Coupled Tensor-Tensor Completion Method with Applications in Drug Repurposing
Authors: Maryam Bagherian, Albert Hung, Ivo Dinov, Joshua Welch
Organizations: Department of Mathematics & Statistics, Idaho State University, Physical Science Complex — 921 S. 8th Ave., Stop 8085 — Pocatello, ID 83209 · Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology · Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor · Statistics Online Computational Resource (SOCR), University of Michigan, Ann Arbor · Department of Computer Science & Engineering, University of Michigan, Ann Arbor
Many biomedical challenges can be posed as tensor completion problems where the observed entries of a multidimensional array (a tensor) are used to impute the missing values. In such settings, incorporating side information about the modes of the tensor, such as gene-gene similarity, can significantly enhance the solutions of the completion problem. Most existing tensor completion methods can only incorporate side information in the form of matrices. In this study, we introduce a novel framework to incorporate side information in the form of tensors. Our new approach, called Coupled Tensor-Tensor Completion (CTTC), leverages the hidden connections among multimodal tensors to improve tensor completion performance. In addition to practical utility, CTTC has theoretical foundations in distance metric learning and group theory. We derive an alternating algorithm to solve the CTTC optimization problem and establish its convergence to a stationary point. Finally, we show that CTTC outperforms state-of-the-art tensor completion methods at predicting drug effects. Results: Compared with other tensor completion methods, including HaLRTC, CTRC, Cell, and NTDDR, CTTC demonstrates superior run-time and RSE tensor completion accuracy on two benchmark datasets, DTD and LINCS.
Tensor factorization (TF) has been widely adopted for high-dimensional sparse data completion tasks. Despite significant progress, neural TF methods often struggle to capture complex cross-mode interactions and remain vulnerable to (extreme) data sparsity. To address these challenges, we propose a novel neural tensor factorization approach, termed Dual-Attention Convolution Expert Networks with Group-Level Contrastive Learning (DCGC). For the first problem, DCGC generates diverse non-linear alignment patterns of latent factors via a multi-channel convolution network, and leverages the gated dual-attention mechanism to drive the model to focus on more important output channels (i.e., convolution experts) and the aligned features. Furthermore, DCGC introduces a group-level contrastive learning strategy that aggregates positive samples with identical feedback levels while separating negative samples across different levels. This strategy injects high-quality self-supervised signals to mitigate data sparsity. Extensive experiments conducted on five datasets demonstrate that our DCGC outperforms the state-of-the-art methods in sparse tensor completion for traffic and recommendation applications. Code to reproduce the experimental results in the paper is available at https://github.com/ku1z/DCGC.
We consider a novel algorithm, for the completion of partially observed low-rank tensors, as a generalization of matrix completion. The proposed low-rank tensor completion (TC) method builds on the conventional nuclear norm (NN) minimization-based low-rank TC paradigm, by leveraging the alternating direction method of multipliers (ADMM) optimization framework. To that extend the original NN minimization problem is reformulated into multiple subproblems, which are then solved iteratively via closed-form proximal operators, making use of over-relaxation and an adaptive penalty parameter update scheme, to further speed up convergence and improve the overall performance of the method. Simulation results demonstrate the superior performance of the new method in terms of normalized mean square error (NMSE), compared to the conventional state-of-the-art (SotA) techniques, including NN minimization approaches, as well as a mixture of the latter with a matrix factorization approach, while its convergence can be significantly improved by initializing the algorithm with the solution of the SotA.
Niclas Führling, Getuar Rexhepi, Giuseppe Thadeu Freitas de Abreu
This paper proposes Spectra-Guided Neural Tucker Factorization (SG-NTF) for High-Dimensional and Incomplete (HDI) tensor completion. Circumventing discrete representational limits, SG-NTF maps scalar timestamps into a continuous spectral space to abstract temporal periodicities. Concurrently, a Spatio-Temporal Co-Gating (STCG) mechanism explicitly filters latent interactions via multiplicative modulation on spatiotemporal contexts. Evaluations on real-world HDI tensors verify that SG-NTF maintains competitive completion accuracy with parameter efficiency.