Augmented Equivariant Attention Networks for Microscopy Image Reconstruction

It is time-consuming and expensive to take high-quality or high-resolution electron microscopy (EM) and fluorescence microscopy (FM) images. Taking these images could be even invasive to samples and may damage certain subtleties in the samples after long or intense exposures, often necessary for achieving high-quality or high resolution in the first place. Advances in deep learning enable us to perform image-to-image transformation tasks for various types of microscopy image reconstruction, computationally producing high-quality images from the physically acquired low-quality ones. When training image-to-image transformation models on pairs of experimentally acquired microscopy images, prior models suffer from performance loss due to their inability to capture inter-image dependencies and common features shared among images. Existing methods that take advantage of shared features in image classification tasks cannot be properly applied to image reconstruction tasks because they fail to preserve the equivariance property under spatial permutations, something essential in image-to-image transformation. To address these limitations, we propose the augmented equivariant attention networks (AEANets) with better capability to capture inter-image dependencies, while preserving the equivariance property. The proposed AEANets captures inter-image dependencies and shared features via two augmentations on the attention mechanism, which are the shared references and the batch-aware attention during training. We theoretically derive the equivariance property of the proposed augmented attention model and experimentally demonstrate its consistent superiority in both quantitative and visual results over the baseline methods.Comment: 11 pages, 8 figure

Deep Causal Reasoning for Recommendations

Traditional recommender systems aim to estimate a user's rating to an item based on observed ratings from the population. As with all observational studies, hidden confounders, which are factors that affect both item exposures and user ratings, lead to a systematic bias in the estimation. Consequently, a new trend in recommender system research is to negate the influence of confounders from a causal perspective. Observing that confounders in recommendations are usually shared among items and are therefore multi-cause confounders, we model the recommendation as a multi-cause multi-outcome (MCMO) inference problem. Specifically, to remedy confounding bias, we estimate user-specific latent variables that render the item exposures independent Bernoulli trials. The generative distribution is parameterized by a DNN with factorized logistic likelihood and the intractable posteriors are estimated by variational inference. Controlling these factors as substitute confounders, under mild assumptions, can eliminate the bias incurred by multi-cause confounders. Furthermore, we show that MCMO modeling may lead to high variance due to scarce observations associated with the high-dimensional causal space. Fortunately, we theoretically demonstrate that introducing user features as pre-treatment variables can substantially improve sample efficiency and alleviate overfitting. Empirical studies on simulated and real-world datasets show that the proposed deep causal recommender shows more robustness to unobserved confounders than state-of-the-art causal recommenders. Codes and datasets are released at https://github.com/yaochenzhu/deep-deconf

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science

Hemingway’s Language Style and Writing Techniques in \u3cem\u3eThe Old Man and the Sea\u3c/em\u3e

Commentary on Hemingway’s deliberate manipulation of language and facts in The Old Man and the Sea resulting in both a seemingly natural prose style and believable fictional narrative

The Spatio-Temporal Characteristics and Influencing Factors of Covid-19 Spread in Shenzhen, China—An Analysis Based on 417 Cases

The global pandemic of COVID-19 has made it the focus of current attention. At present, the law of COVID-19 spread in cities is not clear. Cities have long been difficult areas for epidemic prevention and control because of the high population density, high mobility of people, and high frequency of contacts. This paper analyzed case information for 417 patients with COVID-19 in Shenzhen, China. The nearest neighbor index method, kernel density method, and the standard deviation ellipse method were used to analyze the spatio-temporal characteristics of the COVID-19 spread in Shenzhen. The factors influencing that spread were then explored using the multiple linear regression method. The results show that: (1) The development of COVID-19 epidemic situation in Shenzhen occurred in three stages. The patients showed significant hysteresis from the onset of symptoms to hospitalization and then to diagnosis. Prior to 27 January, there was a relatively long time interval between the onset of symptoms and hospitalization for COVID-19; the interval decreased thereafter. (2) The epidemic site (the place where the patient stays during the onset of the disease) showed an agglomeration in space. The degree of agglomeration constantly increased across the three time nodes of 31 January, 14 February, and 22 February. The epidemic sites formed a “core area” in terms of spatial distribution and spread along the “northwest–southeast” direction of the city. (3) Economic and social factors significantly impacted the spread of COVID-19, while environmental factors have not played a significant role

Value Assessment of Health Losses Caused by PM_2.5 Pollution in Cities of Atmospheric Pollution Transmission Channel in the Beijing–Tianjin–Hebei Region, China

