Text Retrieval with Multi-Stage Re-Ranking Models

The text retrieval is the task of retrieving similar documents to a search query, and it is important to improve retrieval accuracy while maintaining a certain level of retrieval speed. Existing studies have reported accuracy improvements using language models, but many of these do not take into account the reduction in search speed that comes with increased performance. In this study, we propose three-stage re-ranking model using model ensembles or larger language models to improve search accuracy while minimizing the search delay. We ranked the documents by BM25 and language models, and then re-ranks by a model ensemble or a larger language model for documents with high similarity to the query. In our experiments, we train the MiniLM language model on the MS-MARCO dataset and evaluate it in a zero-shot setting. Our proposed method achieves higher retrieval accuracy while reducing the retrieval speed decay

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Unification of Compile-time and Run-time Metaobject Protocols

In this paper, we propose the unification of compile-time and run-time Metaobject Protocols (MOPs), to improve the efficiency and flexibility of object-oriented operating systems. We also propose a reflective programming system, named Cognac, which employs unified MOPs and provides language and runtime facilities for the Apertos object-oriented distributed operating system. In Cognac, each object has a single unified meta-space which defines both the semantics of the source programming language and the execution environment for the object. The definition of the unified meta-space comprises two parts: a compile-time meta-definition which defines how to generate the object binary code, and a run-time metadefinition which defines the run-time execution environment of the object code. Using this technique, the unification of active and passive objects can also be achieved. With this unification, programmers can concentrate on programming an algorithm without having to consider how objects are used and executed. Also, distributed objects can be more easily migrated.

Unification of Active and Passive Objects in an Object-Oriented Operating System

This paper proposes the unification of active and passive objects in object-oriented operating systems. With such a unification, programmers can concentrate on programming an algorithm without having to consider how objects are used and executed. Also, all objects can be migrated in a distributed system. To achieve this unification, meta level scheduling control is introduced, and the scheduling policy is determined at object creation time. We named this system Cognac. In Cognac, the execution domain of an object is an object cluster, in which some metaobjects control the execution of member objects at run-time. The scheduler metaobject manages method invocation and the status of its member objects. Since all objects' attributes are managed by metaobjects, mutual exclusion is guaranteed. 1 Introduction The object-oriented paradigm has become popular and it is now widely accepted as a good tool for constructing large, complex systems, because of its excellent modularity. It is also hel..