Searching to Exploit Memorization Effect in Deep Learning with Noisy Labels.

Sample selection approaches are popular in robust learning from noisy labels. However, how to control the selection process properly so that deep networks can benefit from the memorization effect is a hard problem. In this paper, motivated by the success of automated machine learning (AutoML), we propose to control the selection process by bi-level optimization. Specifically, we parameterize the selection process by exploiting the general patterns of the memorization effect in the upper-level, and then update these parameters using predicting accuracy obtained from model training in the lower-level. We further introduce semi-supervised learning algorithms to utiilize noisy-labeled data as unlabeled data. To solve the bi-level optimization problem efficiently, we consider more information from the validation curvature by the Newton method and cubic regularization method. We provide convergence analysis for both optimization methods. Results show that while both methods can converge to an (approximately) stationary point, the cubic regularization method can find better local optimal than the Newton method with less time. Experiments on both benchmark and real-world data sets demonstrate that the proposed searching method can lead to significant improvements upon existing methods. Compared with existing AutoML approaches, our method is much more efficient on finding a good selection schedule.

Accurate and interpretable drug-drug interaction prediction enabled by knowledge subgraph learning.

BACKGROUND: Discovering potential drug-drug interactions (DDIs) is a long-standing challenge in clinical treatments and drug developments. Recently, deep learning techniques have been developed for DDI prediction. However, they generally require a huge number of samples, while known DDIs are rare. METHODS: In this work, we present KnowDDI, a graph neural network-based method that addresses the above challenge. KnowDDI enhances drug representations by adaptively leveraging rich neighborhood information from large biomedical knowledge graphs. Then, it learns a knowledge subgraph for each drug-pair to interpret the predicted DDI, where each of the edges is associated with a connection strength indicating the importance of a known DDI or resembling strength between a drug-pair whose connection is unknown. Thus, the lack of DDIs is implicitly compensated by the enriched drug representations and propagated drug similarities. RESULTS: Here we show the evaluation results of KnowDDI on two benchmark DDI datasets. Results show that KnowDDI obtains the state-of-the-art prediction performance with better interpretability. We also find that KnowDDI suffers less than existing works given a sparser knowledge graph. This indicates that the propagated drug similarities play a more important role in compensating for the lack of DDIs when the drug representations are less enriched. CONCLUSIONS: KnowDDI nicely combines the efficiency of deep learning techniques and the rich prior knowledge in biomedical knowledge graphs. As an original open-source tool, KnowDDI can help detect possible interactions in a broad range of relevant interaction prediction tasks, such as protein-protein interactions, drug-target interactions and disease-gene interactions, eventually promoting the development of biomedicine and healthcare.

Understanding how drugs interact is crucial for safe healthcare and the development of new medicines. We developed a computational tool that can analyze the data about medicines within large medical databases and predict the impact of being treated by multiple drugs at the same time on the person taking the drugs. Our tool, named KnowDDI, can predict which drugs interact with each other and also provide an explanation for why the interaction is likely to take place. We demonstrated that our tool can identify known drug interactions. It could potentially be used in the future to identify previously unknown or unanticipated interactions that could have negative consequences to people being treated with unusual combinations of medicines.

Property-Aware Relation Networks for Few-Shot Molecular Property Prediction.

Molecular property prediction plays a fundamental role in AI-aided drug discovery to identify candidate molecules, which is also essentially a few-shot problem due to lack of labeled data. In this paper, we propose Property-Aware Relation networks (PAR) to handle this problem. We first introduce a property-aware molecular encoder to transform the generic molecular embeddings to property-aware ones. Then, we design a query-dependent relation graph learning module to estimate molecular relation graph and refine molecular embeddings w.r.t. the target property. Thus, the facts that both property-related information and relationships among molecules change across different properties are utilized to better learn and propagate molecular embeddings. Generally, PAR can be regarded as a combination of metric-based and optimization-based few-shot learning method. We further extend PAR to Transferable PAR (T-PAR) to handle the distribution shift, which is common in drug discovery. The keys are joint sampling and relation graph learning schemes, which simultaneously learn molecular embeddings from both source and target domains. Extensive results on benchmark datasets show that PAR and T-PAR consistently outperform existing methods on few-shot and transferable few-shot molecular property prediction tasks, respectively. Besides, ablation and case studies are conducted to validate the rationality of our designs in PAR and T-PAR.

