Abstract: Objective: Dynamic cone-beam CT (CBCT) imaging is highly desired in image-guided radiation therapy to provide volumetric images with high spatial and temporal resolutions to enable applications including tumor motion tracking/prediction and intra-delivery dose calculation/accumulation. However, the dynamic CBCT reconstruction is a substantially challenging spatiotemporal inverse problem, due to the extremely limited projection sample available for each CBCT reconstruction (one projection for one CBCT volume). Approach: We developed a simultaneous spatial and temporal implicit neural representation (STINR) method for dynamic CBCT reconstruction. STINR mapped the unknown image and the evolution of its motion into spatial and temporal multi-layer perceptrons (MLPs), and iteratively optimized the neuron weighting of the MLPs via acquired projections to represent the dynamic CBCT series. In addition to the MLPs, we also introduced prior knowledge, in form of principal component analysis (PCA)-based patient-specific motion models, to reduce the complexity of the temporal INRs to address the ill-conditioned dynamic CBCT reconstruction problem.

Hypergraph neural networks can model multi-way connections among nodes of the graphs, which are common in real-world applications such as genetic medicine. In particular, genetic pathways or gene sets encode molecular functions driven by multiple genes, naturally represented as hyperedges. Thus, hypergraph-guided embedding can capture functional relations in learned representations. Existing hypergraph neural network models often focus on node-level or graph-level inference. There is an unmet need in learning powerful representations of subgraphs of hypergraphs in real-world applications. For example, a cancer patient can be viewed as a subgraph of genes harboring mutations in the patient, while all the genes are connected by hyperedges that correspond to pathways representing specific molecular functions. For accurate inductive subgraph prediction, we propose SubHypergraph Inductive Neural nEtwork (SHINE). SHINE uses informative genetic pathways that encode molecular functions as hyperedges to connect genes as nodes. SHINE jointly optimizes the objectives of end-to-end subgraph classification and hypergraph nodes' similarity regularization. SHINE simultaneously learns representations for both genes and pathways using strongly dual attention message passing. The learned representations are aggregated via a subgraph attention layer and used to train a multilayer perceptron for inductive subgraph inferencing. We evaluated SHINE against a wide array of state-of-the-art (hyper)graph neural networks, XGBoost, NMF and polygenic risk score models, using large scale NGS and curated datasets. SHINE outperformed all comparison models significantly, and yielded interpretable disease models with functional insights.

Traditional Collaborative Filtering (CF) based methods are applied to understand the personal preferences of users/customers for items or products from the rating matrix. Usually, the rating matrix is sparse in nature. So there are some improved variants of the CF method that apply the increasing amount of side information to handle the sparsity problem. Only linear kernel or only non-linear kernel is applied in most of the available recommendation-related work to understand user-item latent feature embeddings from data. Only linear kernel or only non-linear kernel is not sufficient to learn complex user-item features from side information of users. Recently, some researchers have focused on hybrid models that learn some features with non-linear kernels and some other features with linear kernels. But it is very difficult to understand which features can be learned accurately with linear kernels or with non-linear kernels. To overcome this problem, we propose a novel deep fusion model named FusionDeepMF and the novel attempts of this model are i) learning user-item rating matrix and side information through linear and non-linear kernel simultaneously, ii) application of a tuning parameter determining the trade-off between the dual embeddings that are generated from linear and non-linear kernels. Extensive experiments on online review datasets establish that FusionDeepMF can be remarkably futuristic compared to other baseline approaches. Empirical evidence also shows that FusionDeepMF achieves better performances compared to the linear kernels of Matrix Factorization (MF) and the non-linear kernels of Multi-layer Perceptron (MLP).

