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Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection and pathogenesis. This could further help in the prevention and treatment of virus-related diseases. However, the task of predicting protein-protein interactions between a new virus and human cells is extremely challenging due to scarce data on virus-human interactions and fast mutation rates of most viruses. We developed a multitask transfer learning approach that exploits the information of around 24 million protein sequences and the interaction patterns from the human interactome to counter the problem of small training datasets. Instead of using hand-crafted protein features, we utilize statistically rich protein representations learned by a deep language modeling approach from a massive source of protein sequences. Additionally, we employ an additional objective which aims to maximize the probability of observing human protein-protein interactions. This additional task objective acts as a regularizer and also allows to incorporate domain knowledge to inform the virus-human protein-protein interaction prediction model. Our approach achieved competitive results on 13 benchmark datasets and the case study for the SAR-CoV-2 virus receptor. Experimental results show that our proposed model works effectively for both virus-human and bacteria-human protein-protein interaction prediction tasks. We share our code for reproducibility and future research at //git.l3s.uni-hannover.de/dong/multitask-transfer.

This work develops a multiphase thermomechanical model of porous silica aerogel and implements an uncertainty analysis framework consisting of the Sobol methods for global sensitivity analyses and Bayesian inference using a set of experimental data of silica aerogel. A notable feature of this work is implementing a new noise model within the Bayesian inversion to account for data uncertainty and modeling error. The hyper-parameters in the likelihood balance data misfit and prior contribution to the parameter posteriors and prevent their biased estimation. The results indicate that the uncertainty in solid conductivity and elasticity are the most influential parameters affecting the model output variance. Also, the Bayesian inference shows that despite the microstructural randomness in the thermal measurements, the model captures the data with 2% error. However, the model is inadequate in simulating the stress-strain measurements resulting in significant uncertainty in the computational prediction of a building insulation component.

Approaches based on deep neural networks have achieved striking performance when testing data and training data share similar distribution, but can significantly fail otherwise. Therefore, eliminating the impact of distribution shifts between training and testing data is crucial for building performance-promising deep models. Conventional methods assume either the known heterogeneity of training data (e.g. domain labels) or the approximately equal capacities of different domains. In this paper, we consider a more challenging case where neither of the above assumptions holds. We propose to address this problem by removing the dependencies between features via learning weights for training samples, which helps deep models get rid of spurious correlations and, in turn, concentrate more on the true connection between discriminative features and labels. Extensive experiments clearly demonstrate the effectiveness of our method on multiple distribution generalization benchmarks compared with state-of-the-art counterparts. Through extensive experiments on distribution generalization benchmarks including PACS, VLCS, MNIST-M, and NICO, we show the effectiveness of our method compared with state-of-the-art counterparts.

Over the past decade, knowledge graphs became popular for capturing structured domain knowledge. Relational learning models enable the prediction of missing links inside knowledge graphs. More specifically, latent distance approaches model the relationships among entities via a distance between latent representations. Translating embedding models (e.g., TransE) are among the most popular latent distance approaches which use one distance function to learn multiple relation patterns. However, they are not capable of capturing symmetric relations. They also force relations with reflexive patterns to become symmetric and transitive. In order to improve distance based embedding, we propose multi-distance embeddings (MDE). Our solution is based on the idea that by learning independent embedding vectors for each entity and relation one can aggregate contrasting distance functions. Benefiting from MDE, we also develop supplementary distances resolving the above-mentioned limitations of TransE. We further propose an extended loss function for distance based embeddings and show that MDE and TransE are fully expressive using this loss function. Furthermore, we obtain a bound on the size of their embeddings for full expressivity. Our empirical results show that MDE significantly improves the translating embeddings and outperforms several state-of-the-art embedding models on benchmark datasets.

