Self-Supervised and Controlled Multi-Document Opinion Summarization

We address the problem of unsupervised abstractive summarization of collections of user generated reviews with self-supervision and control. We propose a self-supervised setup that considers an individual document as a target summary for a set of similar documents. This setting makes training simpler than previous approaches by relying only on standard log-likelihood loss. We address the problem of hallucinations through the use of control codes, to steer the generation towards more coherent and relevant summaries.Finally, we extend the Transformer architecture to allow for multiple reviews as input. Our benchmarks on two datasets against graph-based and recent neural abstractive unsupervised models show that our proposed method generates summaries with a superior quality and relevance.This is confirmed in our human evaluation which focuses explicitly on the faithfulness of generated summaries We also provide an ablation study, which shows the importance of the control setup in controlling hallucinations and achieve high sentiment and topic alignment of the summaries with the input reviews.Comment: 18 pages including 5 pages appendi

Origin and evolution of the octoploid strawberry genome.

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry

The Corpus Expansion Toolkit: finding what we want on the web

This thesis presents the Corpus Expansion Toolkit (CET), a generally applicable toolkit that allows researchers to build domain-specific corpora from the web. The main purpose of the work presented in this thesis and the development of the CET is to provide a solution to discovering desired content on the web from possibly unknown locations or a poorly defined domain. Using an iterative process, the CET is able to solve the problem of discovering domain-specific online content and expand a corpus using only a very small number of example documents or characteristic phrases taken from the target domain. Using a human-in-the-loop strategy and a chain of discrete software components the CET also allows the concept of a domain to be iteratively defined using the very online resources used to expand the original corpus. The CET combines feature extraction, search, web crawling and machine learning methods to collected, store, filter and perform information extraction on collected documents. Using a small number of example ‘seed’ documents the CET is able to expand the original corpus by finding more relevant documents from the web and provide a number of tools to support their analysis. This thesis presents a case study-based methodology that introduces the various contributions and components of the CET through the discussion of five case studies covering a wide variety of domains and requirements that the CET has been applied. These case studies hope to illustrate three main use cases, listed below, where the CET is applicable: 1. Domain known – source known 2. Domain known – source unknown 3. Domain unknown – source unknown First, use cases where the sites for document collection are known and the topic of research is clearly defined. Second, instances where the topic of research is clearly defined but where to find relevant documents on the web is unknown. Third, the most extreme use case, where the domain is poorly defined or unknown to the researcher and the location of the information is also unknown. This thesis presents a solution that allows researchers to begin with very little information on a specific topic and iteratively build a clear conception of a domain and translate that to a computational system

Molecular Mechanisms of Crop Domestication Revealed by Comparative Analysis of the Transcriptomes Between Cultivated and Wild Soybeans

Soybean is one of the key crops necessary to meet the food requirement of the increasing global population. However, in order to meet this need, the quality and quantity of soybean yield must be greatly enhanced. Soybean yield advancement depends on the presence of favorable genes in the genome pool that have significantly changed during domestication. To make use of those domesticated genes, this study involved seven cultivated, G. max, and four wild-type, G. soja, soybeans. Their genomes were studied from developing pods to decipher the molecular mechanisms underlying crop domestication. Specifically, their transcriptomes were analyzed comparatively to previous related studies, with the intention of contributing further to the literature. For these goals, several bioinformatics applications were utilized, including De novo transcriptome assembly, transcriptome abundance quantification, and discovery of differentially expressed genes (DEGs) and their functional annotations and network visualizations. The results revealed 1,247 DEGs, 916 of which were upregulated in the cultivated soybean in comparison to wild type. Findings were mostly corresponded to literature review results, especially regarding genes affecting two focused, domesticated-related pod-shattering resistance and seed size traits. These traits were shown to be upregulated in cultivated soybeans and down-regulated in wild type. However, the opposite trend was shown in disease-related genes, which were down-regulated or not even present in the cultivated soybean genome. Further, 47 biochemical functions of the identified DEGs at the cellular level were revealed, providing some knowledge about the molecular mechanisms of genes related to the two aforementioned subjected traits. While our findings provide valuable insight about the molecular mechanisms of soybean domestication attributed to annotation of differentially expressed genes and transcripts, these results must be dissected further and/or reprocessed with a higher number of samples in order to advance the field

Automatic text filtering using limited supervision learning for epidemic intelligence

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