Deep Factor Learning for Accurate Brain Neuroimaging Data Analysis on Discrimination for Structural MRI and Functional MRI.

Analysis of neuroimaging data (e.g., Magnetic Resonance Imaging, structural and functional MRI) plays an important role in monitoring brain dynamics and probing brain structures. Neuroimaging data are multi-featured and non-linear by nature, and it is a natural way to organise these data as tensors prior to performing automated analyses such as discrimination of neurological disorders like Parkinson's Disease (PD) and Attention Deficit and Hyperactivity Disorder (ADHD). However, the existing approaches are often subject to performance bottlenecks (e.g., conventional feature extraction and deep learning based feature construction), as these can lose the structural information that correlates multiple data dimensions or/and demands excessive empirical and application-specific settings. This study proposes a Deep Factor Learning model on a Hilbert Basis tensor (namely, HB-DFL) to automatically derive latent low-dimensional and concise factors of tensors. This is achieved through the application of multiple Convolutional Neural Networks (CNNs) in a non-linear manner along all possible dimensions with no assumed a priori knowledge. HB-DFL leverages the Hilbert basis tensor to enhance the stability of the solution by regularizing the core tensor to allow any component in a certain domain to interact with any component in the other dimensions. The final multi-domain features are handled through another multi-branch CNN to achieve reliable classification, exemplified here using MRI discrimination as a typical case. A case study of MRI discrimination has been performed on public MRI datasets for discrimination of PD and ADHD. Results indicate that 1) HB-DFL outperforms the counterparts in terms of FIT, mSIR and stability (mSC and umSC) of factor learning; 2) HB-DFL identifies PD and ADHD with an accuracy significantly higher than state-of-the-art methods do. Overall, HB-DFL has significant potentials for neuroimaging data analysis applications with its stability of automatic construction of structural features.

Searching a High Performance Feature Extractor for Text Recognition Network.

Feature extractor plays a critical role in text recognition (TR), but customizing its architecture is relatively less explored due to expensive manual tweaking. In this article, inspired by the success of neural architecture search (NAS), we propose to search for suitable feature extractors. We design a domain-specific search space by exploring principles for having good feature extractors. The space includes a 3D-structured space for the spatial model and a transformed-based space for the sequential model. As the space is huge and complexly structured, no existing NAS algorithms can be applied. We propose a two-stage algorithm to effectively search in the space. In the first stage, we cut the space into several blocks and progressively train each block with the help of an auxiliary head. We introduce the latency constrain into the second stage and search sub-network from the trained supernet via natural gradient descent. In experiments, a series of ablation studies are performed to better understand the designed space, search algorithm, and searched architectures. We also compare the proposed method with various state-of-the-art ones on both hand-written and scene TR tasks. Extensive results show that our approach can achieve better recognition performance with less latency. Code is avaliable at https://github.com/AutoML-Research/TREFE.

Bilinear Scoring Function Search for Knowledge Graph Learning.

Learning embeddings for entities and relations in knowledge graph (KG) have benefited many downstream tasks. In recent years, scoring functions, the crux of KG learning, have been human designed to measure the plausibility of triples and capture different kinds of relations in KGs. However, as relations exhibit intricate patterns that are hard to infer before training, none of them consistently perform the best on benchmark tasks. In this paper, inspired by the recent success of automated machine learning (AutoML), we search bilinear scoring functions for different KG tasks through the AutoML techniques. However, it is non-trivial to explore domain-specific information here. We first set up a search space for AutoBLM by analyzing existing scoring functions. Then, we propose a progressive algorithm (AutoBLM) and an evolutionary algorithm (AutoBLM+), which are further accelerated by filter and predictor to deal with the domain-specific properties for KG learning. Finally, we perform extensive experiments on benchmarks in KG completion, multi-hop query, and entity classification tasks. Empirical results show that the searched scoring functions are KG dependent, new to the literature, and outperform the existing scoring functions. AutoBLM+ is better than AutoBLM as the evolutionary algorithm can flexibly explore better structures in the same budget.