Embedding models for deterministic Knowledge Graphs (KG) have been extensively studied, with the purpose of capturing latent semantic relations between entities and incorporating the structured knowledge into machine learning. However, there are many KGs that model uncertain knowledge, which typically model the inherent uncertainty of relations facts with a confidence score, and embedding such uncertain knowledge represents an unresolved challenge. The capturing of uncertain knowledge will benefit many knowledge-driven applications such as question answering and semantic search by providing more natural characterization of the knowledge. In this paper, we propose a novel uncertain KG embedding model UKGE, which aims to preserve both structural and uncertainty information of relation facts in the embedding space. Unlike previous models that characterize relation facts with binary classification techniques, UKGE learns embeddings according to the confidence scores of uncertain relation facts. To further enhance the precision of UKGE, we also introduce probabilistic soft logic to infer confidence scores for unseen relation facts during training. We propose and evaluate two variants of UKGE based on different learning objectives. Experiments are conducted on three real-world uncertain KGs via three tasks, i.e. confidence prediction, relation fact ranking, and relation fact classification. UKGE shows effectiveness in capturing uncertain knowledge by achieving promising results on these tasks, and consistently outperforms baselines on these tasks.

In one-class-learning tasks, only the normal case (foreground) can be modeled with data, whereas the variation of all possible anomalies is too erratic to be described by samples. Thus, due to the lack of representative data, the wide-spread discriminative approaches cannot cover such learning tasks, and rather generative models, which attempt to learn the input density of the foreground, are used. However, generative models suffer from a large input dimensionality (as in images) and are typically inefficient learners. We propose to learn the data distribution of the foreground more efficiently with a multi-hypotheses autoencoder. Moreover, the model is criticized by a discriminator, which prevents artificial data modes not supported by data, and enforces diversity across hypotheses. Our multiple-hypothesesbased anomaly detection framework allows the reliable identification of out-of-distribution samples. For anomaly detection on CIFAR-10, it yields up to 3.9% points improvement over previously reported results. On a real anomaly detection task, the approach reduces the error of the baseline models from 6.8% to 1.5%.

Tracking by detection is a common approach to solving the Multiple Object Tracking problem. In this paper we show how deep metric learning can be used to improve three aspects of tracking by detection. We train a convolutional neural network to learn an embedding function in a Siamese configuration on a large person re-identification dataset offline. It is then used to improve the online performance of tracking while retaining a high frame rate. We use this learned appearance metric to robustly build estimates of pedestrian's trajectories in the MOT16 dataset. In breaking with the tracking by detection model, we use our appearance metric to propose detections using the predicted state of a tracklet as a prior in the case where the detector fails. This method achieves competitive results in evaluation, especially among online, real-time approaches. We present an ablative study showing the impact of each of the three uses of our deep appearance metric.

Machine translation is a popular test bed for research in neural sequence-to-sequence models but despite much recent research, there is still a lack of understanding of these models. Practitioners report performance degradation with large beams, the under-estimation of rare words and a lack of diversity in the final translations. Our study relates some of these issues to the inherent uncertainty of the task, due to the existence of multiple valid translations for a single source sentence, and to the extrinsic uncertainty caused by noisy training data. We propose tools and metrics to assess how uncertainty in the data is captured by the model distribution and how it affects search strategies that generate translations. Our results show that search works remarkably well but that the models tend to spread too much probability mass over the hypothesis space. Next, we propose tools to assess model calibration and show how to easily fix some shortcomings of current models. We release both code and multiple human reference translations for two popular benchmarks.

The aim of knowledge graphs is to gather knowledge about the world and provide a structured representation of this knowledge. Current knowledge graphs are far from complete. To address the incompleteness of the knowledge graphs, link prediction approaches have been developed which make probabilistic predictions about new links in a knowledge graph given the existing links. Tensor factorization approaches have proven promising for such link prediction problems. In this paper, we develop a simple tensor factorization model called SimplE, through a slight modification of the Polyadic Decomposition model from 1927. The complexity of SimplE grows linearly with the size of embeddings. The embeddings learned through SimplE are interpretable, and certain types of expert knowledge in terms of logical rules can be incorporated into these embeddings through weight tying. We prove SimplE is fully-expressive and derive a bound on the size of its embeddings for full expressivity. We show empirically that, despite its simplicity, SimplE outperforms several state-of-the-art tensor factorization techniques.