Cell–cell communications are vital for biological signalling and play important roles in complex diseases. Recent advances in single-cell spatial transcriptomics (SCST) technologies allow examining the spatial cell communication landscapes and hold the promise for disentangling the complex ligand–receptor (L–R) interactions across cells. However, due to frequent dropout events and noisy signals in SCST data, it is challenging and lack of effective and tailored methods to accurately infer cellular communications. Herein, to decipher the cell-to-cell communications from SCST profiles, we propose a novel adaptive graph model with attention mechanisms named spaCI. spaCI incorporates both spatial locations and gene expression profiles of cells to identify the active L–R signalling axis across neighbouring cells. Through benchmarking with currently available methods, spaCI shows superior performance on both simulation data and real SCST datasets. Furthermore, spaCI is able to identify the upstream transcriptional factors mediating the active L–R interactions. For biological insights, we have applied spaCI to the seqFISH+ data of mouse cortex and the NanoString CosMx Spatial Molecular Imager (SMI) data of non-small cell lung cancer samples. spaCI reveals the hidden L–R interactions from the sparse seqFISH+ data, meanwhile identifies the inconspicuous L–R interactions including THBS1−ITGB1 between fibroblast and tumours in NanoString CosMx SMI data. spaCI further reveals that SMAD3 plays an important role in regulating the crosstalk between fibroblasts and tumours, which contributes to the prognosis of lung cancer patients. Collectively, spaCI addresses the challenges in interrogating SCST data for gaining insights into the underlying cellular communications, thus facilitates the discoveries of disease mechanisms, effective biomarkers and therapeutic targets.

Unmanned Aerial Systems, hereafter referred to as UAS, are of great use in hazard events such as wildfire due to their ability to provide high-resolution video imagery over areas deemed too dangerous for manned aircraft and ground crews. This aerial perspective allows for identification of ground-based hazards such as spot fires and fire lines, and to communicate this information with fire fighting crews. Current technology relies on visual interpretation of UAS imagery, with little to no computer-assisted automatic detection. With the help of big labeled data and the significant increase of computing power, deep learning has seen great successes on object detection with fixed patterns, such as people and vehicles. However, little has been done for objects, such as spot fires, with amorphous and irregular shapes. Additional challenges arise when data are collected via UAS as high-resolution aerial images or videos; an ample solution must provide reasonable accuracy with low delays. In this paper, we examined 4K ( $3840\times 2160$ ) videos collected by UAS from a controlled burn and created a set of labeled video sets to be shared for public use. We introduce a coarse-to-fine framework to auto-detect wildfires that are sparse, small, and irregularly-shaped. The coarse detector adaptively selects the sub-regions that are likely to contain the objects of interest while the fine detector passes only the details of the sub-regions, rather than the entire 4K region, for further scrutiny. The proposed two-phase learning therefore greatly reduced time overhead and is capable of maintaining high accuracy. Compared against the real-time one-stage object backbone of YoloV3, the proposed methods improved the mean average precision(mAP) from $0.29$ to $0.67$ , with an average inference speed of 7.44 frames per second. Limitations and future work are discussed with regard to the design and the experiment results.

Recent advancements in spatial imaging technologies have revolutionized the acquisition of high-resolution multichannel images, gene expressions, and spatial locations at the single-cell level. Our study introduces xSiGra, an interpretable graph-based AI model, designed to elucidate interpretable features of identified spatial cell types, by harnessing multimodal features from spatial imaging technologies. By constructing a spatial cellular graph with immunohistology images and gene expression as node attributes, xSiGra employs hybrid graph transformer models to delineate spatial cell types. Additionally, xSiGra integrates a novel variant of gradient-weighted class activation mapping component to uncover interpretable features, including pivotal genes and cells for various cell types, thereby facilitating deeper biological insights from spatial data. Through rigorous benchmarking against existing methods, xSiGra demonstrates superior performance across diverse spatial imaging datasets. Application of xSiGra on a lung tumor slice unveils the importance score of cells, illustrating that cellular activity is not solely determined by itself but also impacted by neighboring cells. Moreover, leveraging the identified interpretable genes, xSiGra reveals endothelial cell subset interacting with tumor cells, indicating its heterogeneous underlying mechanisms within complex cellular interactions.

Regression problems that have closed-form solutions are well understood and can be easily implemented when the dataset is small enough to be all loaded into the RAM. Challenges arise when data is too big to be stored in RAM to compute the closed form solutions. Many techniques were proposed to overcome or alleviate the memory barrier problem but the solutions are often local optimal. In addition, most approaches require accessing the raw data again when updating the models. Parallel computing clusters are also expected if multiple models need to be computed simultaneously. We propose multiple learning approaches that utilize an array of sufficient statistics (SS) to address this big data challenge. This memory oblivious approach breaks the memory barrier when computing regressions with closed-form solutions, including but not limited to linear regression, weighted linear regression, linear regression with Box-Cox transformation (Box-Cox regression) and ridge regression models. The computation and update of the SS array can be handled at per row level or per mini-batch level. And updating a model is as easy as matrix addition and subtraction. Furthermore, multiple SS arrays for different models can be easily computed simultaneously to obtain multiple models at one pass through the dataset. We implemented our approaches on Spark and evaluated over the simulated datasets. Results showed our approaches can achieve closed-form solutions of multiple models at the cost of half training time of the traditional methods for a single model.