We present a novel extension to embedding-based knowledge graph completion models which enables them to perform open-world link prediction, i.e. to predict facts for entities unseen in training based on their textual description. Our model combines a regular link prediction model learned from a knowledge graph with word embeddings learned from a textual corpus. After training both independently, we learn a transformation to map the embeddings of an entity's name and description to the graph-based embedding space. In experiments on several datasets including FB20k, DBPedia50k and our new dataset FB15k-237-OWE, we demonstrate competitive results. Particularly, our approach exploits the full knowledge graph structure even when textual descriptions are scarce, does not require a joint training on graph and text, and can be applied to any embedding-based link prediction model, such as TransE, ComplEx and DistMult.

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation techniques. To facilitate progress in this field, we introduce the Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. We curate tasks into specific training, validation, and test splits to ensure that each task tests biologically relevant generalization that transfers to real-life scenarios. We benchmark a range of approaches to semi-supervised protein representation learning, which span recent work as well as canonical sequence learning techniques. We find that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases. Despite this increase, in several cases features learned by self-supervised pretraining still lag behind features extracted by state-of-the-art non-neural techniques. This gap in performance suggests a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences. TAPE will help the machine learning community focus effort on scientifically relevant problems.

Optimal transport (OT)-based methods have a wide range of applications and have attracted a tremendous amount of attention in recent years. However, most of the computational approaches of OT do not learn the underlying transport map. Although some algorithms have been proposed to learn this map, they rely on kernel-based methods, which makes them prohibitively slow when the number of samples increases. Here, we propose a way to learn an approximate transport map and a parametric approximation of the Wasserstein barycenter. We build an approximated transport mapping by leveraging the closed-form of Gaussian (Bures-Wasserstein) transport; we compute local transport plans between matched pairs of the Gaussian components of each density. The learned map generalizes to out-of-sample examples. We provide experimental results on simulated and real data, comparing our proposed method with other mapping estimation algorithms. Preliminary experiments suggest that our proposed method is not only faster, with a factor 80 overall running time, but it also requires fewer components than state-of-the-art methods to recover the support of the barycenter. From a practical standpoint, it is straightforward to implement and can be used with a conventional machine learning pipeline.

A major challenge in reinforcement learning for continuous state-action spaces is exploration, especially when reward landscapes are very sparse. Several recent methods provide an intrinsic motivation to explore by directly encouraging RL agents to seek novel states. A potential disadvantage of pure state novelty-seeking behavior is that unknown states are treated equally regardless of their potential for future reward. In this paper, we propose that the temporal difference error of predicting primary reward can serve as a secondary reward signal for exploration. This leads to novelty-seeking in the absence of primary reward, and at the same time accelerates exploration of reward-rich regions in sparse (but nonzero) reward landscapes compared to state novelty-seeking. This objective draws inspiration from dopaminergic pathways in the brain that influence animal behavior. We implement this idea with an adversarial method in which Q and Qx are the action-value functions for primary and secondary rewards, respectively. Secondary reward is given by the absolute value of the TD-error of Q. Training is off-policy, based on a replay buffer containing a mixture of trajectories induced by Q and Qx. We characterize performance on a suite of continuous control benchmark tasks against recent state of the art exploration methods and demonstrate comparable or better performance on all tasks, with much faster convergence for Q.

In cases of uncertainty, a multi-class classifier preferably returns a set of candidate classes instead of predicting a single class label with little guarantee. More precisely, the classifier should strive for an optimal balance between the correctness (the true class is among the candidates) and the precision (the candidates are not too many) of its prediction. We formalize this problem within a general decision-theoretic framework that unifies most of the existing work in this area. In this framework, uncertainty is quantified in terms of conditional class probabilities, and the quality of a predicted set is measured in terms of a utility function. We then address the problem of finding the Bayes-optimal prediction, i.e., the subset of class labels with highest expected utility. For this problem, which is computationally challenging as there are exponentially (in the number of classes) many predictions to choose from, we propose efficient algorithms that can be applied to a broad family of utility scores. Two of these algorithms make use of structural information in the form of a class hierarchy, which is often available in prediction problems with many classes. Our theoretical results are complemented by experimental studies, in which we analyze the proposed algorithms in terms of predictive accuracy and runtime efficiency.

