LARCH: Large Language Model-based Automatic Readme Creation with Heuristics

Writing a readme is a crucial aspect of software development as it plays a vital role in managing and reusing program code. Though it is a pain point for many developers, automatically creating one remains a challenge even with the recent advancements in large language models (LLMs), because it requires generating an abstract description from thousands of lines of code. In this demo paper, we show that LLMs are capable of generating a coherent and factually correct readmes if we can identify a code fragment that is representative of the repository. Building upon this finding, we developed LARCH (LLM-based Automatic Readme Creation with Heuristics) which leverages representative code identification with heuristics and weak supervision. Through human and automated evaluations, we illustrate that LARCH can generate coherent and factually correct readmes in the majority of cases, outperforming a baseline that does not rely on representative code identification. We have made LARCH open-source and provided a cross-platform Visual Studio Code interface and command-line interface, accessible at https://github.com/hitachi-nlp/larch. A demo video showcasing LARCH's capabilities is available at https://youtu.be/ZUKkh5ED-O4.Comment: This is a pre-print of a paper accepted at CIKM'23 Demo. Refer to the DOI URL for the original publicatio

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

Controlling keywords and their positions in text generation

One of the challenges in text generation is to control generation as intended by a user. Previous studies have proposed to specify the keywords that should be included in the generated text. However, this is insufficient to generate text which reflect the user intent. For example, placing the important keyword beginning of the text would helps attract the reader's attention, but existing methods do not enable such flexible control. In this paper, we tackle a novel task of controlling not only keywords but also the position of each keyword in the text generation. To this end, we show that a method using special tokens can control the relative position of keywords. Experimental results on summarization and story generation tasks show that the proposed method can control keywords and their positions. We also demonstrate that controlling the keyword positions can generate summary texts that are closer to the user's intent than baseline. We release our code

Developmental morphology of ovules and seeds of Nymphaeales

金沢大学理工研究域自然システム学系Ovule and seed development in six species of Nymphaeales was examined. In the Cabombaceae the two species studied resemble some extant basal angiosperms by having a hood-shaped outer integument. A micropyle-hilum complex results when the outer integument and derived testa are lacking between the micropyle and the funiculus, thus the hood-shaped appearance. In the Nymphaeaceae the outer integument is annular at an early stage and then cup-shaped though it is semiannular at initiation in Nupar japonicum and Nymphaea alba. The micropyle and hilum are separated by an intervening testa. Developmental data on the formation of the outer integument, from semiannular to hood-shaped vs. from annular to cup-shaped, are useful for inferring the morphology of the outer integument from the relative position of the micropyle to the hilum in seed fossils. The oldest (early Cretaceous) probable nymphaealean seeds had the micropyle-hilum complex, suggesting that the hood-shaped outer integument may be primitive in the Nymphaeales. This needs to be tested by examination of this feature in other groups of basal angiosperms

AINTEGUMENTA homolog expression in Gnetum (gymnosperms) and implications for the evolution of ovulate axes in seed plants

金沢大学理工研究域自然システム学系The expression of GpANTL1, a homolog of AINTEGUMENTA (ANT) found in the gymnosperm Gnetum parvifolium, was analyzed by RT-PCR and in situ hybridization. GpANTL1 was expressed in the leaf primordia, root tips, and young ovules. In the ovulate axis, expression was detected as four distinct rings around the outer, middle, and inner envelope primordia as well as around the nucellar tip. This pattern of expression is similar to that of ANT in Arabidopsis thaliana. A comparison of the expression of GpANTL1 with that of PtANTL1 in the conifer Pinus thunbergii suggests that the integrated expression of PtANTL1 may have been caused by congenital fusion of the integument, ovuliferous scale, and bract. © 2008 The Author(s)

ERRγ agonist under mechanical stretching manifests hypertrophic cardiomyopathy phenotypes of engineered cardiac tissue through maturation

iPS細胞から成熟した人工心筋組織の作製方法の開発 肥大型心筋症の治療法開発への利用に期待. 京都大学プレスリリース. 2023-10-06.Stretching and stimulating engineered heart tissues to accurately portray hypertrophic cardiomyopathy. 京都大学プレスリリース. 2023-10-17.Engineered cardiac tissue (ECT) using human induced pluripotent stem cell-derived cardiomyocytes is a promising tool for modeling heart disease. However, tissue immaturity makes robust disease modeling difficult. Here, we established a method for modeling hypertrophic cardiomyopathy (HCM) malignant (MYH7 R719Q) and nonmalignant (MYBPC3 G115∗) pathogenic sarcomere gene mutations by accelerating ECT maturation using an ERRγ agonist, T112, and mechanical stretching. ECTs treated with T112 under 10% elongation stimulation exhibited more organized and mature characteristics. Whereas matured ECTs with the MYH7 R719Q mutation showed broad HCM phenotypes, including hypertrophy, hypercontraction, diastolic dysfunction, myofibril misalignment, fibrotic change, and glycolytic activation, matured MYBPC3 G115∗ ECTs displayed limited phenotypes, which were primarily observed only under our new maturation protocol (i.e., hypertrophy). Altogether, ERRγ activation combined with mechanical stimulation enhanced ECT maturation, leading to a more accurate manifestation of HCM phenotypes, including non-cardiomyocyte activation, consistent with clinical observations

Expression patterns of class I KNOX and YABBY genes in Ruscus aculeatus (Asparagaceae) with implications for phylloclade homology

金沢大学大学院自然科学研究科生物多様性動態学金沢大学理学部STM (RaSTM) and YAB2 (RaYAB2) homologues were isolated from Ruscus aculeatus (Asparagaceae, monocots), and their expressions were analyzed by real-time polymerase chain reaction (PCR) to assess hypotheses on the evolutionary origin of the phylloclade in the Asparagaceae. In young shoot buds, RaSTM is expressed in the shoot apex, while RaYAB2 is expressed in the scale leaf subtending the shoot bud. This expression pattern is shared by other angiosperms, suggesting that the expression patterns of RaSTM and RaYAB2 are useful as molecular markers to identify the shoot and leaf, respectively. RaSTM and RaYAB2 are expressed concomitantly in phylloclade primordia. These results suggest that the phylloclade is not homologous to either the shoot or leaf, but that it has a double organ identity. © Springer-Verlag 2007