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  1. Existing tensor completion formulation mostly relies on partial observations from a single tensor. However, tensors extracted from real-world data often are more complex due to: (i) Partial observation: Only a small subset of tensor elements are available. (ii) Coarse observation: Some tensor modes only present coarse and aggregated patterns (e.g., monthly summary instead of daily reports). In this paper, we are given a subset of the tensor and some aggregated/coarse observations (along one or more modes) and seek to recover the original fine-granular tensor with low-rank factorization. We formulate a coupled tensor completion problem and propose an efficient Multi-resolution Tensor Completion model (MTC) to solve the problem. Our MTC model explores tensor mode properties and leverages the hierarchy of resolutions to recursively initialize an optimization setup, and optimizes on the coupled system using alternating least squares. MTC ensures low computational and space complexity. We evaluate our model on two COVID-19 related spatio-temporal tensors. The experiments show that MTC could provide 65.20% and 75.79% percentage of fitness (PoF) in tensor completion with only 5% fine granular observations, which is 27.96% relative improvement over the best baseline. To evaluate the learned low-rank factors, we also design a tensor prediction task for dailymore »and cumulative disease case predictions, where MTC achieves 50% in PoF and 30% relative improvements over the best baseline.« less
  2. Real-world spatio-temporal data is often incomplete or inaccurate due to various data loading delays. For example, a location-disease-time tensor of case counts can have multiple delayed updates of recent temporal slices for some locations or diseases. Recovering such missing or noisy (under-reported) elements of the input tensor can be viewed as a generalized tensor completion problem. Existing tensor completion methods usually assume that i) missing elements are randomly distributed and ii) noise for each tensor element is i.i.d. zero-mean. Both assumptions can be violated for spatio-temporal tensor data. We often observe multiple versions of the input tensor with different under-reporting noise levels. The amount of noise can be time- or location-dependent as more updates are progressively introduced to the tensor. We model such dynamic data as a multi-version tensor with an extra tensor mode capturing the data updates. We propose a low-rank tensor model to predict the updates over time. We demonstrate that our method can accurately predict the ground-truth values of many real-world tensors. We obtain up to 27.2% lower root mean-squared-error compared to the best baseline method. Finally, we extend our method to track the tensor data over time, leading to significant computational savings.

  3. This paper presents an active distillation method for a local institution (e.g., hospital) to find the best queries within its given budget to distill an on-server black-box model’s predictive knowledge into a local surrogate with transparent parameterization. This allows local institutions to understand better the predictive reasoning of the black-box model in its own local context or to further customize the distilled knowledge with its private dataset that cannot be centralized and fed into the server model. The proposed method thus addresses several challenges of deploying machine learning (ML) in many industrial settings (e.g., healthcare analytics) with strong proprietary constraints. These include: (1) the opaqueness of the server model’s architecture which prevents local users from understanding its predictive reasoning in their local data contexts; (2) the increasing cost and risk of uploading local data on the cloud for analysis; and (3) the need to customize the server model with private onsite data. We evaluated the proposed method on both benchmark and real-world healthcare data where significant improvements over existing local distillation methods were observed. A theoretical analysis of the proposed method is also presented.
  4. Abstract Molecular interaction networks are powerful resources for molecular discovery. They are increasingly used with machine learning methods to predict biologically meaningful interactions. While deep learning on graphs has dramatically advanced the prediction prowess, current graph neural network (GNN) methods are mainly optimized for prediction on the basis of direct similarity between interacting nodes. In biological networks, however, similarity between nodes that do not directly interact has proved incredibly useful in the last decade across a variety of interaction networks. Here, we present SkipGNN, a graph neural network approach for the prediction of molecular interactions. SkipGNN predicts molecular interactions by not only aggregating information from direct interactions but also from second-order interactions, which we call skip similarity. In contrast to existing GNNs, SkipGNN receives neural messages from two-hop neighbors as well as immediate neighbors in the interaction network and non-linearly transforms the messages to obtain useful information for prediction. To inject skip similarity into a GNN, we construct a modified version of the original network, called the skip graph. We then develop an iterative fusion scheme that optimizes a GNN using both the skip graph and the original graph. Experiments on four interaction networks, including drug–drug, drug–target, protein–protein, and gene–diseasemore »interactions, show that SkipGNN achieves superior and robust performance. Furthermore, we show that unlike popular GNNs, SkipGNN learns biologically meaningful embeddings and performs especially well on noisy, incomplete interaction networks.« less
  5. Wren, Jonathan (Ed.)
    Abstract Summary Accurate prediction of drug–target interactions (DTI) is crucial for drug discovery. Recently, deep learning (DL) models for show promising performance for DTI prediction. However, these models can be difficult to use for both computer scientists entering the biomedical field and bioinformaticians with limited DL experience. We present DeepPurpose, a comprehensive and easy-to-use DL library for DTI prediction. DeepPurpose supports training of customized DTI prediction models by implementing 15 compound and protein encoders and over 50 neural architectures, along with providing many other useful features. We demonstrate state-of-the-art performance of DeepPurpose on several benchmark datasets. Availability and implementation Supplementary information Supplementary data are available at Bioinformatics online.
  6. Therapeutics machine learning is an emerging field with incredible opportunities for innovatiaon and impact. However, advancement in this field requires formulation of meaningful learning tasks and careful curation of datasets. Here, we introduce Therapeutics Data Commons (TDC), the first unifying platform to systematically access and evaluate machine learning across the entire range of therapeutics. To date, TDC includes 66 AI-ready datasets spread across 22 learning tasks and spanning the discovery and development of safe and effective medicines. TDC also provides an ecosystem of tools and community resources, including 33 data functions and types of meaningful data splits, 23 strategies for systematic model evaluation, 17 molecule generation oracles, and 29 public leaderboards. All resources are integrated and accessible via an open Python library. We carry out extensive experiments on selected datasets, demonstrating that even the strongest algorithms fall short of solving key therapeutics challenges, including real dataset distributional shifts, multi-scale modeling of heterogeneous data, and robust generalization to novel data points. We envision that TDC can facilitate algorithmic and scientific advances and considerably accelerate machine-learning model development, validation and transition into biomedical and clinical implementation. TDC is an open-science initiative available at this