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A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that…

机器学习 · 计算机科学 2023-04-10 Patrick Emami , Aidan Perreault , Jeffrey Law , David Biagioni , Peter C. St. John

Trained on massive cross-species DNA corpora, DNA large language models (LLMs) learn the fundamental "grammar" and evolutionary patterns of genomic sequences. This makes them powerful priors for DNA sequence modeling, particularly over long…

基因组学 · 定量生物学 2025-11-19 Rui Zhu , Xiaopu Zhou , Haixu Tang , Stephen W. Scherer , Lucila Ohno-Machado

GA LLM is a hybrid framework that combines Genetic Algorithms with Large Language Models to handle structured generation tasks under strict constraints. Each output, such as a plan or report, is treated as a gene, and evolutionary…

计算与语言 · 计算机科学 2025-06-17 William Shum , Rachel Chan , Jonas Lin , Benny Feng , Patrick Lau

This paper presents an improved deep embedding learning method based on convolutional neural network (CNN) for text-independent speaker verification. Two improvements are proposed for x-vector embedding learning: (1) Multi-scale convolution…

音频与语音处理 · 电气工程与系统科学 2020-01-15 Bin Gu , Wu Guo

Language exhibits structure at different scales, ranging from subwords to words, sentences, paragraphs, and documents. To what extent do deep models capture information at these scales, and can we force them to better capture structure…

计算与语言 · 计算机科学 2020-11-11 Alex Tamkin , Dan Jurafsky , Noah Goodman

Ensuring the robustness of deep learning models requires comprehensive and diverse testing. Existing approaches, often based on simple data augmentation techniques or generative adversarial networks, are limited in producing realistic and…

计算机视觉与模式识别 · 计算机科学 2025-02-10 Luciano Baresi , Davide Yi Xian Hu , Muhammad Irfan Mas'udi , Giovanni Quattrocchi

The massive progress of machine learning has seen its application over a variety of domains in the past decade. But how do we develop a systematic, scalable and modular strategy to validate machine-learning systems? We present, to the best…

机器学习 · 计算机科学 2019-11-07 Sakshi Udeshi , Sudipta Chattopadhyay

As generative AI achieves hyper-realism, superficial artifact detection has become obsolete. While prevailing methods rely on resource-intensive fine-tuning of black-box backbones, we propose that forgery detection capability is already…

计算机视觉与模式识别 · 计算机科学 2026-02-02 Jingtong Dou , Chuancheng Shi , Yemin Wang , Shiming Guo , Anqi Yi , Wenhua Wu , Li Zhang , Fei Shen , Tat-Seng Chua

While neural models show remarkable accuracy on individual predictions, their internal beliefs can be inconsistent across examples. In this paper, we formalize such inconsistency as a generalization of prediction error. We propose a…

人工智能 · 计算机科学 2019-09-16 Tao Li , Vivek Gupta , Maitrey Mehta , Vivek Srikumar

Multimodal learning combining pathology images and genomic sequences enhances cancer survival analysis but faces clinical implementation barriers due to limited access to genomic sequencing in under-resourced regions. To enable survival…

计算机视觉与模式识别 · 计算机科学 2025-06-30 Zizhi Chen , Minghao Han , Xukun Zhang , Shuwei Ma , Tao Liu , Xing Wei , Lihua Zhang

Medicine is inherently a multimodal discipline. Medical images can reflect the pathological changes of cancer and tumors, while the expression of specific genes can influence their morphological characteristics. However, most deep learning…

计算机视觉与模式识别 · 计算机科学 2024-06-04 Jiaying Zhou , Mingzhou Jiang , Junde Wu , Jiayuan Zhu , Ziyue Wang , Yueming Jin

Can we leverage LLMs to model the process of discovering novel language model (LM) architectures? Inspired by real research, we propose a multi-agent LLM approach that simulates the conventional stages of research, from ideation and…

人工智能 · 计算机科学 2025-06-26 Junyan Cheng , Peter Clark , Kyle Richardson

The goal of this paper is to use multi-task learning to efficiently scale slot filling models for natural language understanding to handle multiple target tasks or domains. The key to scalability is reducing the amount of training data…

计算与语言 · 计算机科学 2016-08-11 Aaron Jaech , Larry Heck , Mari Ostendorf

Protein sequence design has seen significant advances through discrete diffusion and autoregressive approaches, yet the potential of continuous diffusion remains underexplored. Here, we present DiMA, a latent diffusion framework that…

This paper presents several novel findings on the explainability of vision reflection in large multimodal models (LMMs). First, we show that prompting an LMM to verify the prediction of a specialized vision model can improve recognition…

计算机视觉与模式识别 · 计算机科学 2025-08-12 Guoyuan An , JaeYoon Kim , SungEui Yoon

Existing language models such as n-grams for software code often fail to capture a long context where dependent code elements scatter far apart. In this paper, we propose a novel approach to build a language model for software code to…

软件工程 · 计算机科学 2016-08-10 Hoa Khanh Dam , Truyen Tran , Trang Pham

Binary classifiers are often employed as discriminators in GAN-based unsupervised style transfer systems to ensure that transferred sentences are similar to sentences in the target domain. One difficulty with this approach is that the error…

计算与语言 · 计算机科学 2019-01-31 Zichao Yang , Zhiting Hu , Chris Dyer , Eric P. Xing , Taylor Berg-Kirkpatrick

Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…

其他定量生物学 · 定量生物学 2025-01-29 Wang Liang

This paper proposes an approach to the joint modeling of the short-time Fourier transform magnitude and phase spectrograms with a deep generative model. We assume that the magnitude follows a Gaussian distribution and the phase follows a…

声音 · 计算机科学 2022-07-18 Aditya Arie Nugraha , Kouhei Sekiguchi , Kazuyoshi Yoshii

Prior Unsupervised Domain Adaptation (UDA) methods often aim to train a domain-invariant feature extractor, which may hinder the model from learning sufficiently discriminative features. To tackle this, a line of works based on prompt…

机器学习 · 计算机科学 2025-04-02 Hoang Phan , Lam Tran , Quyen Tran , Trung Le