Bayesian optimization has proven to be an efficient method to optimize expensive-to-evaluate systems. However, depending on the cost of single observations, multi-dimensional optimizations of one or more objectives may still be prohibitively expensive. Multi-fidelity optimization remedies this issue by including multiple, cheaper information sources such as low-resolution approximations in numerical simulations. Acquisition functions for multi-fidelity optimization are typically based on exploration-heavy algorithms that are difficult to combine with optimization towards multiple objectives. Here we show that the expected hypervolume improvement policy can act in many situations as a suitable substitute. We incorporate the evaluation cost either via a two-step evaluation or within a single acquisition function with an additional fidelity-related objective. This permits simultaneous multi-objective and multi-fidelity optimization, which allows to accurately establish the Pareto set and front at fractional cost. Benchmarks show a cost reduction of an order of magnitude or more. Our method thus allows for Pareto optimization of extremely expansive black-box functions. The presented methods are simple and straightforward to implement in existing, optimized Bayesian optimization frameworks and can immediately be extended to batch optimization. The techniques can also be used to combine different continuous and/or discrete fidelity dimensions, which makes them particularly relevant for simulation problems in plasma physics, fluid dynamics and many other branches of scientific computing.
The ubiquity of fluids in the physical world explains the need to accurately simulate their dynamics for many scientific and engineering applications. Traditionally, well established but resource intensive CFD solvers provide such simulations. The recent years have seen a surge of deep learning surrogate models substituting these solvers to alleviate the simulation process. Some approaches to build data-driven surrogates mimic the solver iterative process. They infer the next state of the fluid given its previous one. Others directly infer the state from time input. Approaches also differ in their management of the spatial information. Graph Neural Networks (GNN) can address the specificity of the irregular meshes commonly used in CFD simulations. In this article, we present our ongoing work to design a novel direct time GNN architecture for irregular meshes. It consists of a succession of graphs of increasing size connected by spline convolutions. We test our architecture on the Von K{\'a}rm{\'a}n's vortex street benchmark. It achieves small generalization errors while mitigating error accumulation along the trajectory.
Manually annotating complex scene point cloud datasets is both costly and error-prone. To reduce the reliance on labeled data, a new model called SnapshotNet is proposed as a self-supervised feature learning approach, which directly works on the unlabeled point cloud data of a complex 3D scene. The SnapshotNet pipeline includes three stages. In the snapshot capturing stage, snapshots, which are defined as local collections of points, are sampled from the point cloud scene. A snapshot could be a view of a local 3D scan directly captured from the real scene, or a virtual view of such from a large 3D point cloud dataset. Snapshots could also be sampled at different sampling rates or fields of view (FOVs), thus multi-FOV snapshots, to capture scale information from the scene. In the feature learning stage, a new pre-text task called multi-FOV contrasting is proposed to recognize whether two snapshots are from the same object or not, within the same FOV or across different FOVs. Snapshots go through two self-supervised learning steps: the contrastive learning step with both part and scale contrasting, followed by a snapshot clustering step to extract higher level semantic features. Then a weakly-supervised segmentation stage is implemented by first training a standard SVM classifier on the learned features with a small fraction of labeled snapshots. The trained SVM is used to predict labels for input snapshots and predicted labels are converted into point-wise label assignments for semantic segmentation of the entire scene using a voting procedure. The experiments are conducted on the Semantic3D dataset and the results have shown that the proposed method is capable of learning effective features from snapshots of complex scene data without any labels. Moreover, the proposed method has shown advantages when comparing to the SOA method on weakly-supervised point cloud semantic segmentation.
We study the task of personalizing ASR models to a target non-native speaker/accent while being constrained by a transcription budget on the duration of utterances selected from a large unlabelled corpus. We propose a subset selection approach using the recently proposed submodular mutual information functions, in which we identify a diverse set of utterances that match the target speaker/accent. This is specified through a few target utterances and achieved by modeling the relationship between the target subset and the selected subset using submodular mutual information functions. This method is applied at both the speaker and accent levels. We personalize the model by fine tuning it with utterances selected and transcribed from the unlabelled corpus. Our method is able to consistently identify utterances from the target speaker/accent using just speech features. We show that the targeted subset selection approach improves upon random sampling by as much as 2% to 5% (absolute) depending on the speaker and accent and is 2x to 4x more label-efficient compared to random sampling. We also compare with a skyline where we specifically pick from the target and our method generally outperforms the oracle in its selections.