Neural machine translation models are used to automatically generate a document from given source code since this can be regarded as a machine translation task. Source code summarization is one of the components for automatic document generation, which generates a summary in natural language from given source code. This suggests that techniques used in neural machine translation, such as Long Short-Term Memory (LSTM), can be used for source code summarization. However, there is a considerable difference between source code and natural language: Source code is essentially {\em structured}, having loops and conditional branching, etc. Therefore, there is some obstacle to apply known machine translation models to source code. Abstract syntax trees (ASTs) capture these structural properties and play an important role in recent machine learning studies on source code. Tree-LSTM is proposed as a generalization of LSTMs for tree-structured data. However, there is a critical issue when applying it to ASTs: It cannot handle a tree that contains nodes having an arbitrary number of children and their order simultaneously, which ASTs generally have such nodes. To address this issue, we propose an extension of Tree-LSTM, which we call \emph{Multi-way Tree-LSTM} and apply it for source code summarization. As a result of computational experiments, our proposal achieved better results when compared with several state-of-the-art techniques.

This short note highlights some links between two lines of research within the emerging topic of trustworthy machine learning: differential privacy and robustness to adversarial examples. By abstracting the definitions of both notions, we show that they build upon the same theoretical ground and hence results obtained so far in one domain can be transferred to the other. More precisely, our analysis is based on two key elements: probabilistic mappings (also called randomized algorithms in the differential privacy community), and the Renyi divergence which subsumes a large family of divergences. We first generalize the definition of robustness against adversarial examples to encompass probabilistic mappings. Then we observe that Renyi-differential privacy (a generalization of differential privacy recently proposed in~\cite{Mironov2017RenyiDP}) and our definition of robustness share several similarities. We finally discuss how can both communities benefit from this connection to transfer technical tools from one research field to the other.

Data collection and labeling is one of the main challenges in employing machine learning algorithms in a variety of real-world applications with limited data. While active learning methods attempt to tackle this issue by labeling only the data samples that give high information, they generally suffer from large computational costs and are impractical in settings where data can be collected in parallel. Batch active learning methods attempt to overcome this computational burden by querying batches of samples at a time. To avoid redundancy between samples, previous works rely on some ad hoc combination of sample quality and diversity. In this paper, we present a new principled batch active learning method using Determinantal Point Processes, a repulsive point process that enables generating diverse batches of samples. We develop tractable algorithms to approximate the mode of a DPP distribution, and provide theoretical guarantees on the degree of approximation. We further demonstrate that an iterative greedy method for DPP maximization, which has lower computational costs but worse theoretical guarantees, still gives competitive results for batch active learning. Our experiments show the value of our methods on several datasets against state-of-the-art baselines.

We consider a problem of manifold estimation from noisy observations. We suggest a novel adaptive procedure, which simultaneously reconstructs a smooth manifold from the observations and estimates projectors onto the tangent spaces. Many manifold learning procedures locally approximate a manifold by a weighted average over a small neighborhood. However, in the presence of large noise, the assigned weights become so corrupted that the averaged estimate shows very poor performance. We adjust the weights so they capture the manifold structure better. We propose a computationally efficient procedure, which iteratively refines the weights on each step, such that, after several iterations, we obtain the "oracle" weights, so the quality of the final estimates does not suffer even in the presence of relatively large noise. We also provide a theoretical study of the procedure and prove its optimality deriving both new upper and lower bounds for manifold estimation under the Hausdorff loss.

The power of neural networks lies in their ability to generalize to unseen data, yet the underlying reasons for this phenomenon remain elusive. Numerous rigorous attempts have been made to explain generalization, but available bounds are still quite loose, and analysis does not always lead to true understanding. The goal of this work is to make generalization more intuitive. Using visualization methods, we discuss the mystery of generalization, the geometry of loss landscapes, and how the curse (or, rather, the blessing) of dimensionality causes optimizers to settle into minima that generalize well.