We present two machine learning methodologies that are capable of predicting diffusion Monte Carlo (DMC) energies with small datasets (~60 DMC calculations in total). The first uses voxel deep neural networks (VDNNs) to predict DMC energy densities using Kohn-Sham density functional theory (DFT) electron densities as input. The second uses kernel ridge regression (KRR) to predict atomic contributions to the DMC total energy using atomic environment vectors as input (we used atom centred symmetry functions, atomic environment vectors from the ANI models, and smooth overlap of atomic positions). We first compare the methodologies on pristine graphene lattices, where we find the KRR methodology performs best in comparison to gradient boosted decision trees, random forest, gaussian process regression, and multilayer perceptrons. In addition, KRR outperforms VDNNs by an order of magnitude. Afterwards, we study the generalizability of KRR to predict the energy barrier associated with a Stone-Wales defect. Lastly, we move from 2D to 3D materials and use KRR to predict total energies of liquid water. In all cases, we find that the KRR models are more accurate than Kohn-Sham DFT and all mean absolute errors are less than chemical accuracy.

Long-latency load requests continue to limit the performance of high-performance processors. To increase the latency tolerance of a processor, architects have primarily relied on two key techniques: sophisticated data prefetchers and large on-chip caches. In this work, we show that: 1) even a sophisticated state-of-the-art prefetcher can only predict half of the off-chip load requests on average across a wide range of workloads, and 2) due to the increasing size and complexity of on-chip caches, a large fraction of the latency of an off-chip load request is spent accessing the on-chip cache hierarchy. The goal of this work is to accelerate off-chip load requests by removing the on-chip cache access latency from their critical path. To this end, we propose a new technique called Hermes, whose key idea is to: 1) accurately predict which load requests might go off-chip, and 2) speculatively fetch the data required by the predicted off-chip loads directly from the main memory, while also concurrently accessing the cache hierarchy for such loads. To enable Hermes, we develop a new lightweight, perceptron-based off-chip load prediction technique that learns to identify off-chip load requests using multiple program features (e.g., sequence of program counters). For every load request, the predictor observes a set of program features to predict whether or not the load would go off-chip. If the load is predicted to go off-chip, Hermes issues a speculative request directly to the memory controller once the load's physical address is generated. If the prediction is correct, the load eventually misses the cache hierarchy and waits for the ongoing speculative request to finish, thus hiding the on-chip cache hierarchy access latency from the critical path of the off-chip load. Our evaluation shows that Hermes significantly improves performance of a state-of-the-art baseline. We open-source Hermes.

Black-box models, such as deep neural networks, exhibit superior predictive performances, but understanding their behavior is notoriously difficult. Many explainable artificial intelligence methods have been proposed to reveal the decision-making processes of black box models. However, their applications in high-stakes domains remain limited. Recently proposed neural additive models (NAM) have achieved state-of-the-art interpretable machine learning. NAM can provide straightforward interpretations with slight performance sacrifices compared with multi-layer perceptron. However, NAM can only model 1$^{\text{st}}$-order feature interactions; thus, it cannot capture the co-relationships between input features. To overcome this problem, we propose a novel interpretable machine learning method called higher-order neural additive models (HONAM) and a feature interaction method for high interpretability. HONAM can model arbitrary orders of feature interactions. Therefore, it can provide the high predictive performance and interpretability that high-stakes domains need. In addition, we propose a novel hidden unit to effectively learn sharp-shape functions. We conducted experiments using various real-world datasets to examine the effectiveness of HONAM. Furthermore, we demonstrate that HONAM can achieve fair AI with a slight performance sacrifice. The source code for HONAM is publicly available.

