Mediation analysis is an important tool to study causal associations in biomedical and other scientific areas and has recently gained attention in microbiome studies. Using a microbiome study of acute myeloid leukemia (AML) patients, we investigate whether the effect of induction chemotherapy intensity levels on the infection status is mediated by the microbial taxa abundance. The unique characteristics of the microbial mediators -- high-dimensionality, zero-inflation, and dependence -- call for new methodological developments in mediation analysis. The presence of an exposure-induced mediator-outcome confounder, antibiotic use, further requires a delicate treatment in the analysis. To address these unique challenges in our motivating AML microbiome study, we propose a novel nonparametric identification formula for the interventional indirect effect (IIE), a measure recently developed for studying mediation effects. We develop the corresponding estimation algorithm using the inverse probability weighting method. We also test the presence of mediation effects via constructing the standard normal bootstrap confidence intervals. Simulation studies show that the proposed method has good finite-sample performance in terms of the IIE estimation, and type-I error rate and power of the corresponding test. In the AML microbiome study, our findings suggest that the effect of induction chemotherapy intensity levels on infection is mainly mediated by patients' gut microbiome.
In machine learning systems, privileged features refer to the features that are available during offline training but inaccessible for online serving. Previous studies have recognized the importance of privileged features and explored ways to tackle online-offline discrepancies. A typical practice is privileged features distillation (PFD): train a teacher model using all features (including privileged ones) and then distill the knowledge from the teacher model using a student model (excluding the privileged features), which is then employed for online serving. In practice, the pointwise cross-entropy loss is often adopted for PFD. However, this loss is insufficient to distill the ranking ability for CTR prediction. First, it does not consider the non-i.i.d. characteristic of the data distribution, i.e., other items on the same page significantly impact the click probability of the candidate item. Second, it fails to consider the relative item order ranked by the teacher model's predictions, which is essential to distill the ranking ability. To address these issues, we first extend the pointwise-based PFD to the listwise-based PFD. We then define the calibration-compatible property of distillation loss and show that commonly used listwise losses do not satisfy this property when employed as distillation loss, thus compromising the model's calibration ability, which is another important measure for CTR prediction. To tackle this dilemma, we propose Calibration-compatible LIstwise Distillation (CLID), which employs carefully-designed listwise distillation loss to achieve better ranking ability than the pointwise-based PFD while preserving the model's calibration ability. We theoretically prove it is calibration-compatible. Extensive experiments on public datasets and a production dataset collected from the display advertising system of Alibaba further demonstrate the effectiveness of CLID.
Deep learning models are known to suffer from the problem of bias, and researchers have been exploring methods to address this issue. However, most of these methods require prior knowledge of the bias and are not always practical. In this paper, we focus on a more practical setting with no prior information about the bias. Generally, in this setting, there are a large number of bias-aligned samples that cause the model to produce biased predictions and a few bias-conflicting samples that do not conform to the bias. If the training data is limited, the influence of the bias-aligned samples may become even stronger on the model predictions, and we experimentally demonstrate that existing debiasing techniques suffer severely in such cases. In this paper, we examine the effects of unknown bias in small dataset regimes and present a novel approach to mitigate this issue. The proposed approach directly addresses the issue of the extremely low occurrence of bias-conflicting samples in limited data settings through the synthesis of hybrid samples that can be used to reduce the effect of bias. We perform extensive experiments on several benchmark datasets and experimentally demonstrate the effectiveness of our proposed approach in addressing any unknown bias in the presence of limited data. Specifically, our approach outperforms the vanilla, LfF, LDD, and DebiAN debiasing methods by absolute margins of 10.39%, 9.08%, 8.07%, and 9.67% when only 10% of the Corrupted CIFAR-10 Type 1 dataset is available with a bias-conflicting sample ratio of 0.05.
Safeguarding privacy in sensitive training data is paramount, particularly in the context of generative modeling. This is done through either differentially private stochastic gradient descent, or with a differentially private metric for training models or generators. In this paper, we introduce a novel differentially private generative modeling approach based on parameter-free gradient flows in the space of probability measures. The proposed algorithm is a new discretized flow which operates through a particle scheme, utilizing drift derived from the sliced Wasserstein distance and computed in a private manner. Our experiments show that compared to a generator-based model, our proposed model can generate higher-fidelity data at a low privacy budget, offering a viable alternative to generator-based approaches.
Unsupervised domain adaptation has recently emerged as an effective paradigm for generalizing deep neural networks to new target domains. However, there is still enormous potential to be tapped to reach the fully supervised performance. In this paper, we present a novel active learning strategy to assist knowledge transfer in the target domain, dubbed active domain adaptation. We start from an observation that energy-based models exhibit free energy biases when training (source) and test (target) data come from different distributions. Inspired by this inherent mechanism, we empirically reveal that a simple yet efficient energy-based sampling strategy sheds light on selecting the most valuable target samples than existing approaches requiring particular architectures or computation of the distances. Our algorithm, Energy-based Active Domain Adaptation (EADA), queries groups of targe data that incorporate both domain characteristic and instance uncertainty into every selection round. Meanwhile, by aligning the free energy of target data compact around the source domain via a regularization term, domain gap can be implicitly diminished. Through extensive experiments, we show that EADA surpasses state-of-the-art methods on well-known challenging benchmarks with substantial improvements, making it a useful option in the open world. Code is available at //github.com/BIT-DA/EADA.
