DeepMind, a Google-owned artificial intelligence (AI) company based in the United Kingdom, made scientific history when it announced last November that it had a solution to a 50-year-old grand challenge in biology--protein folding. This AI machine learning breakthrough may help accelerate the discovery of new medications and novel treatments for diseases. On July 15, 2021 DeepMind revealed details on how its AI works in a new peer-reviewed paper published in Nature, and made its revolutionary AlphaFold version 2.0 model available as open-source on GitHub. The three-dimensional (3D) shape and function of proteins are determined by the sequence of its amino acids. AlphaFold predicts three-dimensional (3D) models of protein structures.

A major obstacle to the integration of deep learning models for chest x-ray interpretation into clinical settings is the lack of understanding of their failure modes. In this work, we first investigate whether there are patient subgroups that chest x-ray models are likely to misclassify. We find that patient age and the radiographic finding of lung lesion, pneumothorax or support devices are statistically relevant features for predicting misclassification for some chest x-ray models. Second, we develop misclassification predictors on chest x-ray models using their outputs and clinical features. We find that our best performing misclassification identifier achieves an AUROC close to 0.9 for most diseases. Third, employing our misclassification identifiers, we develop a corrective algorithm to selectively flip model predictions that have high likelihood of misclassification at inference time. We observe F1 improvement on the prediction of Consolidation (0.008 [95% CI 0.005, 0.010]) and Edema (0.003, [95% CI 0.001, 0.006]). By carrying out our investigation on ten distinct and high-performing chest x-ray models, we are able to derive insights across model architectures and offer a generalizable framework applicable to other medical imaging tasks.

In this paper, we describe a reproduction of the Relational Graph Convolutional Network (RGCN). Using our reproduction, we explain the intuition behind the model. Our reproduction results empirically validate the correctness of our implementations using benchmark Knowledge Graph datasets on node classification and link prediction tasks. Our explanation provides a friendly understanding of the different components of the RGCN for both users and researchers extending the RGCN approach. Furthermore, we introduce two new configurations of the RGCN that are more parameter efficient. The code and datasets are available at https://github.com/thiviyanT/torch-rgcn.

Objective: Temporal electronic health records (EHRs) can be a wealth of information for secondary uses, such as clinical events prediction or chronic disease management. However, challenges exist for temporal data representation. We therefore sought to identify these challenges and evaluate novel methodologies for addressing them through a systematic examination of deep learning solutions. Methods: We searched five databases (PubMed, EMBASE, the Institute of Electrical and Electronics Engineers [IEEE] Xplore Digital Library, the Association for Computing Machinery [ACM] digital library, and Web of Science) complemented with hand-searching in several prestigious computer science conference proceedings. We sought articles that reported deep learning methodologies on temporal data representation in structured EHR data from January 1, 2010, to August 30, 2020. We summarized and analyzed the selected articles from three perspectives: nature of time series, methodology, and model implementation. Results: We included 98 articles related to temporal data representation using deep learning. Four major challenges were identified, including data irregularity, data heterogeneity, data sparsity, and model opacity. We then studied how deep learning techniques were applied to address these challenges. Finally, we discuss some open challenges arising from deep learning. Conclusion: Temporal EHR data present several major challenges for clinical prediction modeling and data utilization. To some extent, current deep learning solutions can address these challenges. Future studies can consider designing comprehensive and integrated solutions. Moreover, researchers should incorporate additional clinical domain knowledge into study designs and enhance the interpretability of the model to facilitate its implementation in clinical practice.

The rapid increase in computational power on edge devices has set forth federated learning (FL) as an elegant alternative to traditional cloud/data center based analytics. FL brings training to the edge, where devices collaboratively extract knowledge and learn complex models (most often deep learning models) with the orchestration of a central server while keeping their personal data stored locally. This paradigm shifts not only reduces privacy concerns but also sets forth many intrinsic advantages including cost efficiency, diversity, and reduced communication, amongst many others [39, 18]. The earliest and perhaps most popular FL algorithm is FederatedAveraging (fedavg) [28]. In fedavg, the central server broadcasts a global model (set of weights) to selected edge devices, these devices run updates based on their local data, and the server then takes a weighted average of the resulting local models to update the global model.