A set of exposure–response coefficients between fine particulate matter (PM2.5) pollution and different health endpoints were determined through the meta-analysis method based on 2254 studies collected from the Web of Science database. With data including remotely-sensed PM2.5 concentration, demographic data, health data, and survey data, a Poisson regression model was used to assess the health losses and their economic value caused by PM2.5 pollution in cities of atmospheric pollution transmission channel in the Beijing–Tianjin–Hebei region, China. The results showed the following: (1) Significant exposure–response relationships existed between PM2.5 pollution and a set of health endpoints, including all-cause death, death from circulatory disease, death from respiratory disease, death from lung cancer, hospitalization for circulatory disease, hospitalization for respiratory disease, and outpatient emergency treatment. Each increase of 10 μg/m3 in PM2.5 concentration led to an increase of 5.69% (95% CI (confidence interval): 4.12%, 7.85%), 6.88% (95% CI: 4.94%, 9.58%), 4.71% (95% CI: 2.93%, 7.57%), 9.53% (95% CI: 6.84%, 13.28%), 5.33% (95% CI: 3.90%, 7.27%), 5.50% (95% CI: 4.09%, 7.38%), and 6.35% (95% CI: 4.71%, 8.56%) for above-mentioned health endpoints, respectively. (2) PM2.5 pollution posed a serious threat to residents’ health. In 2016, the number of deaths, hospitalizations, and outpatient emergency visits induced by PM2.5 pollution in cities of atmospheric pollution transmission channel in the Beijing–Tianjin–Hebei region reached 309,643, 1,867,240, and 47,655,405, respectively, accounting for 28.36%, 27.02% and 30.13% of the total number of deaths, hospitalizations, and outpatient emergency visits, respectively. (3) The economic value of health losses due to PM2.5 pollution in the study area was approximately $28.1 billion, accounting for 1.52% of the gross domestic product. The economic value of health losses was higher in Beijing, Tianjin, Shijiazhuang, Zhengzhou, Handan, Baoding, and Cangzhou, but lower in Taiyuan, Yangquan, Changzhi, Jincheng, and Hebi

Estimating Relations of Vegetation, Climate Change, and Human Activity: A Case Study in the 400 mm Annual Precipitation Fluctuation Zone, China

The 400 mm annual precipitation fluctuation zone (75°55′–127°6′E and 26°55′–53°6′N) is located in central and western China, which is a transition area from traditional agricultural to animal husbandry. It is extremely sensitive to climatic changes. The corresponding changes of the ecosystem, represented by vegetation, under the dual influences of climate change and human activities are important issues in the study of the regional ecological environment. Based on the Savitzky–Golay (S–G) filtering method, the Global Inventory Modeling and Mapping Studies (GIMMS) Normalized Differential Vegetation Index (NDVI) dataset (NDVI3g) was reconstructed in this paper. Sen’s slope estimation, Mann–Kendall (M–K), multiple regression residual analysis, and the Hurst index were used to quantify the impacts of climate change and human activities on vegetation; in addition, the future persistence characteristics of the vegetation changes trend were analyzed. Vegetation changes in the study area had an obvious spatio-temporal heterogeneity. On an annual scale, the vegetation increased considerably, with a growth rate of 0.50%/10a. The multi-year mean value of NDVI and growth rate of cultivated land were the highest, followed by the forest land and grassland. On a seasonal scale, the vegetation cover increased most significantly in autumn, followed by spring and summer. In the southeastern and central parts of the study area, the vegetation cover increased significantly (P < 0.05), while it decreased significantly in the northeastern and southwestern parts. In summer, the NDVI value of all vegetation types (cultivated land, forest land and grassland) reached the maximum. The change rate of NDVI value for cultivated land reached the highest in autumn (1.57%/10a), forest land reached the highest in spring (1.15%/10a), and grassland reached the highest in autumn (0.49%/10a). The NDVI of cultivated land increased in all seasons, while forest land (−0.31%/10a) and grassland (−0.009%/10a) decreased in winter. Partial correlation analysis between vegetation and precipitation, temperature found that the areas with positive correlation accounted for 66.29% and 55.05% of the total area, respectively. Under the influence of climate change alone, 62.79% of the study area showed an increasing tendency, among which 46.79% showed a significant upward trend (P < 0.05). The NDVI decreased in 37.21% of the regions and decreased significantly in 14.88% of the regions (P < 0.05). Under the influence of human activities alone, the vegetation in the study area showed an upward trend in 59.61%, with a significant increase in 41.35% (P < 0.05), a downward trend in 40.39%, and a significant downward trend in 7.95% (P < 0.05). Vegetation growth is highly unstable and prone to drastic changes, depending on the environmental conditions