Abstract Syntax Tree for Programming Language Understanding and Representation: How Far Are We?

Programming language understanding and representation (a.k.a code representation learning) has always been a hot and challenging task in software engineering. It aims to apply deep learning techniques to produce numerical representations of the source code features while preserving its semantics. These representations can be used for facilitating subsequent code-related tasks. The abstract syntax tree (AST), a fundamental code feature, illustrates the syntactic information of the source code and has been widely used in code representation learning. However, there is still a lack of systematic and quantitative evaluation of how well AST-based code representation facilitates subsequent code-related tasks. In this paper, we first conduct a comprehensive empirical study to explore the effectiveness of the AST-based code representation in facilitating follow-up code-related tasks. To do so, we compare the performance of models trained with code token sequence (Token for short) based code representation and AST-based code representation on three popular types of code-related tasks. Surprisingly, the overall quantitative statistical results demonstrate that models trained with AST-based code representation consistently perform worse across all three tasks compared to models trained with Token-based code representation. Our further quantitative analysis reveals that models trained with AST-based code representation outperform models trained with Token-based code representation in certain subsets of samples across all three tasks. We also conduct comprehensive experiments to evaluate and reveal the impact of the choice of AST parsing/preprocessing/encoding methods on AST-based code representation and subsequent code-related tasks. Our study provides future researchers with detailed guidance on how to select solutions at each stage to fully exploit AST.Comment: submitted to ACM Transactions on Software Engineering and Methodology. arXiv admin note: text overlap with arXiv:2103.10668 by other author

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.

Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.This work is part of the ‘‘SpatioTemporal Omics Consortium’’ (STOC) paper package. A list of STOC members is available at: http://sto-consortium.org. We would like to thank the MOTIC China Group, Rongqin Ke (Huaqiao University, Xiamen, China), Jiazuan Ni (Shenzhen University, Shenzhen, China), Wei Huang (Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China), and Jonathan S. Weissman (Whitehead Institute, Boston, USA) for their help. This work was supported by the grant of Top Ten Foundamental Research Institutes of Shenzhen, the Shenzhen Key Laboratory of Single-Cell Omics (ZDSYS20190902093613831), and the Guangdong Provincial Key Laboratory of Genome Read and Write (2017B030301011); Longqi Liu was supported by the National Natural Science Foundation of China (31900466) and Miguel A. Esteban’s laboratory at the Guangzhou Institutes of Biomedicine and Health by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16030502), National Natural Science Foundation of China (92068106), and the Guangdong Basic and Applied Basic Research Foundation (2021B1515120075).S

One-pot Synthesis of 2-bromopropionyl Esterified Cellulose Nanofibrils as Versatile Coatings, Reactants and Macroinitiators

Nanocelluloses, the crystalline domains isolated from native cellulose, have gained increasing attention due to their uniquely ultra-high elastic modulus, low axial thermal expansion coefficient, and biocompatibility. All nanocelluloses in the market are hydrophilic and incompatible with most organic liquids and most synthesized polymers, limiting their applications which stated in the 1st chapter. In the 2nd chapter one-pot synthesis of 2-bromopropionyl esterified cellulose nanofibrils (Br-CNFs) coupled with in-situ disintegration by ultrasonication was developed and streamlined in processing and/or matrix media. This coupled functionalization and ultrasonication approach has been optimized to prepare Br-CNFs with tunable levels of esterification in high yields and imaged by atomic force microscopy (AFM) and transmission electron microscopy (TEM). The structures of Br-CNFs were further characterized by Fourier-transform infrared (FTIR) and liquid phase proton nuclear magnetic resonance (1H NMR) spectroscopy. Thermal properties and crystallinity of Br-CNFs were characterized by thermogravimetric analysis (TGA) and X-ray diffraction (XRD), respectively. In the 3rd chapter, the organic compatibility and reactivity of these Br-CNFs have been demonstrated in their polyol role in replacing soft segment or as chain extender in synthesizing polyurethanes with significantly improved modulus (3x), strength (4x), and strain (1.5x) at merely 0.3 w% as polyol or 1.8 w% as extender. The Br bearing esters of these high specific surface Br-CNFs make them excellent macroinitiators for atom transfer radical polymerization (ATRP) of defined lengths of surface polymer grafts on crystalline cellulose, all described in 4th chapter. Br-CNF-g-PLMA from ATRP surface grafting of polylauryl methacrylate (PLMA) have shown to exhibit combined shear thinning behavior of Br-CNF proved by flow behavior index n< 1 and drag reducing effects of PLMA with up to 21071x increased viscosity. Moreover, in the 5th chapter Br-CNFs have shown to be effective hydrophobic coatings on non-porous carbon and cellulose fabrics to respective water contact angles up to 105° and 88° as well as moderately improved the fabric’s modulus (1.4x) and strength (1.2x). The multiple functionalities of these one-pot synthesized Br-CNFs have shown to be excellent surface modifiers (thin films, coatings), reactants or precursors for polyurethanes (polyols, crosslinkers), and ATRP macroinitiators for polymer sheath-nanocellulose core viscosity modifiers and drag reducers for diverse applications

Tunable poly(lauryl methacrylate) surface grafting via SI-ATRP on a one-pot synthesized cellulose nanofibril macroinitiator core as a shear-thinning rheology modifier and drag reducer

