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Recent advancements in single-cell RNA-sequencing (scRNA-seq) have enhanced our understanding of cell heterogeneity at a high resolution. With the ability to sequence over 10,000 cells per hour, researchers can collect large scRNA-seq datasets for different participants, offering an opportunity to study the temporal progression of individual-level single-cell data. However, the presence of excessive zeros, a common issue in scRNA-seq, significantly impacts regression/association analysis, potentially leading to biased estimates in downstream analysis. Addressing these challenges, we introduce the Zero Inflated Smoothing Spline (ZISS) method, specifically designed to model single-cell temporal data. The ZISS method encompasses two components for modeling gene expression patterns over time and handling excessive zeros. Our approach employs the smoothing spline ANOVA model, providing robust estimates of mean functions and zero probabilities for irregularly observed single-cell temporal data compared to existing methods in our simulation studies and real data analysis.

For object re-identification (re-ID), learning from synthetic data has become a promising strategy to cheaply acquire large-scale annotated datasets and effective models, with few privacy concerns. Many interesting research problems arise from this strategy, e.g., how to reduce the domain gap between synthetic source and real-world target. To facilitate developing more new approaches in learning from synthetic data, we introduce the Alice benchmarks, large-scale datasets providing benchmarks as well as evaluation protocols to the research community. Within the Alice benchmarks, two object re-ID tasks are offered: person and vehicle re-ID. We collected and annotated two challenging real-world target datasets: AlicePerson and AliceVehicle, captured under various illuminations, image resolutions, etc. As an important feature of our real target, the clusterability of its training set is not manually guaranteed to make it closer to a real domain adaptation test scenario. Correspondingly, we reuse existing PersonX and VehicleX as synthetic source domains. The primary goal is to train models from synthetic data that can work effectively in the real world. In this paper, we detail the settings of Alice benchmarks, provide an analysis of existing commonly-used domain adaptation methods, and discuss some interesting future directions. An online server has been set up for the community to evaluate methods conveniently and fairly. Datasets and the online server details are available at https://sites.google.com/view/alice-benchmarks., Comment: ICLR 2024. Datasets and the online server details are available at https://sites.google.com/view/alice-benchmarks

Analyzing model performance in various unseen environments is a critical research problem in the machine learning community. To study this problem, it is important to construct a testbed with out-of-distribution test sets that have broad coverage of environmental discrepancies. However, existing testbeds typically either have a small number of domains or are synthesized by image corruptions, hindering algorithm design that demonstrates real-world effectiveness. In this paper, we introduce CIFAR-10-Warehouse, consisting of 180 datasets collected by prompting image search engines and diffusion models in various ways. Generally sized between 300 and 8,000 images, the datasets contain natural images, cartoons, certain colors, or objects that do not naturally appear. With CIFAR-10-W, we aim to enhance the evaluation and deepen the understanding of two generalization tasks: domain generalization and model accuracy prediction in various out-of-distribution environments. We conduct extensive benchmarking and comparison experiments and show that CIFAR-10-W offers new and interesting insights inherent to these tasks. We also discuss other fields that would benefit from CIFAR-10-W., Comment: ICLR 2024. https://sites.google.com/view/CIFAR-10-warehouse/

Hand-crafted image quality metrics, such as PSNR and SSIM, are commonly used to evaluate model privacy risk under reconstruction attacks. Under these metrics, reconstructed images that are determined to resemble the original one generally indicate more privacy leakage. Images determined as overall dissimilar, on the other hand, indicate higher robustness against attack. However, there is no guarantee that these metrics well reflect human opinions, which, as a judgement for model privacy leakage, are more trustworthy. In this paper, we comprehensively study the faithfulness of these hand-crafted metrics to human perception of privacy information from the reconstructed images. On 5 datasets ranging from natural images, faces, to fine-grained classes, we use 4 existing attack methods to reconstruct images from many different classification models and, for each reconstructed image, we ask multiple human annotators to assess whether this image is recognizable. Our studies reveal that the hand-crafted metrics only have a weak correlation with the human evaluation of privacy leakage and that even these metrics themselves often contradict each other. These observations suggest risks of current metrics in the community. To address this potential risk, we propose a learning-based measure called SemSim to evaluate the Semantic Similarity between the original and reconstructed images. SemSim is trained with a standard triplet loss, using an original image as an anchor, one of its recognizable reconstructed images as a positive sample, and an unrecognizable one as a negative. By training on human annotations, SemSim exhibits a greater reflection of privacy leakage on the semantic level. We show that SemSim has a significantly higher correlation with human judgment compared with existing metrics. Moreover, this strong correlation generalizes to unseen datasets, models and attack methods., Comment: 15 pages, 9 figures and 3 tables

