Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from http://scikit-learn.sourceforge.net.

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Scikit-learn: Machine Learning in Python

Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from this http URL.

More than twelve years have elapsed since the first public release of WEKA. In that time, the software has been rewritten entirely from scratch, evolved substantially and now accompanies a text on data mining [35]. These days, WEKA enjoys widespread acceptance in both academia and business, has an active community, and has been downloaded more than 1.4 million times since being placed on Source-Forge in April 2000. This paper provides an introduction to the WEKA workbench, reviews the history of the project, and, in light of the recent 3.6 stable release, briefly discusses what has been added since the last stable version (Weka 3.4) released in 2003.

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The WEKA data mining software: an update

Tree boosting is a highly effective and widely used machine learning method. In this paper, we describe a scalable end-to-end tree boosting system called XGBoost, which is used widely by data scientists to achieve state-of-the-art results on many machine learning challenges. We propose a novel sparsity-aware algorithm for sparse data and weighted quantile sketch for approximate tree learning. More importantly, we provide insights on cache access patterns, data compression and sharding to build a scalable tree boosting system. By combining these insights, XGBoost scales beyond billions of examples using far fewer resources than existing systems.

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XGBoost: A Scalable Tree Boosting System

While the Transformer architecture has become the de-facto standard for natural language processing tasks, its applications to computer vision remain limited. In vision, attention is either applied in conjunction with convolutional networks, or used to replace certain components of convolutional networks while keeping their overall structure in place. We show that this reliance on CNNs is not necessary and a pure transformer applied directly to sequences of image patches can perform very well on image classification tasks. When pre-trained on large amounts of data and transferred to multiple mid-sized or small image recognition benchmarks (ImageNet, CIFAR-100, VTAB, etc.), Vision Transformer (ViT) attains excellent results compared to state-of-the-art convolutional networks while requiring substantially fewer computational resources to train.

An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale

While relation extraction has traditionally been viewed as a task relying solely on textual data, recent work has shown that by taking as input existing facts in the form of entity-relation triples from both knowledge bases and textual data, the performance of relation extraction can be improved significantly. Following this new paradigm, we propose a tensor decomposition approach for knowledge base embedding that is highly scalable, and is especially suitable for relation extraction. By leveraging relational domain knowledge about entity type information, our learning algorithm is significantly faster than previous approaches and is better able to discover new relations missing from the database. In addition, when applied to a relation extraction task, our approach alone is comparable to several existing systems, and improves the weighted mean average precision of a state-of-theart method by 10 points when used as a subcomponent.

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Typed Tensor Decomposition of Knowledge Bases for Relation Extraction

Graph neural networks (GNNs) have been demonstrated to be powerful in modeling graph-structured data However, training GNNs usually requires abundant task-specific labeled data, which is often arduously expensive to obtain One effective way to reduce the labeling effort is to pre-train an expressive GNN model on unlabeled data with self-supervision and then transfer the learned model to downstream tasks with only a few labels In this paper, we present the GPT-GNN framework to initialize GNNs by generative pre-training GPT-GNN introduces a self-supervised attributed graph generation task to pre-train a GNN so that it can capture the structural and semantic properties of the graph We factorize the likelihood of the graph generation into two components: 1) Attribute Generation and 2) Edge Generation By modeling both components, GPT-GNN captures the inherent dependency between node attributes and graph structure during the generative process Comprehensive experiments on the billion-scale Open Academic Graph and Amazon recommendation data demonstrate that GPT-GNN significantly outperforms state-of-the-art GNN models without pre-training by up to 91% across various downstream tasks

GPT-GNN: Generative Pre-Training of Graph Neural Networks

Efficient training of direct multi-class formulations of linear Support Vector Machines is very useful in applications such as text classification with a huge number examples as well as features. This paper presents a fast dual method for this training. The main idea is to sequentially traverse through the training set and optimize the dual variables associated with one example at a time. The speed of training is enhanced further by shrinking and cooling heuristics. Experiments indicate that our method is much faster than state of the art solvers such as bundle, cutting plane and exponentiated gradient methods.

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A sequential dual method for large scale multi-class linear svms

Motivation Sequence-based protein-protein interaction (PPI) prediction represents a fundamental computational biology problem. To address this problem, extensive research efforts have been made to extract predefined features from the sequences. Based on these features, statistical algorithms are learned to classify the PPIs. However, such explicit features are usually costly to extract, and typically have limited coverage on the PPI information. Results We present an end-to-end framework, PIPR (Protein-Protein Interaction Prediction Based on Siamese Residual RCNN), for PPI predictions using only the protein sequences. PIPR incorporates a deep residual recurrent convolutional neural network in the Siamese architecture, which leverages both robust local features and contextualized information, which are significant for capturing the mutual influence of proteins sequences. PIPR relieves the data pre-processing efforts that are required by other systems, and generalizes well to different application scenarios. Experimental evaluations show that PIPR outperforms various state-of-the-art systems on the binary PPI prediction problem. Moreover, it shows a promising performance on more challenging problems of interaction type prediction and binding affinity estimation, where existing approaches fall short. Availability and implementation The implementation is available at https://github.com/muhaochen/seq_ppi.git. Supplementary information Supplementary data are available at Bioinformatics online.

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Multifaceted protein-protein interaction prediction based on Siamese residual RCNN.

Multilingual knowledge graph (KG) embeddings provide latent semantic representations of entities and structured knowledge with cross-lingual inferences, which benefit various knowledge-driven cross-lingual NLP tasks. However, precisely learning such cross-lingual inferences is usually hindered by the low coverage of entity alignment in many KGs. Since many multilingual KGs also provide literal descriptions of entities, in this paper, we introduce an embedding-based approach which leverages a weakly aligned multilingual KG for semi-supervised cross-lingual learning using entity descriptions. Our approach performs co-training of two embedding models, i.e. a multilingual KG embedding model and a multilingual literal description embedding model. The models are trained on a large Wikipedia-based trilingual dataset where most entity alignment is unknown to training. Experimental results show that the performance of the proposed approach on the entity alignment task improves at each iteration of co-training, and eventually reaches a stage at which it significantly surpasses previous approaches. We also show that our approach has promising abilities for zero-shot entity alignment, and cross-lingual KG completion.

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Kai-Wei Chang

Papers

Typed Tensor Decomposition of Knowledge Bases for Relation Extraction

GPT-GNN: Generative Pre-Training of Graph Neural Networks

A sequential dual method for large scale multi-class linear svms

Multifaceted protein-protein interaction prediction based on Siamese residual RCNN.

Co-training Embeddings of Knowledge Graphs and Entity Descriptions for Cross-lingual Entity Alignment