The optimally one-pot synthesized 2-bromoproponyl esterified cellulose nanofibril (Br-CNF) has been validated as a robust macroinitiator for self-surface-initiated atom transfer radical polymerization (SI-ATRP) of lauryl methacrylate (LMA) in tunable graft lengths and high conversions of up to 92.7%. SI-ATRP of LMA surface brushes on Br-CNF followed first order kinetics in lengths at up to 46 degree of polymerization (DP) based on mass balance or 31 DP by solution-state 1H NMR in DMSO-d6. With increasing PLMA graft lengths, Br-CNF-g-PLMA cast films exhibited increasing hydrophobicity with water contact angles from 80.9° to 110.6°. The novel Br-CNF-g-PLMA exhibited dual shear thinning behavior of the Br-CNF core as evident by n < 1 flow behavior index and drag reducing properties of PLMA grafts with increased viscosity at up to 21 071×. Br-CNF-g-PLMA with 46 DP could be fully dispersed in silicon pump oil to function as a drag reducer to enhance viscosity up to 5× at 25, 40, and 55 °C. The novel macroinitiator capability of Br-CNF in SI-ATRP of vinyl monomers and the bottlebrush-like LMA surface grafted Br-CNF as highly effective viscosity modifier and drag reducer further demonstrate the versatile functionality of Br-CNF beyond hydrophobic coatings and reactive polyols previously reported

2-Bromopropionyl Esterified Cellulose Nanofibrils as Chain Extenders or Polyols in Stoichiometrically Optimized Syntheses of High-Strength Polyurethanes.

2-Bromopropionyl bromide esterified cellulose nanofibrils (Br-CNFs) facilely synthesized from one-pot esterification of cellulose and in situ ultrasonication exhibited excellent N,N-dimethylformamide (DMF) dispersibility and reactivity to partially replace either chain extender or soft segment diol in the stoichiometrically optimized syntheses of polyurethanes (PUs). PUs polymerized with Br-CNF to replace either 11 mol% 1,4-butadiol chain extender OHs or 1.8 mol% polytetramethylene ether glycol OHs, i.e., 1.5 or 0.3 wt% Br-CNF in PUs, exhibited an over 3 times increased modulus, nearly 4 times higher strength, and a 50% increase in strain. In either role, the experimental modulus exceeding those predicted by the Halpin-Tsai model gave evidence of the stoichiometrically optimized covalent bonding with Br-CNF, while the improved strain was attributed to increased hydrogen-bonding interactions between Br-CNF and the soft segment. These new Br-CNFs not only offer novel synthetic strategies to incorporate nanocelluloses in polyurethanes but also maximize their reinforcing effects via their versatile polyol reactant and cross-linking roles, demonstrating promising applications in the synthesis of other polymers

One-pot synthesis of 2-bromopropionyl esterified cellulose nanofibrils as hydrophobic coating and film.

Hydrophobic 2-bromopropionyl esterified cellulose nanofibrils (Br-CNFs) have been facilely produced via one-pot esterification of cellulose with 2-bromopropionyl bromide (BPB) then in situ disintegrated by ultrasonication in the same reaction media. Br-CNFs optimally produced by this robust esterification-ultrasonication approach, i.e., 5 : 1 BPB to anhydroglucose (AGU) molar ratio, 23 °C, 6 h and ultrasonication (50% amplitude, 30 min), were 4.6 nm thick, 29.3 nm wide, and 1 μm long in 71% yield and 48% crystallinity. Successful 2-bromopropionyl esterification of cellulose was confirmed by FTIR and 1H NMR. The degree of substitution (DS) of surface hydroxyl to 2-bromopropanoate was determined to be between 0.53 (DSs) based on XRD and Br-CNF dimensions and 0.56 (DSNMR) from solution-state 1H NMR. Br-CNF dispersions in DMF exhibited Newtonian behaviors at concentrations below and shear thinning behaviors above 0.5%, enabling homogeneous deposition at dilute concentrations up to 0.01% into a few nm ultra-thin layers as well as blade coating of gel into ca. 100 μm thick film, all similarly hydrophobic with surface water contact angles (WCAs) in the range of 70-75°. The ultra-high modulus and strength film from gel coating further showed the potential for dual high-strength and hydrophobic applications of Br-CNFs

2‑Bromopropionyl Esterified Cellulose Nanofibrils as Chain Extenders or Polyols in Stoichiometrically Optimized Syntheses of High-Strength Polyurethanes

2-Bromopropionyl bromide esterified cellulose nanofibrils (Br-CNFs) facilely synthesized from one-pot esterification of cellulose and in situ ultrasonication exhibited excellent N,N-dimethylformamide (DMF) dispersibility and reactivity to partially replace either chain extender or soft segment diol in the stoichiometrically optimized syntheses of polyurethanes (PUs). PUs polymerized with Br-CNF to replace either 11 mol% 1,4-butadiol chain extender OHs or 1.8 mol% polytetramethylene ether glycol OHs, i.e., 1.5 or 0.3 wt% Br-CNF in PUs, exhibited an over 3 times increased modulus, nearly 4 times higher strength, and a 50% increase in strain. In either role, the experimental modulus exceeding those predicted by the Halpin–Tsai model gave evidence of the stoichiometrically optimized covalent bonding with Br-CNF, while the improved strain was attributed to increased hydrogen-bonding interactions between Br-CNF and the soft segment. These new Br-CNFs not only offer novel synthetic strategies to incorporate nanocelluloses in polyurethanes but also maximize their reinforcing effects via their versatile polyol reactant and cross-linking roles, demonstrating promising applications in the synthesis of other polymers