There is a growing interest in characterizing circular data found in biological systems. Such data are wide ranging and varied, from signal phase in neural recordings to nucleotide sequences in round genomes. Traditional clustering algorithms are often inadequate due to their limited ability to distinguish differences in the periodic component. Current clustering schemes that work in a polar coordinate system have limitations, such as being only angle-focused or lacking generality. To overcome these limitations, we propose a new analysis framework that utilizes projections onto a cylindrical coordinate system to better represent objects in a polar coordinate system. Using the mathematical properties of circular data, we show our approach always finds the correct clustering result within the reconstructed dataset, given sufficient periodic repetitions of the data. Our approach is generally applicable and adaptable and can be incorporated into most state-of-the-art clustering algorithms. We demonstrate on synthetic and real data that our method generates more appropriate and consistent clustering results compared to standard methods. In summary, our proposed analysis framework overcomes the limitations of existing polar coordinate-based clustering methods and provides a more accurate and efficient way to cluster circular data., Comment: Manuscript is under review in IEEE Transactions on Computational Biology and Bioinformatics. Copyright holder is credited to IEEE

Modern transformer-based models designed for computer vision have outperformed humans across a spectrum of visual tasks. However, critical tasks, such as medical image interpretation or autonomous driving, still require reliance on human judgments. This work demonstrates how human visual input, specifically fixations collected from an eye-tracking device, can be integrated into transformer models to improve accuracy across multiple driving situations and datasets. First, we establish the significance of fixation regions in left-right driving decisions, as observed in both human subjects and a Vision Transformer (ViT). By comparing the similarity between human fixation maps and ViT attention weights, we reveal the dynamics of overlap across individual heads and layers. This overlap is exploited for model pruning without compromising accuracy. Thereafter, we incorporate information from the driving scene with fixation data, employing a "joint space-fixation" (JSF) attention setup. Lastly, we propose a "fixation-attention intersection" (FAX) loss to train the ViT model to attend to the same regions that humans fixated on. We find that the ViT performance is improved in accuracy and number of training epochs when using JSF and FAX. These results hold significant implications for human-guided artificial intelligence., Comment: 25 pages, 9 figures, 3 tables

The layered, air-stable van der Waals antiferromagnetic compound CrSBr exhibits pronounced coupling between its optical, electronic, and magnetic properties. As an example, exciton dynamics can be significantly influenced by lattice vibrations through exciton-phonon coupling. Using low-temperature photoluminescence spectroscopy, we demonstrate the effective coupling between excitons and phonons in nanometer-thick CrSBr. By careful analysis, we identify that the satellite peaks predominantly arise from the interaction between the exciton and an optical phonon with a frequency of 118 cm-1 (~14.6 meV) due to the out-of-plane vibration of Br atoms. Power-dependent and temperature-dependent photoluminescence measurements support exciton-phonon coupling and indicate a coupling between magnetic and optical properties, suggesting the possibility of carrier localization in the material. The presence of strong coupling between the exciton and the lattice may have important implications for the design of light-matter interactions in magnetic semiconductors and provides new insights into the exciton dynamics in CrSBr. This highlights the potential for exploiting exciton-phonon coupling to control the optical properties of layered antiferromagnetic materials., Comment: 21 pages, together with suppl

Label-free model evaluation, or AutoEval, estimates model accuracy on unlabeled test sets, and is critical for understanding model behaviors in various unseen environments. In the absence of image labels, based on dataset representations, we estimate model performance for AutoEval with regression. On the one hand, image feature is a straightforward choice for such representations, but it hampers regression learning due to being unstructured (\ie no specific meanings for component at certain location) and of large-scale. On the other hand, previous methods adopt simple structured representations (like average confidence or average feature), but insufficient to capture the data characteristics given their limited dimensions. In this work, we take the best of both worlds and propose a new semi-structured dataset representation that is manageable for regression learning while containing rich information for AutoEval. Based on image features, we integrate distribution shapes, clusters, and representative samples for a semi-structured dataset representation. Besides the structured overall description with distribution shapes, the unstructured description with clusters and representative samples include additional fine-grained information facilitating the AutoEval task. On three existing datasets and 25 newly introduced ones, we experimentally show that the proposed representation achieves competitive results. Code and dataset are available at https://github.com/sxzrt/Semi-Structured-Dataset-Representations., Comment: 10 pages, 8 figures, 3 tables

Ultraviolet-C light-emitting diodes (UVC-LEDs) have great application in pathogen inactivation under various kinds of situations, especially in the fight against the COVID-19. Unfortunately, its epitaxial wafers are so far limited to 2-inch size, which greatly increases the cost of massive production. In this work, we report the 4-inch crack-free high-power UVC-LED wafer. This achievement relies on a proposed strain-tailored strategy, where a three-dimensional to two-dimensional (3D-2D) transition layer is introduced during the homo-epitaxy of AlN on high temperature annealed (HTA)-AlN template, which successfully drives the original compressive strain into tensile one and thus solves the challenge of realizing high quality Al$_{0.6}$Ga$_{0.4}$N layer with a flat surface. This smooth Al$_{0.6}$Ga$_{0.4}$N layer is nearly pseudomorphically grown on the strain-tailored HTA-AlN template, leading to 4-inch UVC-LED wafers with outstanding performances. Our strategy succeeds in compromising the bottlenecked contradictory in producing large-sized UVC-LED wafer on pronounced crystalline AlN template: The compressive strain in HTA-AlN allows for crack-free 4-inch wafer, but at the same time leads to a deterioration of the AlGaN morphology and crystal quality. The launch of 4-inch wafers makes the chip fabrication process of UVC-LEDs matches the mature blue one, and will definitely speed up the universal of UVC-LED in daily life.

