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1. Learning Data-Driven Drug-Target-Disease Interaction via Neural Tensor Network

   https://doi.org/10.24963/ijcai.2020/477  

   Chen, Huiyuan; Li, Jing (July 2020, International Joint Conference on Artificial Intelligence (IJCAI))

   null (Ed.)

   Precise medicine recommendations provide more effective treatments and cause fewer drug side effects. A key step is to understand the mechanistic relationships among drugs, targets, and diseases. Tensor-based models have the ability to explore relationships of drug-target-disease based on large amount of labeled data. However, existing tensor models fail to capture complex nonlinear dependencies among tensor data. In addition, rich medical knowledge are far less studied, which may lead to unsatisfied results. Here we propose a Neural Tensor Network (NeurTN) to assist personalized medicine treatments. NeurTN seamlessly combines tensor algebra and deep neural networks, which offers a more powerful way to capture the nonlinear relationships among drugs, targets, and diseases. To leverage medical knowledge, we augment NeurTN with geometric neural networks to capture the structural information of both drugs’ chemical structures and targets’ sequences. Extensive experiments on real-world datasets demonstrate the effectiveness of the NeurTN model. 

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2. Beyond single-species models: leveraging multispecies forecasts to navigate the dynamics of ecological predictability

   https://doi.org/10.7717/peerj.18929  

   Clark, Nicholas J; Ernest, S_K Morgan; Senyondo, Henry; Simonis, Juniper; White, Ethan P; Yenni, Glenda M; Karunarathna, K_A_N K (January 2025, PeerJ)

   BackgroundForecasting the responses of natural populations to environmental change is a key priority in the management of ecological systems. This is challenging because the dynamics of multi-species ecological communities are influenced by many factors. Populations can exhibit complex, nonlinear responses to environmental change, often over multiple temporal lags. In addition, biotic interactions, and other sources of multi-species dependence, are major contributors to patterns of population variation. Theory suggests that near-term ecological forecasts of population abundances can be improved by modelling these dependencies, but empirical support for this idea is lacking. MethodsWe test whether models that learn from multiple species, both to estimate nonlinear environmental effects and temporal interactions, improve ecological forecasts compared to simpler single species models for a semi-arid rodent community. Using dynamic generalized additive models, we analyze time series of monthly captures for nine rodent species over 25 years. ResultsModel comparisons provide strong evidence that multi-species dependencies improve both hindcast and forecast performance, as models that captured these effects gave superior predictions than models that ignored them. We show that changes in abundance for some species can have delayed, nonlinear effects on others, and that lagged, nonlinear effects of temperature and vegetation greenness are key drivers of changes in abundance for this system. ConclusionsOur findings highlight that multivariate models are useful not only to improve near-term ecological forecasts but also to ask targeted questions about ecological interactions and drivers of change. This study emphasizes the importance of jointly modelling species’ shared responses to the environment and their delayed temporal interactions when teasing apart community dynamics. 

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3. Nonlinear System Identification via Tensor Completion

   https://doi.org/10.1609/aaai.v34i04.5868  

   Kargas, Nikos; Sidiropoulos, Nicholas D. (June 2020, Proceedings of the AAAI Conference on Artificial Intelligence)

   Function approximation from input and output data pairs constitutes a fundamental problem in supervised learning. Deep neural networks are currently the most popular method for learning to mimic the input-output relationship of a general nonlinear system, as they have proven to be very effective in approximating complex highly nonlinear functions. In this work, we show that identifying a general nonlinear function y = ƒ(x1,…,xN) from input-output examples can be formulated as a tensor completion problem and under certain conditions provably correct nonlinear system identification is possible. Specifically, we model the interactions between the N input variables and the scalar output of a system by a single N-way tensor, and setup a weighted low-rank tensor completion problem with smoothness regularization which we tackle using a block coordinate descent algorithm. We extend our method to the multi-output setting and the case of partially observed data, which cannot be readily handled by neural networks. Finally, we demonstrate the effectiveness of the approach using several regression tasks including some standard benchmarks and a challenging student grade prediction task. 

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4. HyperSoRec: Exploiting Hyperbolic User and Item Representations with Multiple Aspects for Social-aware Recommendation

   https://doi.org/10.1145/3463913  

   Wang, Hao; Lian, Defu; Tong, Hanghang; Liu, Qi; Huang, Zhenya; Chen, Enhong (April 2022, ACM Transactions on Information Systems)

   Social recommendation has achieved great success in many domains including e-commerce and location-based social networks. Existing methods usually explore the user-item interactions or user-user connections to predict users’ preference behaviors. However, they usually learn both user and item representations in Euclidean space, which has large limitations for exploring the latent hierarchical property in the data. In this article, we study a novel problem of hyperbolic social recommendation, where we aim to learn the compact but strong representations for both users and items. Meanwhile, this work also addresses two critical domain-issues, which are under-explored. First, users often make trade-offs with multiple underlying aspect factors to make decisions during their interactions with items. Second, users generally build connections with others in terms of different aspects, which produces different influences with aspects in social network. To this end, we propose a novel graph neural network (GNN) framework with multiple aspect learning, namely, HyperSoRec. Specifically, we first embed all users, items, and aspects into hyperbolic space with superior representations to ensure their hierarchical properties. Then, we adapt a GNN with novel multi-aspect message-passing-receiving mechanism to capture different influences among users. Next, to characterize the multi-aspect interactions of users on items, we propose an adaptive hyperbolic metric learning method by introducing learnable interactive relations among different aspects. Finally, we utilize the hyperbolic translational distance to measure the plausibility in each user-item pair for recommendation. Experimental results on two public datasets clearly demonstrate that our HyperSoRec not only achieves significant improvement for recommendation performance but also shows better representation ability in hyperbolic space with strong robustness and reliability. 

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5. Regularized and smooth double core tensor factorization for heterogeneous data

   Tarzanagh, Davoud Ataee; Michalidis, George (January 2022, Journal of machine learning research)

   We introduce a general tensor model suitable for data analytic tasks for heterogeneous datasets, wherein there are joint low-rank structures within groups of observations, but also discriminative structures across different groups. To capture such complex structures, a double core tensor (DCOT) factorization model is introduced together with a family of smoothing loss functions. By leveraging the proposed smoothing function, the model accurately estimates the model factors, even in the presence of missing entries. A linearized ADMM method is employed to solve regularized versions of DCOT factorizations, that avoid large tensor operations and large memory storage requirements. Further, we establish theoretically its global convergence, together with consistency of the estimates of the model parameters. The effectiveness of the DCOT model is illustrated on several realworld examples including image completion, recommender systems, subspace clustering, and detecting modules in heterogeneous Omics multi-modal data, since it provides more insightful decompositions than conventional tensor methods. 

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