Can our brain signals faithfully reflect the original visual stimuli, even including high-frequency details? Although human perceptual and cognitive capacities enable us to process and remember visual information, these abilities are constrained by several factors, such as limited attentional resources and finite capacity of visual memory. When visual stimuli are processed by human visual system into brain signals, some information is inevitably lost, leading to a discrepancy known as the System GAP. Additionally, perceptual and cognitive dynamics, along with technical noise in signal acquisition, degrade the fidelity of brain signals relative to the visual stimuli, known as the Random GAP. When encoded brain representations are directly aligned with the corresponding pretrained image features, the System GAP and Random GAP between paired data challenge the model, requiring it to bridge these gaps. However, due to limited paired data, these gaps are difficult for the model to learn, leading to overfitting and poor generalization to new data. To address these GAPs, we propose a simple yet effective approach called the Uncertainty-Aware Blur Prior (UBP). It estimates the uncertainty within the paired data, reflecting the mismatch between brain signals and visual stimuli. Based on uncertainty, UBP dynamically blurs the high-frequency details of the original images, reducing the impact of mismatch and improving alignment. Our method achieves a top-1 accuracy of 50.9% and a top-5 accuracy of 79.7% on the zero-shot brain-to-image retrieval task, surpassing previous state-of-the-art methods. Code is available at https://github.com/HaitaoWuTJU/Uncertainty-Aware-Blur-Prior.

MOTIVATION: Clustering analysis for single-cell RNA sequencing (scRNA-seq) data is an important step in revealing cellular heterogeneity. Many clustering methods have been proposed to discover heterogenous cell types from scRNA-seq data. However, adaptive clustering with accurate cluster number reflecting intrinsic biology nature from large-scale scRNA-seq data remains quite challenging. RESULTS: Here, we propose a single-cell Deep Adaptive Clustering (scDAC) model by coupling the Autoencoder (AE) and the Dirichlet Process Mixture Model (DPMM). By jointly optimizing the model parameters of AE and DPMM, scDAC achieves adaptive clustering with accurate cluster numbers on scRNA-seq data. We verify the performance of scDAC on five subsampled datasets with different numbers of cell types and compare it with 15 widely used clustering methods across nine scRNA-seq datasets. Our results demonstrate that scDAC can adaptively find accurate numbers of cell types or subtypes and outperforms other methods. Moreover, the performance of scDAC is robust to hyperparameter changes. AVAILABILITY AND IMPLEMENTATION: The scDAC is implemented in Python. The source code is available at https://github.com/labomics/scDAC.

Deep hashing reaps the benefits of deep learning and hashing technology, and has become the mainstream of large-scale image retrieval. It generally encodes image into hash code with feature similarity preserving, that is, geometric-structure preservation, and achieves promising retrieval results. In this article, we find that existing geometric-structure preservation manner inadequately ensures feature discrimination, while improving feature discrimination of hash code essentially determines hash learning retrieval performance. This fact principally spurs us to propose a discriminative geometric-structure-based deep hashing method (DGDH), which investigates three novel loss terms based on class centers to induce the so-called discriminative geometrical structure. In detail, the margin-aware center loss assembles samples in the same class to the corresponding class centers for intraclass compactness, then a linear classifier based on class center serves to boost interclass separability, and the radius loss further puts different class centers on a hypersphere to tentatively reduce quantization errors. An efficient alternate optimization algorithm with guaranteed desirable convergence is proposed to optimize DGDH. We theoretically analyze the robustness and generalization of the proposed method. The experiments on five popular benchmark datasets demonstrate superior image retrieval performance of the proposed DGDH over several state of the arts.

Sequence logos are used to visually display conservations and variations in short sequences. They can indicate the fixed patterns or conserved motifs in a batch of DNA or protein sequences. However, most of the popular sequence logo generators are based on the assumption that all the input sequences are from the same homologous group, which will lead to an overlook of the heterogeneity among the sequences during the sequence logo making process. Heterogeneous groups of sequences may represent clades of different evolutionary origins, or genes families with different functions. Therefore, it is essential to divide the sequences into different phylogenetic or functional groups to reveal their specific sequence motifs and conservation patterns. To solve these problems, we developed MetaLogo, which can automatically cluster the input sequences after multiple sequence alignment and phylogenetic tree construction, and then output sequence logos for multiple groups and aligned them in one figure. User-defined grouping is also supported by MetaLogo to allow users to investigate functional motifs in a more delicate and dynamic perspective. MetaLogo can highlight both the homologous and nonhomologous sites among sequences. MetaLogo can also be used to annotate the evolutionary positions and gene functions of unknown sequences, together with their local sequence characteristics. We provide users a public MetaLogo web server (http://metalogo.omicsnet.org), a standalone Python package (https://github.com/labomics/MetaLogo), and also a built-in web server available for local deployment. Using MetaLogo, users can draw informative, customized and publishable sequence logos without any programming experience to present and investigate new knowledge on specific sequence sets.