Link prediction on knowledge graphs (KGs) is a key research topic. Previous work mainly focused on binary relations, paying less attention to higher-arity relations although they are ubiquitous in real-world KGs. This paper considers link prediction upon n-ary relational facts and proposes a graph-based approach to this task. The key to our approach is to represent the n-ary structure of a fact as a small heterogeneous graph, and model this graph with edge-biased fully-connected attention. The fully-connected attention captures universal inter-vertex interactions, while with edge-aware attentive biases to particularly encode the graph structure and its heterogeneity. In this fashion, our approach fully models global and local dependencies in each n-ary fact, and hence can more effectively capture associations therein. Extensive evaluation verifies the effectiveness and superiority of our approach. It performs substantially and consistently better than current state-of-the-art across a variety of n-ary relational benchmarks. Our code is publicly available.
Mining graph data has become a popular research topic in computer science and has been widely studied in both academia and industry given the increasing amount of network data in the recent years. However, the huge amount of network data has posed great challenges for efficient analysis. This motivates the advent of graph representation which maps the graph into a low-dimension vector space, keeping original graph structure and supporting graph inference. The investigation on efficient representation of a graph has profound theoretical significance and important realistic meaning, we therefore introduce some basic ideas in graph representation/network embedding as well as some representative models in this chapter.
Representation learning on a knowledge graph (KG) is to embed entities and relations of a KG into low-dimensional continuous vector spaces. Early KG embedding methods only pay attention to structured information encoded in triples, which would cause limited performance due to the structure sparseness of KGs. Some recent attempts consider paths information to expand the structure of KGs but lack explainability in the process of obtaining the path representations. In this paper, we propose a novel Rule and Path-based Joint Embedding (RPJE) scheme, which takes full advantage of the explainability and accuracy of logic rules, the generalization of KG embedding as well as the supplementary semantic structure of paths. Specifically, logic rules of different lengths (the number of relations in rule body) in the form of Horn clauses are first mined from the KG and elaborately encoded for representation learning. Then, the rules of length 2 are applied to compose paths accurately while the rules of length 1 are explicitly employed to create semantic associations among relations and constrain relation embeddings. Besides, the confidence level of each rule is also considered in optimization to guarantee the availability of applying the rule to representation learning. Extensive experimental results illustrate that RPJE outperforms other state-of-the-art baselines on KG completion task, which also demonstrate the superiority of utilizing logic rules as well as paths for improving the accuracy and explainability of representation learning.
Most existing knowledge graphs suffer from incompleteness, which can be alleviated by inferring missing links based on known facts. One popular way to accomplish this is to generate low-dimensional embeddings of entities and relations, and use these to make inferences. ConvE, a recently proposed approach, applies convolutional filters on 2D reshapings of entity and relation embeddings in order to capture rich interactions between their components. However, the number of interactions that ConvE can capture is limited. In this paper, we analyze how increasing the number of these interactions affects link prediction performance, and utilize our observations to propose InteractE. InteractE is based on three key ideas -- feature permutation, a novel feature reshaping, and circular convolution. Through extensive experiments, we find that InteractE outperforms state-of-the-art convolutional link prediction baselines on FB15k-237. Further, InteractE achieves an MRR score that is 9%, 7.5%, and 23% better than ConvE on the FB15k-237, WN18RR and YAGO3-10 datasets respectively. The results validate our central hypothesis -- that increasing feature interaction is beneficial to link prediction performance. We make the source code of InteractE available to encourage reproducible research.
Embedding entities and relations into a continuous multi-dimensional vector space have become the dominant method for knowledge graph embedding in representation learning. However, most existing models ignore to represent hierarchical knowledge, such as the similarities and dissimilarities of entities in one domain. We proposed to learn a Domain Representations over existing knowledge graph embedding models, such that entities that have similar attributes are organized into the same domain. Such hierarchical knowledge of domains can give further evidence in link prediction. Experimental results show that domain embeddings give a significant improvement over the most recent state-of-art baseline knowledge graph embedding models.
Recently, ensemble has been applied to deep metric learning to yield state-of-the-art results. Deep metric learning aims to learn deep neural networks for feature embeddings, distances of which satisfy given constraint. In deep metric learning, ensemble takes average of distances learned by multiple learners. As one important aspect of ensemble, the learners should be diverse in their feature embeddings. To this end, we propose an attention-based ensemble, which uses multiple attention masks, so that each learner can attend to different parts of the object. We also propose a divergence loss, which encourages diversity among the learners. The proposed method is applied to the standard benchmarks of deep metric learning and experimental results show that it outperforms the state-of-the-art methods by a significant margin on image retrieval tasks.