When recognizing emotions, subtle nuances of emotion displays often cause ambiguity or uncertainty in emotion perception. Unfortunately, the ambiguity or uncertainty cannot be reflected in hard emotion labels. Emotion predictions with uncertainty can be useful for risk controlling, but they are relatively scarce in current deep models for emotion recognition. To address this issue, we propose to apply the multi-generational self-distillation algorithm to emotion recognition task towards better uncertainty estimation performance. We firstly use deep ensembles to capture uncertainty, as an approximation to Bayesian methods. Secondly, the deep ensemble provides soft labels to its student models, while the student models can learn from the uncertainty embedded in those soft labels. Thirdly, we iteratively train deep ensembles to further improve the performance of emotion recognition and uncertainty estimation. In the end, our algorithm results in a single student model that can estimate in-domain uncertainty and a student ensemble that can detect out-of-domain samples. We trained our Efficient Multitask Emotion Networks (EMENet) on the Aff-wild2 dataset, and conducted extensive experiments on emotion recognition and uncertainty estimation. Our algorithm gives more reliable uncertainty estimates than Temperature Scaling and Monte Carol Dropout.

Recent work introduced deep kernel processes as an entirely kernel-based alternative to NNs (Aitchison et al. 2020). Deep kernel processes flexibly learn good top-layer representations by alternately sampling the kernel from a distribution over positive semi-definite matrices and performing nonlinear transformations. A particular deep kernel process, the deep Wishart process (DWP), is of particular interest because its prior is equivalent to deep Gaussian process (DGP) priors. However, inference in DWPs has not yet been possible due to the lack of sufficiently flexible distributions over positive semi-definite matrices. Here, we give a novel approach to obtaining flexible distributions over positive semi-definite matrices by generalising the Bartlett decomposition of the Wishart probability density. We use this new distribution to develop an approximate posterior for the DWP that includes dependency across layers. We develop a doubly-stochastic inducing-point inference scheme for the DWP and show experimentally that inference in the DWP gives improved performance over doing inference in a DGP with the equivalent prior.

Real-time state estimation of dynamical systems is a fundamental task in signal processing and control. For systems that are well-represented by a fully known linear Gaussian state space (SS) model, the celebrated Kalman filter (KF) is a low complexity optimal solution. However, both linearity of the underlying SS model and accurate knowledge of it are often not encountered in practice. Here, we present KalmanNet, a real-time state estimator that learns from data to carry out Kalman filtering under non-linear dynamics with partial information. By incorporating the structural SS model with a dedicated recurrent neural network module in the flow of the KF, we retain data efficiency and interpretability of the classic algorithm while implicitly learning complex dynamics from data. We numerically demonstrate that KalmanNet overcomes nonlinearities and model mismatch, outperforming classic filtering methods operating with both mismatched and accurate domain knowledge.

We consider the task of feature selection for reconstruction which consists in choosing a small subset of features from which whole data instances can be reconstructed. This is of particular importance in several contexts involving for example costly physical measurements, sensor placement or information compression. To break the intrinsic combinatorial nature of this problem, we formulate the task as optimizing a binary mask distribution enabling an accurate reconstruction. We then face two main challenges. One concerns differentiability issues due to the binary distribution. The second one corresponds to the elimination of redundant information by selecting variables in a correlated fashion which requires modeling the covariance of the binary distribution. We address both issues by introducing a relaxation of the problem via a novel reparameterization of the logitNormal distribution. We demonstrate that the proposed method provides an effective exploration scheme and leads to efficient feature selection for reconstruction through evaluation on several high dimensional image benchmarks. We show that the method leverages the intrinsic geometry of the data, facilitating reconstruction.

Many RGB-T trackers attempt to attain robust feature representation by utilizing an adaptive weighting scheme (or attention mechanism). Different from these works, we propose a new dynamic modality-aware filter generation module (named MFGNet) to boost the message communication between visible and thermal data by adaptively adjusting the convolutional kernels for various input images in practical tracking. Given the image pairs as input, we first encode their features with the backbone network. Then, we concatenate these feature maps and generate dynamic modality-aware filters with two independent networks. The visible and thermal filters will be used to conduct a dynamic convolutional operation on their corresponding input feature maps respectively. Inspired by residual connection, both the generated visible and thermal feature maps will be summarized with input feature maps. The augmented feature maps will be fed into the RoI align module to generate instance-level features for subsequent classification. To address issues caused by heavy occlusion, fast motion, and out-of-view, we propose to conduct a joint local and global search by exploiting a new direction-aware target-driven attention mechanism. The spatial and temporal recurrent neural network is used to capture the direction-aware context for accurate global attention prediction. Extensive experiments on three large-scale RGB-T tracking benchmark datasets validated the effectiveness of our proposed algorithm. The project page of this paper is available at https://sites.google.com/view/mfgrgbttrack/.