3, Wengong Jin4,5

  • 1Interdepartmental Program in Computational Biology & Bioinformatics, Yale University, New Haven, Connecticut 06511, USA.

Genome Research
|February 3, 2026
PubMed
Summary
This summary is machine-generated.

spRefine, a deep learning framework, effectively denoises and imputes spatial transcriptomic data. This enhances data integration and improves spatial ageing clock accuracy, revealing new aging-related biological insights.

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Area of Science:

  • Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • Spatial transcriptomics analysis faces challenges like high noise and missing data.
  • The cost of spatial data limits its widespread application compared to single-cell data.

Purpose of the Study:

  • To introduce spRefine, a deep learning framework for denoising and imputing spatial transcriptomic data.
  • To improve cell- and spot-level data representations and enhance data integration.

Main Methods:

  • Utilized genomic language models within a deep learning framework.
  • Applied spRefine for joint denoising and imputation of spatial transcriptomic datasets.

Main Results:

  • spRefine generated more robust cell- and spot-level representations.
  • The framework significantly improved spatial transcriptomic data integration.
  • Enhanced accuracy in spatial ageing clock estimations was achieved.

Conclusions:

  • spRefine offers a powerful approach for preprocessing spatial transcriptomic data.
  • The framework facilitates novel biological signal discovery and analysis of aging effects.
  • spRefine provides new insights into aging-related processes, including neuronal function loss.