Most examinations of neural networks' learned latent spaces typically employ dimensionality reduction techniques such as t-distributed stochastic neighbor embedding (t-SNE) or uniform manifold approximation and projection (UMAP). These methods distort the local neighborhood in the visualization, making it hard to distinguish the structure of a subset of samples in the latent space. In response to this challenge, we introduce the k* distribution and its corresponding visualization technique. This method uses local neighborhood analysis to guarantee the preservation of the structure of sample distributions for individual classes within the subset of the learned latent space. This facilitates easy comparison of different k* distributions, enabling analysis of how various classes are processed by the same neural network. Our study reveals three distinct distributions of samples within the learned latent space subset: 1) fractured; 2) overlapped; and 3) clustered, providing a more profound understanding of the existing contemporary visualizations. Experiments show that the distribution of samples within the network's learned latent space significantly varies depending on the class. Furthermore, we illustrate that our analysis can be applied to explore the latent space of diverse neural network architectures, various layers within neural networks, transformations applied to input samples, and the distribution of training and testing data for neural networks. Thus, the k* distribution should aid in visualizing the structure inside neural networks and further foster their understanding.
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http://dx.doi.org/10.1109/TNNLS.2024.3446509 | DOI Listing |
PLoS Comput Biol
January 2025
Department of Anatomy and Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan.
Mathematical modeling has been utilized to explain biological pattern formation, but the selections of models and parameters have been made empirically. In the present study, we propose a data-driven approach to validate the applicability of mathematical models. Specifically, we developed methods to automatically select the appropriate mathematical models based on the patterns of interest and to estimate the model parameters.
View Article and Find Full Text PDFR Soc Open Sci
January 2025
School of Physics, The University of Sydney, Sydney, Australia.
Clustering short text is a difficult problem, owing to the low word co-occurrence between short text documents. This work shows that large language models (LLMs) can overcome the limitations of traditional clustering approaches by generating embeddings that capture the semantic nuances of short text. In this study, clusters are found in the embedding space using Gaussian mixture modelling.
View Article and Find Full Text PDFNeural Netw
January 2025
College of Mechatronics and Control Engineering, Shenzhen University, Shenzhen, Guangdong, China.
Multi-view classification integrates features from different views to optimize classification performance. Most of the existing works typically utilize semantic information to achieve view fusion but neglect the spatial information of data itself, which accommodates data representation with correlation information and is proven to be an essential aspect. Thus robust independent subspace analysis network, optimized by sparse and soft orthogonal optimization, is first proposed to extract the latent spatial information of multi-view data with subspace bases.
View Article and Find Full Text PDFSci Adv
January 2025
Department of Biomedical Engineering, Duke University, Durham, NC, USA.
Designing binders to target undruggable proteins presents a formidable challenge in drug discovery. In this work, we provide an algorithmic framework to design short, target-binding linear peptides, requiring only the amino acid sequence of the target protein. To do this, we propose a process to generate naturalistic peptide candidates through Gaussian perturbation of the peptidic latent space of the ESM-2 protein language model and subsequently screen these novel sequences for target-selective interaction activity via a contrastive language-image pretraining (CLIP)-based contrastive learning architecture.
View Article and Find Full Text PDFHumans excel at applying learned behavior to unlearned situations. A crucial component of this generalization behavior is our ability to compose/decompose a whole into reusable parts, an attribute known as compositionality. One of the fundamental questions in robotics concerns this characteristic: How can linguistic compositionality be developed concomitantly with sensorimotor skills through associative learning, particularly when individuals only learn partial linguistic compositions and their corresponding sensorimotor patterns? To address this question, we propose a brain-inspired neural network model that integrates vision, proprioception, and language into a framework of predictive coding and active inference on the basis of the free-energy principle.
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