MOTIVATION: One of the key applications of Unique Molecular Identifiers (UMIs) in high-throughput sequencing is to correct for PCR amplification bias and removal of PCR duplicates, thereby improving quantification in DNA-seq and RNA-seq applications. Accurately grouping error-bearing UMIs that originate from the same input molecule through a UMI deduplication method is a critical step in this process. However, many existing UMI deduplication tools rely on simple Hamming distance comparisons or suboptimal clustering algorithms, often resulting in erroneous UMI groupings, particularly in error-prone long-read sequencing or ultra-high-depth short-read sequencing. RESULTS: We introduce UMI-nea, a tool that utilizes Levenshtein distance comparisons and a novel clustering approach to optimize multithreading workflows. Compared against three other indel-aware UMI deduplication tools, UMI-nea achieves more accurate UMI groupings with efficient run time. It demonstrates robust performance across diverse sequencing platforms, depths, and UMI lengths. Additionally, UMI-nea incorporates a data-guided adaptive UMI filter, further enhancing quantification accuracy. AVAILABILITY AND IMPLEMENTATION: UMI-nea is available on github https://github.com/Qiaseq-research/UMI-nea.git or Zenodo https://doi.org/10.5281/zenodo.16745758. Sequencing data are stored at https://qiagenpublic.blob.core.windows.net/umi-nea-datasets/.

Heterogeneous domain adaptation (HDA) is expected to achieve effective knowledge transfer from a label-rich source domain to a heterogeneous target domain with scarce labeled data. Most prior HDA methods strive to align the cross-domain feature distributions by learning domain invariant representations without considering the intrinsic semantic correlations among categories, which inevitably results in the suboptimal adaptation performance across domains. Therefore, to address this issue, we propose a novel semantic correlation transfer (SCT) method for HDA, which not only matches the marginal and conditional distributions between domains to mitigate the large domain discrepancy, but also transfers the category correlation knowledge underlying the source domain to target by maximizing the pairwise class similarity across source and target. Technically, the domainwise and classwise centroids (prototypes) are first computed and aligned according to the feature embeddings. Then, based on the derived classwise prototypes, we leverage the cosine similarity of each two classes in both domains to transfer the supervised source semantic correlation knowledge among different categories to target effectively. As a result, the feature transferability and category discriminability can be simultaneously improved during the adaptation process. Comprehensive experiments and ablation studies on standard HDA tasks, such as text-to-image, image-to-image, and text-to-text, have demonstrated the superiority of our proposed SCT against several state-of-the-art HDA methods.

The demand for indoor synthesis has increased significantly in recent years because of the emergence of computational design. This work designs and develops MyRoom, a Unity plugin that can import layout datasets for indoor synthesis and procedurally generate and interactively design indoor scenes. MyRoom enables users to easily edit and visualize non-intuitive layout description data, making it easier to generate and manipulate indoor scenes in Unity. MyRoom provides a user-friendly interface and powerful tools for designing and optimizing indoor layouts, including an automatic layout generator, making it ideal for game developers, interior designers, and researchers in the digital world-building industry. With MyRoom, users can streamline the process of creating high-quality indoor scenes in games and achieve their design goals efficiently.

Partial domain adaptation (PDA) attempts to learn transferable models from a large-scale labeled source domain to a small unlabeled target domain with fewer classes, which has attracted a recent surge of interest in transfer learning. Most conventional PDA approaches endeavor to design delicate source weighting schemes by leveraging target predictions to align cross-domain distributions in the shared class space. Accordingly, two crucial issues are overlooked in these methods. First, target prediction is a double-edged sword, and inaccurate predictions will result in negative transfer inevitably. Second, not all target samples have equal transferability during the adaptation; thus, "ambiguous" target data predicted with high uncertainty should be paid more attentions. In this article, we propose a critical classes and samples discovering network (CSDN) to identify the most relevant source classes and critical target samples, such that more precise cross-domain alignment in the shared label space could be enforced by co-training two diverse classifiers. Specifically, during the training process, CSDN introduces an adaptive source class weighting scheme to select the most relevant classes dynamically. Meanwhile, based on the designed target ambiguous score, CSDN emphasizes more on ambiguous target samples with larger inconsistent predictions to enable fine-grained alignment. Taking a step further, the weighting schemes in CSDN can be easily coupled with other PDA and DA methods to further boost their performance, thereby demonstrating its flexibility. Extensive experiments verify that CSDN attains excellent results compared to state of the arts on four highly competitive benchmark datasets.

In this letter, a singular value decomposition (SVD)-based method for estimating the equivalent number of looks (ENL) in synthetic aperture radar (SAR) images is proposed. First, SAR images are logarithmically scaled to change the multiplicative speckle into additive noise. Assuming that the multiplicative speckle is a gamma random variable with unit mean, a monotone function is established between the ENL and the variance of the additive noise, thus transforming the ENL estimation problem into estimating the variance of the additive noise. Then SVD is applied to the logarithmic image in a window with certain size to obtain its singular values. By making use of an empirical linear relationship between the average of the smallest singular values and the standard deviation of the noise in the logarithmic image, the variance of the additive noise is finally estimated. Experiments of both simulated and real SAR images demonstrated the effectiveness of the proposed method.