Contrary to the common belief that light-induced halide ion segregation in a mixed halide al-loy occurs within the illuminated area, we find that the Br ions released by light diffuse away from the area, which generates a counter-balancing Coulombic force between the anion deficit and surplus region, together resulting in a macro/mesoscopic size anion ring surrounding the center, showing a photoluminescence ring. Upon removing the illumination, the displaced anions return to the illuminated area, and the restoring force leads to a damped ultra-low-frequency oscillatory ion motion, which may be the first observation of an ionic plasma oscillation in solids.

Very often for the same scientific question, there may exist different techniques or experiments that measure the same numerical quantity. Historically, various methods have been developed to exploit the information within each type of data independently. However, statistical data fusion methods that could effectively integrate multi-source data under a unified framework are lacking. In this paper, we propose a novel data fusion method, called B-scaling, for integrating multi-source data. Consider $K$ measurements that are generated from different sources but measure the same latent variable through some linear or nonlinear ways. We seek to find a representation of the latent variable, named B-mean, which captures the common information contained in the $K$ measurements while takes into account the nonlinear mappings between them and the latent variable. We also establish the asymptotic property of the B-mean and apply the proposed method to integrate multiple histone modifications and DNA methylation levels for characterizing epigenomic landscape. Both numerical and empirical studies show that B-scaling is a powerful data fusion method with broad applications., Comment: To be published in Annals of Applied Statistics

The scalability of highly efficient organic-inorganic perovskite solar cells (PSCs) is one of the remaining challenges of solar module manufacturing. Various scalable methods have been explored to strive for uniform perovskite films of high crystal quality on large-area substrates. However, each of these methods have individual drawbacks, limiting the successful commercialization of perovskite photovoltaics. Here, we report a fully scalable hybrid process, which combines vapor- and solution-based techniques to deposit high quality uniform perovskite films on large-area substrates. This two-step process does not use toxic solvents, and it further allows facile implementation of passivation strategies and additives. We fabricated PSCs based on this process and used blade coating to deposit both charge transporting layers (SnO2 and Spiro-OMeTAD) without hazardous solvents in ambient air. The fabricated PSCs have yielded open-circuit voltage up to 1.16 V and power conversion efficiency of 18.7 % with good uniformity on 5 cm x 5 cm substrates.

Consider a scenario where we are supplied with a number of ready-to-use models trained on a certain source domain and hope to directly apply the most appropriate ones to different target domains based on the models' relative performance. Ideally we should annotate a validation set for model performance assessment on each new target environment, but such annotations are often very expensive. Under this circumstance, we introduce the problem of ranking models in unlabeled new environments. For this problem, we propose to adopt a proxy dataset that 1) is fully labeled and 2) well reflects the true model rankings in a given target environment, and use the performance rankings on the proxy sets as surrogates. We first select labeled datasets as the proxy. Specifically, datasets that are more similar to the unlabeled target domain are found to better preserve the relative performance rankings. Motivated by this, we further propose to search the proxy set by sampling images from various datasets that have similar distributions as the target. We analyze the problem and its solutions on the person re-identification (re-ID) task, for which sufficient datasets are publicly available, and show that a carefully constructed proxy set effectively captures relative performance ranking in new environments. Code is available at \url{https://github.com/sxzrt/Proxy-Set}., Comment: 13 pages, 10 figures, ICCV2021

The divide-and-conquer method has been widely used for estimating large-scale kernel ridge regression estimates. Unfortunately, when the response variable is highly skewed, the divide-and-conquer kernel ridge regression (dacKRR) may overlook the underrepresented region and result in unacceptable results. We combine a novel response-adaptive partition strategy with the oversampling technique synergistically to overcome the limitation. Through the proposed novel algorithm, we allocate some carefully identified informative observations to multiple nodes (local processors). Although the oversampling technique has been widely used for addressing discrete label skewness, extending it to the dacKRR setting is nontrivial. We provide both theoretical and practical guidance on how to effectively over-sample the observations under the dacKRR setting. Furthermore, we show the proposed estimate has a smaller risk than that of the classical dacKRR estimate under mild conditions. Our theoretical findings are supported by both simulated and real-data analyses.