Emerging drug interaction prediction enabled by a flow-based graph neural network with biomedical network.

Drug-drug interactions (DDIs) for emerging drugs offer possibilities for treating and alleviating diseases, and accurately predicting these with computational methods can improve patient care and contribute to efficient drug development. However, many existing computational methods require large amounts of known DDI information, which is scarce for emerging drugs. Here we propose EmerGNN, a graph neural network that can effectively predict interactions for emerging drugs by leveraging the rich information in biomedical networks. EmerGNN learns pairwise representations of drugs by extracting the paths between drug pairs, propagating information from one drug to the other, and incorporating the relevant biomedical concepts on the paths. The edges of the biomedical network are weighted to indicate the relevance for the target DDI prediction. Overall, EmerGNN has higher accuracy than existing approaches in predicting interactions for emerging drugs and can identify the most relevant information on the biomedical network.

Bridging the Gap of AutoGraph Between Academia and Industry: Analyzing AutoGraph Challenge at KDD Cup 2020.

Graph structured data is ubiquitous in daily life and scientific areas and has attracted increasing attention. Graph Neural Networks (GNNs) have been proved to be effective in modeling graph structured data and many variants of GNN architectures have been proposed. However, much human effort is often needed to tune the architecture depending on different datasets. Researchers naturally adopt Automated Machine Learning on Graph Learning, aiming to reduce human effort and achieve generally top-performing GNNs, but their methods focus more on the architecture search. To understand GNN practitioners' automated solutions, we organized AutoGraph Challenge at KDD Cup 2020, emphasizing automated graph neural networks for node classification. We received top solutions, especially from industrial technology companies like Meituan, Alibaba, and Twitter, which are already open sourced on GitHub. After detailed comparisons with solutions from academia, we quantify the gaps between academia and industry on modeling scope, effectiveness, and efficiency, and show that (1) academic AutoML for Graph solutions focus on GNN architecture search while industrial solutions, especially the winning ones in the KDD Cup, tend to obtain an overall solution (2) with only neural architecture search, academic solutions achieve on average 97.3% accuracy of industrial solutions (3) academic solutions are cheap to obtain with several GPU hours while industrial solutions take a few months' labors. Academic solutions also contain much fewer parameters.

Codabench: Flexible, easy-to-use, and reproducible meta-benchmark platform.

Obtaining a standardized benchmark of computational methods is a major issue in data-science communities. Dedicated frameworks enabling fair benchmarking in a unified environment are yet to be developed. Here, we introduce Codabench, a meta-benchmark platform that is open sourced and community driven for benchmarking algorithms or software agents versus datasets or tasks. A public instance of Codabench is open to everyone free of charge and allows benchmark organizers to fairly compare submissions under the same setting (software, hardware, data, algorithms), with custom protocols and data formats. Codabench has unique features facilitating easy organization of flexible and reproducible benchmarks, such as the possibility of reusing templates of benchmarks and supplying compute resources on demand. Codabench has been used internally and externally on various applications, receiving more than 130 users and 2,500 submissions. As illustrative use cases, we introduce four diverse benchmarks covering graph machine learning, cancer heterogeneity, clinical diagnosis, and reinforcement learning.

Non-Local Meets Global: An Iterative Paradigm for Hyperspectral Image Restoration.

