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Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate…

Genomics · Quantitative Biology 2023-09-06 Nathan Ng , Ji Won Park , Jae Hyeon Lee , Ryan Lewis Kelly , Stephen Ra , Kyunghyun Cho

Coverage analysis is widely used but can suffer from high overhead. This overhead is especially acute in the context of Python, which is already notoriously slow (a recent study observes a roughly 30x slowdown vs. native code). We find that…

Software Engineering · Computer Science 2023-06-01 Juan Altmayer Pizzorno , Emery D Berger

This article introduces a novel concatenated coding scheme called sparse regression LDPC (SR-LDPC) codes. An SR-LDPC code consists of an outer non-binary LDPC code and an inner sparse regression code (SPARC) whose respective field size and…

Information Theory · Computer Science 2024-10-28 Jamison R. Ebert , Jean-Francois Chamberland , Krishna R. Narayanan

An iterative algorithm is presented for soft-input-soft-output (SISO) decoding of Reed-Solomon (RS) codes. The proposed iterative algorithm uses the sum product algorithm (SPA) in conjunction with a binary parity check matrix of the RS…

Information Theory · Computer Science 2009-09-29 Jing Jiang , Krishna R. Narayanan

Depth completion involves recovering a dense depth map from a sparse map and an RGB image. Recent approaches focus on utilizing color images as guidance images to recover depth at invalid pixels. However, color images alone are not enough…

Computer Vision and Pattern Recognition · Computer Science 2026-04-16 Danish Nazir , Marcus Liwicki , Didier Stricker , Muhammad Zeshan Afzal

Dependency parsing is a crucial step towards deep language understanding and, therefore, widely demanded by numerous Natural Language Processing applications. In particular, left-to-right and top-down transition-based algorithms that rely…

Computation and Language · Computer Science 2022-10-27 Daniel Fernández-González , Carlos Gómez-Rodríguez

Motivated by the philosophy and phenomenal success of compressed sensing, the problem of reconstructing a matrix from a sampling of its entries has attracted much attention recently. Such a problem can be viewed as an information-theoretic…

Information Theory · Computer Science 2009-05-15 Zhisu Zhu , Anthony Man-Cho So , Yinyu Ye

Speculative decoding (SD) has been demonstrated as an effective technique for lossless LLM inference acceleration. Retrieval-based SD methods, one kind of model-free method, have yielded promising speedup, but they often rely on incomplete…

Computation and Language · Computer Science 2024-12-17 Yuxuan Hu , Ke Wang , Xiaokang Zhang , Fanjin Zhang , Cuiping Li , Hong Chen , Jing Zhang

We present a novel bottom-up method for the synthesis of functional recursive programs. While bottom-up synthesis techniques can work better than top-down methods in certain settings, there is no prior technique for synthesizing recursive…

Programming Languages · Computer Science 2021-12-10 Anders Miltner , Adrian Trejo Nuñez , Ana Brendel , Swarat Chaudhuri , Isil Dillig

The recent development of deep learning methods provides a new approach to optimize the belief propagation (BP) decoding of linear codes. However, the limitation of existing works is that the scale of neural networks increases rapidly with…

Information Theory · Computer Science 2021-02-11 Jincheng Dai , Kailin Tan , Zhongwei Si , Kai Niu , Mingzhe Chen , H. Vincent Poor , Shuguang Cui

Autoregressive next token prediction language models offer powerful capabilities but face significant challenges in practical deployment due to the high computational and memory costs of inference, particularly during the decoding stage. We…

Large language models (LLMs) have achieved impressive results on multi-step mathematical reasoning, yet at the cost of high computational overhead. This challenge is particularly acute for test-time scaling methods such as parallel…

Machine Learning · Computer Science 2026-03-24 Yuanlin Chu , Bo Wang , Xiang Liu , Hong Chen , Aiwei Liu , Xuming Hu

The utilization of statistical machine translation (SMT) has grown enormously over the last decade, many using open-source software developed by the NLP community. As commercial use has increased, there is need for software that is…

Computation and Language · Computer Science 2016-10-20 Hieu Hoang , Nikolay Bogoychev , Lane Schwartz , Marcin Junczys-Dowmunt

Despite the widely successful applications, bootstrapping and fine-tuning semantic parsers are still a tedious process with challenges such as costly data annotation and privacy risks. In this paper, we suggest an alternative,…

Computation and Language · Computer Science 2020-10-19 Ziyu Yao , Yiqi Tang , Wen-tau Yih , Huan Sun , Yu Su

Tasks like code generation and semantic parsing require mapping unstructured (or partially structured) inputs to well-formed, executable outputs. We introduce abstract syntax networks, a modeling framework for these problems. The outputs…

Computation and Language · Computer Science 2017-04-26 Maxim Rabinovich , Mitchell Stern , Dan Klein

Given a relation and a ranking of its tuples, but no information about the ranking function, we are interested in synthesizing simple scoring functions that reproduce the ranking. Our system RankHow identifies linear scoring functions that…

Databases · Computer Science 2025-04-30 Zixuan Chen , Panagiotis Manolios , Mirek Riedewald

As a new communication paradigm, semantic communication has received widespread attention in communication fields. However, since the decoding of semantic signals relies on contextual knowledge, misalignment between the starting position of…

Signal Processing · Electrical Eng. & Systems 2023-12-19 Xiaoyi Liu , Haotai Liang , Chen Dong , Xiaodong Xu

One of the recent best attempts at Text-to-SQL is the pre-trained language model. Due to the structural property of the SQL queries, the seq2seq model takes the responsibility of parsing both the schema items (i.e., tables and columns) and…

Computation and Language · Computer Science 2023-04-11 Haoyang Li , Jing Zhang , Cuiping Li , Hong Chen

Large language models (LLMs) often face a bottleneck in inference speed due to their reliance on auto-regressive decoding. Recently, parallel decoding has shown significant promise in enhancing inference efficiency. However, we have…

Computation and Language · Computer Science 2024-10-18 Yuxuan Liu , Wenyuan Li , Laizhong Cui , Hailiang Yang

In the domain of semantic parsing, significant progress has been achieved in Text-to-SQL and question-answering tasks, both of which focus on extracting information from data sources in their native formats. However, the inherent…

Machine Learning · Computer Science 2025-04-08 Saleh Almohaimeed , Shenyang Liu , May Alsofyani , Saad Almohaimeed , Liqiang Wang
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