The identification of active binding drugs for target proteins (termed as drug-target interaction prediction) is the key challenge in virtual screening, which plays an essential role in drug discovery. Although recent deep learning-based approaches achieved better performance than molecular docking, existing models often neglect certain aspects of the intermolecular information, hindering the performance of prediction. We recognize this problem and propose a novel approach named Intermolecular Graph Transformer (IGT) that employs a dedicated attention mechanism to model intermolecular information with a three-way Transformer-based architecture. IGT outperforms state-of-the-art approaches by 9.1% and 20.5% over the second best for binding activity and binding pose prediction respectively, and shows superior generalization ability to unseen receptor proteins. Furthermore, IGT exhibits promising drug screening ability against SARS-CoV-2 by identifying 83.1% active drugs that have been validated by wet-lab experiments with near-native predicted binding poses.
Deep representation learning on non-Euclidean data types, such as graphs, has gained significant attention in recent years. Invent of graph neural networks has improved the state-of-the-art for both node and the entire graph representation in a vector space. However, for the entire graph representation, most of the existing graph neural networks are trained on a graph classification loss in a supervised way. But obtaining labels of a large number of graphs is expensive for real world applications. Thus, we aim to propose an unsupervised graph neural network to generate a vector representation of an entire graph in this paper. For this purpose, we combine the idea of hierarchical graph neural networks and mutual information maximization into a single framework. We also propose and use the concept of periphery representation of a graph and show its usefulness in the proposed algorithm which is referred as GraPHmax. We conduct thorough experiments on several real-world graph datasets and compare the performance of GraPHmax with a diverse set of both supervised and unsupervised baseline algorithms. Experimental results show that we are able to improve the state-of-the-art for multiple graph level tasks on several real-world datasets, while remain competitive on the others.
Graph Neural Networks (GNNs) have been shown to be a powerful tool for generating predictions from biological data. Their application to neuroimaging data such as functional magnetic resonance imaging (fMRI) scans has been limited. However, applying GNNs to fMRI scans may substantially improve predictive accuracy and could be used to inform clinical diagnosis in the future. In this paper, we present a novel approach to representing resting-state fMRI data as a graph containing nodes and edges without omitting any of the voxels and thus reducing information loss. We compare multiple GNN architectures and show that they can successfully predict the disease and sex of a person. We hope to provide a basis for future work to exploit the power of GNNs when applied to brain imaging data.
Visual-inertial SLAM has been studied widely due to the advantage of its lightweight, cost-effectiveness, and rich information compared to other sensors. A multi-state constrained filter (MSCKF) and its Schmidt version have been developed to address the computational cost, which treats keyframes as static nuisance parameters, leading to sub-optimal performance. We propose a new Compressed-MSCKF which can achieve improved accuracy with moderate computational costs. By keeping the information gain with compressed form, it can limit to $\mathcal{O}(L)$ with $L$ being the number of local keyframes. The performance of the proposed system has been evaluated using a MATLAB simulator.
Keyphrase provides accurate information of document content that is highly compact, concise, full of meanings, and widely used for discourse comprehension, organization, and text retrieval. Though previous studies have made substantial efforts for automated keyphrase extraction and generation, surprisingly, few studies have been made for \textit{keyphrase completion} (KPC). KPC aims to generate more keyphrases for document (e.g. scientific publication) taking advantage of document content along with a very limited number of known keyphrases, which can be applied to improve text indexing system, etc. In this paper, we propose a novel KPC method with an encoder-decoder framework. We name it \textit{deep keyphrase completion} (DKPC) since it attempts to capture the deep semantic meaning of the document content together with known keyphrases via a deep learning framework. Specifically, the encoder and the decoder in DKPC play different roles to make full use of the known keyphrases. The former considers the keyphrase-guiding factors, which aggregates information of known keyphrases into context. On the contrary, the latter considers the keyphrase-inhibited factor to inhibit semantically repeated keyphrase generation. Extensive experiments on benchmark datasets demonstrate the efficacy of our proposed model.
Deep learning can provide rapid brain age estimation based on brain magnetic resonance imaging (MRI). However, most studies use one neural network to extract the global information from the whole input image, ignoring the local fine-grained details. In this paper, we propose a global-local transformer, which consists of a global-pathway to extract the global-context information from the whole input image and a local-pathway to extract the local fine-grained details from local patches. The fine-grained information from the local patches are fused with the global-context information by the attention mechanism, inspired by the transformer, to estimate the brain age. We evaluate the proposed method on 8 public datasets with 8,379 healthy brain MRIs with the age range of 0-97 years. 6 datasets are used for cross-validation and 2 datasets are used for evaluating the generality. Comparing with other state-of-the-art methods, the proposed global-local transformer reduces the mean absolute error of the estimated ages to 2.70 years and increases the correlation coefficient of the estimated age and the chronological age to 0.9853. In addition, our proposed method provides regional information of which local patches are most informative for brain age estimation. Our source code is available on: \url{https://github.com/shengfly/global-local-transformer}.