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Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based…

Quantitative Methods · Quantitative Biology 2023-10-19 Zuobai Zhang , Chuanrui Wang , Minghao Xu , Vijil Chenthamarakshan , Aurélie Lozano , Payel Das , Jian Tang

Speech is the surface form of a finite set of phonetic units, which can be represented by discrete codes. We propose the Code BERT (CoBERT) approach for self-supervised speech representation learning. The idea is to convert an utterance to…

Sound · Computer Science 2023-07-06 Chutong Meng , Junyi Ao , Tom Ko , Mingxuan Wang , Haizhou Li

We address the problem of predicting edit completions based on a learned model that was trained on past edits. Given a code snippet that is partially edited, our goal is to predict a completion of the edit for the rest of the snippet. We…

Programming Languages · Computer Science 2020-10-13 Shaked Brody , Uri Alon , Eran Yahav

Automated program repair (APR) attempts to generate correct patches and has drawn wide attention from both academia and industry in the past decades. However, APR is continuously struggling with the patch overfitting issue due to the weak…

Software Engineering · Computer Science 2026-04-07 Quanjun Zhang , Haichuan Hu , Chunrong Fang , Ye Shang , Tao Zheng , Zhenyu Chen , Yun Yang , Liang Xiao

We describe a method for utilizing the known structure of input data to make learning more efficient. Our work is in the domain of programming languages, and we use deep neural networks to do program analysis. Computer programs include a…

Neural and Evolutionary Computing · Computer Science 2019-04-01 Zehra Sura , Tong Chen , Hyojin Sung

Code summaries help developers comprehend programs and reduce their time to infer the program functionalities during software maintenance. Recent efforts resort to deep learning techniques such as sequence-to-sequence models for generating…

Computation and Language · Computer Science 2023-02-08 Shuzheng Gao , Cuiyun Gao , Yulan He , Jichuan Zeng , Lun Yiu Nie , Xin Xia , Michael R. Lyu

Deep learning appears as an appealing solution for Automatic Synthesizer Programming (ASP), which aims to assist musicians and sound designers in programming sound synthesizers. However, integrating software synthesizers into training…

Sound · Computer Science 2025-09-10 Paolo Combes , Stefan Weinzierl , Klaus Obermayer

Pre-trained transformer models shine in many natural language processing tasks and therefore are expected to bear the representation of the input sentence or text meaning. These sentence-level embeddings are also important in…

Computation and Language · Computer Science 2025-02-21 Lukas Stankevičius , Mantas Lukoševičius

Analyzing sequential data is crucial in many domains, particularly due to the abundance of data collected from the Internet of Things paradigm. Time series classification, the task of categorizing sequential data, has gained prominence,…

Machine Learning · Computer Science 2024-06-21 Venkata Ragavendra Vavilthota , Ranjith Ramanathan , Sathyanarayanan N. Aakur

DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…

Genomics · Quantitative Biology 2025-12-16 Zhiyuan Peng , Naifan Zhang , Yuanbo Tang , Yang Li

The representation of graphs is commonly based on the adjacency matrix concept. This formulation is the foundation of most algebraic and computational approaches to graph processing. The advent of deep learning language models offers a wide…

Artificial Intelligence · Computer Science 2025-12-16 Ezequiel Lopez-Rubio

We introduce ProcGen3D, a new approach for 3D content creation by generating procedural graph abstractions of 3D objects, which can then be decoded into rich, complex 3D assets. Inspired by the prevalent use of procedural generators in…

Computer Vision and Pattern Recognition · Computer Science 2025-11-11 Xinyi Zhang , Daoyi Gao , Naiqi Li , Angela Dai

Deep learning has been actively studied for time series forecasting, and the mainstream paradigm is based on the end-to-end training of neural network architectures, ranging from classical LSTM/RNNs to more recent TCNs and Transformers.…

Machine Learning · Computer Science 2022-05-06 Gerald Woo , Chenghao Liu , Doyen Sahoo , Akshat Kumar , Steven Hoi

Source code summarization aims to generate natural language descriptions of code snippets. Many existing studies learn the syntactic and semantic knowledge of code snippets from their token sequences and Abstract Syntax Trees (ASTs). They…

Software Engineering · Computer Science 2022-03-29 Yuexiu Gao , Chen Lyu

Personalized instruction aims to provide learners with support that adapts to their individual knowledge and progress toward learning objectives. Discovering and tracing Knowledge Components (KCs) is an important step in building accurate…

Machine Learning · Computer Science 2026-04-02 Muntasir Hoq , Griffin Pitts , Tirth Bhatt , Aum Pandya , Andrew Lan , Peter Brusilovsky , Bita Akram

Data-efficiency and generalization are key challenges in deep learning and deep reinforcement learning as many models are trained on large-scale, domain-specific, and expensive-to-label datasets. Self-supervised models trained on…

Machine Learning · Computer Science 2021-06-10 Mina Khan , P Srivatsa , Advait Rane , Shriram Chenniappa , Rishabh Anand , Sherjil Ozair , Pattie Maes

A code generation system generates programming language code based on an input natural language description. State-of-the-art approaches rely on neural networks for code generation. However, these code generators suffer from two problems.…

Machine Learning · Computer Science 2019-12-02 Zeyu Sun , Qihao Zhu , Yingfei Xiong , Yican Sun , Lili Mou , Lu Zhang

Source code summarization -- creating natural language descriptions of source code behavior -- is a rapidly-growing research topic with applications to automatic documentation generation, program comprehension, and software maintenance.…

Software Engineering · Computer Science 2019-02-07 Alexander LeClair , Siyuan Jiang , Collin McMillan

With the rise of machine learning, there is a great deal of interest in treating programs as data to be fed to learning algorithms. However, programs do not start off in a form that is immediately amenable to most off-the-shelf learning…

Software Engineering · Computer Science 2018-08-21 Jordan Henkel , Shuvendu K. Lahiri , Ben Liblit , Thomas Reps

Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of…

Machine Learning · Computer Science 2023-01-04 Lirong Wu , Yufei Huang , Haitao Lin , Stan Z. Li