The success of training computer-vision models heavily relies on the support of large-scale, real-world images with annotations. Yet such an annotation-ready dataset is difficult to curate in pathology due to the privacy protection and excessive annotation burden. To aid in computational pathology, synthetic data generation, curation, and annotation present a cost-effective means to quickly enable data diversity that is required to boost model performance at different stages. In this study, we introduce a large-scale synthetic pathological image dataset paired with the annotation for nuclei semantic segmentation, termed as Synthetic Nuclei and annOtation Wizard (SNOW). The proposed SNOW is developed via a standardized workflow by applying the off-the-shelf image generator and nuclei annotator. The dataset contains overall 20k image tiles and 1,448,522 annotated nuclei with the CC-BY license. We show that SNOW can be used in both supervised and semi-supervised training scenarios. Extensive results suggest that synthetic-data-trained models are competitive under a variety of model training settings, expanding the scope of better using synthetic images for enhancing downstream data-driven clinical tasks.

We present FengWu, an advanced data-driven global medium-range weather forecast system based on Artificial Intelligence (AI). Different from existing data-driven weather forecast methods, FengWu solves the medium-range forecast problem from a multi-modal and multi-task perspective. Specifically, a deep learning architecture equipped with model-specific encoder-decoders and cross-modal fusion Transformer is elaborately designed, which is learned under the supervision of an uncertainty loss to balance the optimization of different predictors in a region-adaptive manner. Besides this, a replay buffer mechanism is introduced to improve medium-range forecast performance. With 39-year data training based on the ERA5 reanalysis, FengWu is able to accurately reproduce the atmospheric dynamics and predict the future land and atmosphere states at 37 vertical levels on a 0.25° latitude-longitude resolution. Hindcasts of 6-hourly weather in 2018 based on ERA5 demonstrate that FengWu performs better than GraphCast in predicting 80% of the 880 reported predictands, e.g., reducing the root mean square error (RMSE) of 10-day lead global z500 prediction from 733 to 651 m2/s2. In addition, the inference cost of each iteration is merely 600ms on NVIDIA Tesla A100 hardware. The results suggest that FengWu can significantly improve the forecast skill and extend the skillful global medium-range weather forecast out to 10.75 days lead (with ACC of z500 > 0.6) for the first time.

Most natural and synthetic antibodies are ‘unseen’. That is, the demonstration of their neutralization effects with any antigen requires laborious and costly wet-lab experiments. The existing methods that learn antibody representations from known antibody–antigen interactions are unsuitable for unseen antibodies owing to the absence of interaction instances. The DeepAAI method proposed herein learns unseen antibody representations by constructing two adaptive relation graphs among antibodies and antigens and applying Laplacian smoothing between unseen and seen antibodies’ representations. Rather than using static protein descriptors, DeepAAI learns representations and relation graphs ‘dynamically’, optimized towards the downstream tasks of neutralization prediction and 50% inhibition concentration estimation. The performance of DeepAAI is demonstrated on human immunodeficiency virus, severe acute respiratory syndrome coronavirus 2, influenza and dengue. Moreover, the relation graphs have rich interpretability. The antibody relation graph implies similarity in antibody neutralization reactions, and the antigen relation graph indicates the relation among a virus’s different variants. We accordingly recommend probable broad-spectrum antibodies against new variants of these viruses.

The model was developed on 459 colon tumour whole-slide images from TCGA-COAD, and externally validated on 165 rectum tumour whole-slide images from TCGA-READ and 161 colon tumour whole-slide images from CPTAC-COAD. For TCGA cohorts, our method accurately predicted the molecular classes of the gene mutations (area under the curve [AUCs] from 82·54 [95% CI 77·41–87·14] to 87·08 [83·28–90·82] on TCGA-COAD, and AUCs from 70·46 [61·37–79·61] to 81·80 [72·20–89·70] on TCGA-READ), along with genes with copy number alterations (AUCs from 81·98 [73·34–89·68] to 90·55 [86·02–94·89] on TCGA-COAD, and AUCs from 62·05 [48·94–73·46] to 76·48 [64·78–86·71] on TCGA-READ), microsatellite instability (MSI) status classification (AUC 83·92 [77·41–87·59] on TCGA-COAD, and AUC 61·28 [53·28–67·93] on TCGA-READ), and protein expressions (AUCs from 85·57 [81·16–89·44] to 89·64 [86·29–93·19] on TCGA-COAD, and AUCs from 51·77 [42·53–61·83] to 59·79 [50·79–68·57] on TCGA-READ). For the CPTAC-COAD cohort, our model predicted a panel of gene mutations with AUC values from 63·74 (95% CI 52·92–75·37) to 82·90 (73·69–90·71), genes with copy number alterations with AUC values from 62·39 (51·37–73·76) to 86·08 (79·67–91·74), and MSI status prediction with AUC value of 73·15 (63·21–83·13).

Protein side chains are vitally important to many biological processes such as protein–protein interaction. In this study, we evaluate the performance of our previous released side-chain modeling method OPUS-Mut, together with some other methods, on three oligomer datasets, CASP14 (11), CAMEO-Homo (65) and CAMEO-Hetero (21). The results show that OPUS-Mut outperforms other methods measured by all residues or by the interfacial residues. We also demonstrate our method on evaluating protein–protein docking pose on a dataset Oligomer-Dock (75) created using the top 10 predictions from ZDOCK 3.0.2. Our scoring function correctly identifies the native pose as the top-1 in 45 out of 75 targets. Different from traditional scoring functions, our method is based on the overall side-chain packing favorableness in accordance with the local packing environment. It emphasizes the significance of side chains and provides a new and effective scoring term for studying protein–protein interaction.

3D visual perception tasks, including 3D detection and map segmentation based on multi-camera images, are essential for autonomous driving systems. In this work, we present a new framework termed BEVFormer, which learns unified BEV representations with spatiotemporal transformers to support multiple autonomous driving perception tasks. In a nutshell, BEVFormer exploits both spatial and temporal information by interacting with spatial and temporal space through predefined grid-shaped BEV queries. To aggregate spatial information, we design a spatial cross-attention that each BEV query extracts the spatial features from the regions of interest across camera views. For temporal information, we propose a temporal self-attention to recurrently fuse the history BEV information. Our approach achieves the new state-of-the-art 56.9% in terms of NDS metric on the nuScenes test set, which is 9.0 points higher than previous best arts and on par with the performance of LiDAR-based baselines. We further show that BEVFormer remarkably improves the accuracy of velocity estimation and recall of objects under low visibility conditions. The code will be released at https://github.com/zhiqi-li/BEVFormer