Numerical Strategies of Computing the Luminosity Distance

We propose two efficient numerical methods of evaluating the luminosity distance in the spatially flat {\Lambda}CDM universe. The first method is based on the Carlson symmetric form of elliptic integrals, which is highly accurate and can replace numerical quadratures. The second method, using a modified version of Hermite interpolation, is less accurate but involves only basic numerical operations and can be easily implemented. We compare our methods with other numerical approximation schemes and explore their respective features and limitations. Possible extensions of these methods to other cosmological models are also discussed.Comment: 4 pages, 2 figures. v2: A minor error in the last equation has been corrected (conclusions are not affected). v3: Accepted by MNRA

Masked Images Are Counterfactual Samples for Robust Fine-tuning

Deep learning models are challenged by the distribution shift between the training data and test data. Recently, the large models pre-trained on diverse data demonstrate unprecedented robustness to various distribution shifts. However, fine-tuning on these models can lead to a trade-off between in-distribution (ID) performance and out-of-distribution (OOD) robustness. Existing methods for tackling this trade-off do not explicitly address the OOD robustness problem. In this paper, based on causal analysis on the aforementioned problems, we propose a novel fine-tuning method, which use masked images as counterfactual samples that help improving the robustness of the fine-tuning model. Specifically, we mask either the semantics-related or semantics-unrelated patches of the images based on class activation map to break the spurious correlation, and refill the masked patches with patches from other images. The resulting counterfactual samples are used in feature-based distillation with the pre-trained model. Extensive experiments verify that regularizing the fine-tuning with the proposed masked images can achieve a better trade-off between ID and OOD performance, surpassing previous methods on the OOD performance. Our code will be publicly available.Comment: Accepted by CVPR 2023 (v2: improve the clarity

CSMD: a computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples

Motivation Microbiome analyses of clinical samples with low microbial biomass are challenging because of the very small quantities of microbial DNA relative to the human host, ubiquitous contaminating DNA in sequencing experiments and the large and rapidly growing microbial reference databases. Results We present computational subtraction-based microbiome discovery (CSMD), a bioinformatics pipeline specifically developed to generate accurate species-level microbiome profiles for clinical samples with low microbial loads. CSMD applies strategies for the maximal elimination of host sequences with minimal loss of microbial signal and effectively detects microorganisms present in the sample with minimal false positives using a stepwise convergent solution. CSMD was benchmarked in a comparative evaluation with other classic tools on previously published well-characterized datasets. It showed higher sensitivity and specificity in host sequence removal and higher specificity in microbial identification, which led to more accurate abundance estimation. All these features are integrated into a free and easy-to-use tool. Additionally, CSMD applied to cell-free plasma DNA showed that microbial diversity within these samples is substantially broader than previously believed. Availability and implementation CSMD is freely available at https://github.com/liuyu8721/csmd

Exploring Format Consistency for Instruction Tuning

Instruction tuning has emerged as a promising approach to enhancing large language models in following human instructions. It is shown that increasing the diversity and number of instructions in the training data can consistently enhance generalization performance, which facilitates a recent endeavor to collect various instructions and integrate existing instruction tuning datasets into larger collections. However, different users have their unique ways of expressing instructions, and there often exist variations across different datasets in the instruction styles and formats, i.e., format inconsistency. In this work, we study how format inconsistency may impact the performance of instruction tuning. We propose a framework called "Unified Instruction Tuning" (UIT), which calls OpenAI APIs for automatic format transfer among different instruction tuning datasets. We show that UIT successfully improves the generalization performance on unseen instructions, which highlights the importance of format consistency for instruction tuning. To make the UIT framework more practical, we further propose a novel perplexity-based denoising method to reduce the noise of automatic format transfer. We also train a smaller offline model that achieves comparable format transfer capability than OpenAI APIs to reduce costs in practice