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Register a new userword2vec Skip-Gram with Negative Sampling is a Weighted Logistic PCA
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We show that the skip-gram formulation of word2vec trained with negative sampling is equivalent to a weighted logistic PCA. This connection allows us to better understand the objective, compare it to other word embedding methods, and extend it to higher dimensional models.
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We simulate first- and second-order context overlap and show that Skip-Gram with Negative Sampling is similar to Singular Value Decomposition in capturing second-order co-occurrence information, while Pointwise Mutual Information is agnostic to it. We support the results with an empirical study finding that the models react differently when provided with additional second-order information. Our findings reveal a basic property of Skip-Gram with Negative Sampling and point towards an explanation of its success on a variety of tasks.
Network representation learning, as an approach to learn low dimensional representations of vertices, has attracted considerable research attention recently. It has been proven extremely useful in many machine learning tasks over large graph. Most existing methods focus on learning the structural representations of vertices in a static network, but cannot guarantee an accurate and efficient embedding in a dynamic network scenario. To address this issue, we present an efficient incremental skip-gram algorithm with negative sampling for dynamic network embedding, and provide a set of theoretical analyses to characterize the performance guarantee. Specifically, we first partition a dynamic network into the updated, including addition/deletion of links and vertices, and the retained networks over time. Then we factorize the objective function of network embedding into the added, vanished and retained parts of the network. Next we provide a new stochastic gradient-based method, guided by the partitions of the network, to update the nodes and the parameter vectors. The proposed algorithm is proven to yield an objective function value with a bounded difference to that of the original objective function. Experimental results show that our proposal can significantly reduce the training time while preserving the comparable performance. We also demonstrate the correctness of the theoretical analysis and the practical usefulness of the dynamic network embedding. We perform extensive experiments on multiple real-world large network datasets over multi-label classification and link prediction tasks to evaluate the effectiveness and efficiency of the proposed framework, and up to 22 times speedup has been achieved.
We investigate the integration of word embeddings as classification features in the setting of large scale text classification. Such representations have been used in a plethora of tasks, however their application in classification scenarios with thousands of classes has not been extensively researched, partially due to hardware limitations. In this work, we examine efficient composition functions to obtain document-level from word-level embeddings and we subsequently investigate their combination with the traditional one-hot-encoding representations. By presenting empirical evidence on large, multi-class, multi-label classification problems, we demonstrate the efficiency and the performance benefits of this combination.
Compared to the conditional mean as a simple point estimator, the conditional density function is more informative to describe the distributions with multi-modality, asymmetry or heteroskedasticity. In this paper, we propose a novel parametric conditional density estimation method by showing the connection between the general density and the likelihood function of inhomogeneous Poisson process models. The maximum likelihood estimates can be obtained via weighted logistic regressions, and the computation can be significantly relaxed by combining a block-wise alternating maximization scheme and local case-control sampling. We also provide simulation studies for illustration.
Background: The inception of next generations sequencing technologies have exponentially increased the volume of biological sequence data. Protein sequences, being quoted as the `language of life, has been analyzed for a multitude of applications and inferences. Motivation: Owing to the rapid development of deep learning, in recent years there have been a number of breakthroughs in the domain of Natural Language Processing. Since these methods are capable of performing different tasks when trained with a sufficient amount of data, off-the-shelf models are used to perform various biological applications. In this study, we investigated the applicability of the popular Skip-gram model for protein sequence analysis and made an attempt to incorporate some biological insights into it. Results: We propose a novel $k$-mer embedding scheme, Align-gram, which is capable of mapping the similar $k$-mers close to each other in a vector space. Furthermore, we experiment with other sequence-based protein representations and observe that the embeddings derived from Align-gram aids modeling and training deep learning models better. Our experiments with a simple baseline LSTM model and a much complex CNN model of DeepGoPlus shows the potential of Align-gram in performing different types of deep learning applications for protein sequence analysis.
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