We present an error-neural-modeling-based strategy for approximating two-dimensional curvature in the level-set method. Our main contribution is a redesigned hybrid solver [Larios-C\'ardenas and Gibou, J. Comput. Phys. (May 2022), 10.1016/j.jcp.2022.111291] that relies on numerical schemes to enable machine-learning operations on demand. In particular, our routine features double predicting to harness curvature symmetry invariance in favor of precision and stability. The core of this solver is a multilayer perceptron trained on circular- and sinusoidal-interface samples. Its role is to quantify the error in numerical curvature approximations and emit corrected estimates for select grid vertices along the free boundary. These corrections arise in response to preprocessed context level-set, curvature, and gradient data. To promote neural capacity, we have adopted sample negative-curvature normalization, reorientation, and reflection-based augmentation. In the same manner, our system incorporates dimensionality reduction, well-balancedness, and regularization to minimize outlying effects. Our training approach is likewise scalable across mesh sizes. For this purpose, we have introduced dimensionless parametrization and probabilistic subsampling during data production. Together, all these elements have improved the accuracy and efficiency of curvature calculations around under-resolved regions. In most experiments, our strategy has outperformed the numerical baseline at twice the number of redistancing steps while requiring only a fraction of the cost.

Reasoning is a fundamental problem for computers and deeply studied in Artificial Intelligence. In this paper, we specifically focus on answering multi-hop logical queries on Knowledge Graphs (KGs). This is a complicated task because, in real-world scenarios, the graphs tend to be large and incomplete. Most previous works have been unable to create models that accept full First-Order Logical (FOL) queries, which include negative queries, and have only been able to process a limited set of query structures. Additionally, most methods present logic operators that can only perform the logical operation they are made for. We introduce a set of models that use Neural Networks to create one-point vector embeddings to answer the queries. The versatility of neural networks allows the framework to handle FOL queries with Conjunction ($\wedge$), Disjunction ($\vee$) and Negation ($\neg$) operators. We demonstrate experimentally the performance of our model through extensive experimentation on well-known benchmarking datasets. Besides having more versatile operators, the models achieve a 10\% relative increase over the best performing state of the art and more than 30\% over the original method based on single-point vector embeddings.

A distinctive representation of image patches in form of features is a key component of many computer vision and robotics tasks, such as image matching, image retrieval, and visual localization. State-of-the-art descriptors, from hand-crafted descriptors such as SIFT to learned ones such as HardNet, are usually high dimensional; 128 dimensions or even more. The higher the dimensionality, the larger the memory consumption and computational time for approaches using such descriptors. In this paper, we investigate multi-layer perceptrons (MLPs) to extract low-dimensional but high-quality descriptors. We thoroughly analyze our method in unsupervised, self-supervised, and supervised settings, and evaluate the dimensionality reduction results on four representative descriptors. We consider different applications, including visual localization, patch verification, image matching and retrieval. The experiments show that our lightweight MLPs achieve better dimensionality reduction than PCA. The lower-dimensional descriptors generated by our approach outperform the original higher-dimensional descriptors in downstream tasks, especially for the hand-crafted ones. The code will be available at https://github.com/PRBonn/descriptor-dr.

When dealing with clinical text classification on a small dataset recent studies have confirmed that a well-tuned multilayer perceptron outperforms other generative classifiers, including deep learning ones. To increase the performance of the neural network classifier, feature selection for the learning representation can effectively be used. However, most feature selection methods only estimate the degree of linear dependency between variables and select the best features based on univariate statistical tests. Furthermore, the sparsity of the feature space involved in the learning representation is ignored. Goal: Our aim is therefore to access an alternative approach to tackle the sparsity by compressing the clinical representation feature space, where limited French clinical notes can also be dealt with effectively. Methods: This study proposed an autoencoder learning algorithm to take advantage of sparsity reduction in clinical note representation. The motivation was to determine how to compress sparse, high-dimensional data by reducing the dimension of the clinical note representation feature space. The classification performance of the classifiers was then evaluated in the trained and compressed feature space. Results: The proposed approach provided overall performance gains of up to 3% for each evaluation. Finally, the classifier achieved a 92% accuracy, 91% recall, 91% precision, and 91% f1-score in detecting the patient's condition. Furthermore, the compression working mechanism and the autoencoder prediction process were demonstrated by applying the theoretic information bottleneck framework.