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.

Graph-based semi-supervised learning is the problem of propagating labels from a small number of labelled data points to a larger set of unlabelled data. This paper is concerned with the consistency of optimization-based techniques for such problems, in the limit where the labels have small noise and the underlying unlabelled data is well clustered. We study graph-based probit for binary classification, and a natural generalization of this method to multi-class classification using one-hot encoding. The resulting objective function to be optimized comprises the sum of a quadratic form defined through a rational function of the graph Laplacian, involving only the unlabelled data, and a fidelity term involving only the labelled data.

In this work, we explain the working mechanism of MixUp in terms of adversarial training. We introduce a new class of adversarial training schemes, which we refer to as directional adversarial training, or DAT. In a nutshell, a DAT scheme perturbs a training example in the direction of another example but keeps its original label as the training target. We prove that MixUp is equivalent to a special subclass of DAT, in that it has the same expected loss function and corresponds to the same optimization problem asymptotically. This understanding not only serves to explain the effectiveness of MixUp, but also reveals a more general family of MixUp schemes, which we call Untied MixUp. We prove that the family of Untied MixUp schemes is equivalent to the entire class of DAT schemes. We establish empirically the existence of Untied Mixup schemes which improve upon MixUp.

We present a novel reinforcement learning-based natural media painting algorithm. Our goal is to reproduce a reference image using brush strokes and we encode the objective through observations. Our formulation takes into account that the distribution of the reward in the action space is sparse and training a reinforcement learning algorithm from scratch can be difficult. We present an approach that combines self-supervised learning and reinforcement learning to effectively transfer negative samples into positive ones and change the reward distribution. We demonstrate the benefits of our painting agent to reproduce reference images with brush strokes. The training phase takes about one hour and the runtime algorithm takes about 30 seconds on a GTX1080 GPU reproducing a 1000 800 image with 20,000 strokes.

We propose a simple and efficient method to combine semi-supervised learning with weakly-supervised learning for deep neural networks. Designing deep neural networks for weakly-supervised learning is always accompanied by a tradeoff between fine-information and coarse-level classification accuracy. While using unlabeled data for semi-supervised learning, in contrast to seeking for this tradeoff, we design two extremely different models for different targets, one of which just pursues finer information for the final target. Another one is more professional to achieve higher coarse-level classification accuracy so that it is regarded as a more professional teacher to teach the former model using unlabeled data. We present an end-to-end semi-supervised learning process termed guided learning for these two different models so that improve the training efficiency. Our approach improves the $1^{st}$ place result on Task4 of the DCASE2018 challenge from $32.4\%$ to $38.3\%$, achieving start-of-art performance.

In this direction, patterns of concepts can be used to justify (and explain) Neural Multi-Space (NeMuS) is a weighted multispace "shortcuts" to generate recursive hypothesis from very large representation for a portion of first-order sets of relations without the need to compute the entire path logic designed for use with machine learning and to justify it. This is critical when the background knowledge neural network methods. It was demonstrated that has huge amounts of data. It could be adequately handled it can be used to perform reasoning based on regions as regions of concepts and categories, similar to the human forming patterns of refutation and also in brain map organization. This will allow symbolic deduction the process of inductive learning in ILP-like style.

High-capacity networks are solving many different machine learning tasks, ranging from large-scale image classification, segmentation and image generation, to natural speech understanding and realistic text-to-speech, arguably passing some formulations of a Turing Test. A few general trends are easily identified in academia and industry: deeper networks show increasingly better results, as long as they are fed with ever bigger amounts of data, and labelled data in particular. Computational and economic costs increase linearly with the size of the dataset and for this reason, starting 2015 a number of unsupervised approaches aiming at the exploitation of unlabelled data are growing in popularity. The intuition behind many of these techniques is to emulate the ability of human brains to self determine the goal of a task and improve towards it. Starting 2015 advancements in algorithms able to exploit labels inherently contained within an unlabelled dataset gave rise to what is now referenced as self-supervised learning.

Recent advances in semi-supervised learning methods rely on estimating the categories of unlabeled data using a model trained on the labeled data (pseudo-labeling) and using the unlabeled data for various consistency-based regularization. In this work, we propose to explicitly leverage the structure of the data manifold based on a Manifold Graph constructed over the image instances within the feature space. Specifically, we propose an architecture based on graph networks that jointly optimizes feature extraction, graph connectivity, and feature propagation and aggregation to unlabeled data in an end-to-end manner. Further, we present a novel Prototype Generator for producing a diverse set of prototypes that compactly represent each category, which supports feature propagation. To evaluate our method, we first contribute a strong baseline that combines two consistency-based regularizers that already achieves state-of-the-art results especially with fewer labels. We then show that when combined with these regularizers, the proposed method facilitates the propagation of information from generated prototypes to image data to further improve results. We provide extensive qualitative and quantitative experimental results on semi-supervised benchmarks demonstrating the improvements arising from our design and show that our method achieves state-of-the-art performance when compared with existing methods using a single model and comparable with ensemble methods. Specifically, we achieve error rates of 3.35% on SVHN, 8.27% on CIFAR-10, and 33.83% on CIFAR-100. With much fewer labels, we surpass the state of the arts by significant margins of 41% relative error decrease on average.

While supervised learning has tremendously improved AI performance in image classification, a major drawback is its reliance on large-scale labeled datasets. This has prompted researchers to explore the potential of unsupervised learning and semi-supervised learning -- techniques that forego data annotation but have their own drawback: diminished accuracy. A new paper from Google's UK-based research company DeepMind addresses this with a model based on Contrastive Predictive Coding (CPC) that outperforms the fully-supervised AlexNet model in Top-1 and Top-5 accuracy on ImageNet. CPC was introduced by DeepMind in 2018. The unsupervised learning approach uses a powerful autoregressive model to extract representations of high-dimensional data to predict future samples.

We propose a new approach to address the text classification problems when learning with partial labels is beneficial. Instead of offering each training sample a set of candidate labels, we assign negative-oriented labels to the ambiguous training examples if they are unlikely fall into certain classes. We construct our new maximum likelihood estimators with self-correction property, and prove that under some conditions, our estimators converge faster. Also we discuss the advantages of applying one of our estimator to a fully supervised learning problem. The proposed method has potential applicability in many areas, such as crowdsourcing, natural language processing and medical image analysis.