Non-local low-rank tensor approximation has been developed as a state-of-the-art method for hyperspectral image (HSI) restoration, which includes the tasks of denoising, compressed HSI reconstruction and inpainting. Unfortunately, while its restoration performance benefits from more spectral bands, its runtime also substantially increases. In this paper, we claim that the HSI lies in a global spectral low-rank subspace, and the spectral subspaces of each full band patch group should lie in this global low-rank subspace. This motivates us to propose a unified paradigm combining the spatial and spectral properties for HSI restoration. The proposed paradigm enjoys performance superiority from the non-local spatial denoising and light computation complexity from the low-rank orthogonal basis exploration. An efficient alternating minimization algorithm with rank adaptation is developed. It is done by first solving a fidelity term-related problem for the update of a latent input image, and then learning a low-dimensional orthogonal basis and the related reduced image from the latent input image. Subsequently, non-local low-rank denoising is developed to refine the reduced image and orthogonal basis iteratively. Finally, the experiments on HSI denoising, compressed reconstruction, and inpainting tasks, with both simulated and real datasets, demonstrate its superiority with respect to state-of-the-art HSI restoration methods.

Efficient Low-Rank Semidefinite Programming With Robust Loss Functions.

In real-world applications, it is important for machine learning algorithms to be robust against data outliers or corruptions. In this paper, we focus on improving the robustness of a large class of learning algorithms that are formulated as low-rank semi-definite programming (SDP) problems. Traditional formulations use the square loss, which is notorious for being sensitive to outliers. We propose to replace this with more robust noise models, including the l1-loss and other nonconvex losses. However, the resultant optimization problem becomes difficult as the objective is no longer convex or smooth. To alleviate this problem, we design an efficient algorithm based on majorization-minimization. The crux is on constructing a good optimization surrogate, and we show that this surrogate can be efficiently obtained by the alternating direction method of multipliers (ADMM). By properly monitoring ADMM's convergence, the proposed algorithm is empirically efficient and also theoretically guaranteed to converge to a critical point. Extensive experiments are performed on four machine learning applications using both synthetic and real-world data sets. Results show that the proposed algorithm is not only fast but also has better performance than the state-of-the-arts.

Large-Scale Low-Rank Matrix Learning with Nonconvex Regularizers.

Low-rank modeling has many important applications in computer vision and machine learning. While the matrix rank is often approximated by the convex nuclear norm, the use of nonconvex low-rank regularizers has demonstrated better empirical performance. However, the resulting optimization problem is much more challenging. Recent state-of-the-art requires an expensive full SVD in each iteration. In this paper, we show that for many commonly-used nonconvex low-rank regularizers, the singular values obtained from the proximal operator can be automatically threshold. This allows the proximal operator to be efficiently approximated by the power method. We then develop a fast proximal algorithm and its accelerated variant with inexact proximal step. It can be guaranteed that the squared distance between consecutive iterates converges at a rate of $O(1/T)$O(1/T), where $T$T is the number of iterations. Furthermore, we show the proposed algorithm can be parallelized, and the resultant algorithm achieves nearly linear speedup w.r.t. the number of threads. Extensive experiments are performed on matrix completion and robust principal component analysis. Significant speedup over the state-of-the-art is observed.

Scalable Online Convolutional Sparse Coding.

Convolutional sparse coding (CSC) improves sparse coding by learning a shift-invariant dictionary from the data. However, most existing CSC algorithms operate in the batch mode and are computationally expensive. In this paper, we alleviate this problem by online learning. The key is a reformulation of the CSC objective so that convolution can be handled easily in the frequency domain, and much smaller history matrices are needed. To solve the resultant optimization problem, we use the alternating direction method of multipliers (ADMMs), and its subproblems have efficient closed-form solutions. Theoretical analysis shows that the learned dictionary converges to a stationary point of the optimization problem. Extensive experiments are performed on both the standard CSC benchmark data sets and much larger data sets such as the ImageNet. Results show that the proposed algorithm outperforms the state-of-the-art batch and online CSC methods. It is more scalable, has faster convergence, and better reconstruction performance.