NBLDA: Negative Binomial Linear Discriminant Analysis for RNA-Seq Data

RNA-sequencing (RNA-Seq) has become a powerful technology to characterize gene expression profiles because it is more accurate and comprehensive than microarrays. Although statistical methods that have been developed for microarray data can be applied to RNA-Seq data, they are not ideal due to the discrete nature of RNA-Seq data. The Poisson distribution and negative binomial distribution are commonly used to model count data. Recently, Witten (2011) proposed a Poisson linear discriminant analysis for RNA-Seq data. The Poisson assumption may not be as appropriate as negative binomial distribution when biological replicates are available and in the presence of overdispersion (i.e., when the variance is larger than the mean). However, it is more complicated to model negative binomial variables because they involve a dispersion parameter that needs to be estimated. In this paper, we propose a negative binomial linear discriminant analysis for RNA-Seq data. By Bayes' rule, we construct the classifier by fitting a negative binomial model, and propose some plug-in rules to estimate the unknown parameters in the classifier. The relationship between the negative binomial classifier and the Poisson classifier is explored, with a numerical investigation of the impact of dispersion on the discriminant score. Simulation results show the superiority of our proposed method. We also analyze four real RNA-Seq data sets to demonstrate the advantage of our method in real-world applications

The Extraction of Trajectories from Real Texts Based on Linear Classification

Proceedings of the 16th Nordic Conference of Computational Linguistics NODALIDA-2007. Editors: Joakim Nivre, Heiki-Jaan Kaalep, Kadri Muischnek and Mare Koit. University of Tartu, Tartu, 2007. ISBN 978-9985-4-0513-0 (online) ISBN 978-9985-4-0514-7 (CD-ROM) pp. 121-127

Document-Level Relation Extraction with Reconstruction

In document-level relation extraction (DocRE), graph structure is generally used to encode relation information in the input document to classify the relation category between each entity pair, and has greatly advanced the DocRE task over the past several years. However, the learned graph representation universally models relation information between all entity pairs regardless of whether there are relationships between these entity pairs. Thus, those entity pairs without relationships disperse the attention of the encoder-classifier DocRE for ones with relationships, which may further hind the improvement of DocRE. To alleviate this issue, we propose a novel encoder-classifier-reconstructor model for DocRE. The reconstructor manages to reconstruct the ground-truth path dependencies from the graph representation, to ensure that the proposed DocRE model pays more attention to encode entity pairs with relationships in the training. Furthermore, the reconstructor is regarded as a relationship indicator to assist relation classification in the inference, which can further improve the performance of DocRE model. Experimental results on a large-scale DocRE dataset show that the proposed model can significantly improve the accuracy of relation extraction on a strong heterogeneous graph-based baseline.Comment: 9 pages, 5 figures, 6 tables. Accepted by AAAI 2021 (Long Paper

SVIT: Scaling up Visual Instruction Tuning

Thanks to the emerging of foundation models, the large language and vision models are integrated to acquire the multimodal ability of visual captioning, dialogue, question answering, etc. Although existing multimodal models present impressive performance of visual understanding and reasoning, their limits are still largely under-explored due to the scarcity of high-quality instruction tuning data. To push the limits of multimodal capability, we Sale up Visual Instruction Tuning (SVIT) by constructing a dataset of 3.2 million visual instruction tuning data including 1.6M conversation question-answer (QA) pairs and 1.6M complex reasoning QA pairs and 106K detailed image descriptions. Besides the volume, the proposed dataset is also featured by the high quality and rich diversity, which is generated by prompting GPT-4 with the abundant manual annotations of images. We empirically verify that training multimodal models on SVIT can significantly improve the multimodal performance in terms of visual perception, reasoning and planing