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Currently, many studies view DNA sequences as a special type of language and utilize Transformers to model them. These studies use fixed-length k-mer segmentation and BPE subword tokenization but lack a systematic evaluation to determine…

Computation and Language · Computer Science 2025-07-22 Chenlei Gong , Yuanhe Tian , Lei Mao , Yan Song

Time-frequency (TF) domain dual-path models achieve high-fidelity speech separation. While some previous state-of-the-art (SoTA) models rely on RNNs, this reliance means they lack the parallelizability, scalability, and versatility of…

Audio and Speech Processing · Electrical Eng. & Systems 2024-08-08 Kohei Saijo , Gordon Wichern , François G. Germain , Zexu Pan , Jonathan Le Roux

Transformers require positional encodings to represent sequence order, yet most prior work focuses on designing new positional encodings rather than examining how positional information is fused with token embeddings. In this paper, we…

Machine Learning · Computer Science 2026-01-12 Mohamed Amine Hallam , Kuo-Kun Tseng

Although large language models (LLMs) have achieved significant progress in handling long-context inputs, they still suffer from the ``lost-in-the-middle'' problem, where crucial information in the middle of the context is often…

Computation and Language · Computer Science 2025-03-07 Zhenghua Wang , Yiran Ding , Changze Lv , Zhibo Xu , Tianlong Li , Tianyuan Shi , Xiaoqing Zheng , Xuanjing Huang

Position modeling plays a critical role in Transformers. In this paper, we focus on length extrapolation, i.e., training on short texts while evaluating longer sequences. We define attention resolution as an indicator of extrapolation. Then…

Computation and Language · Computer Science 2022-12-21 Yutao Sun , Li Dong , Barun Patra , Shuming Ma , Shaohan Huang , Alon Benhaim , Vishrav Chaudhary , Xia Song , Furu Wei

In Transformers, Position Embeddings (PEs) significantly influence Length Generalization (LG) performance, yet their fundamental role remains unclear. In this work, we investigate the limitations and capabilities of PEs in achieving LG. We…

Machine Learning · Computer Science 2025-10-07 Yang Chen , Yitao Liang , Zhouchen Lin

Comorbidity, the co-occurrence of multiple medical conditions in a single patient, profoundly impacts disease management and outcomes. Understanding these complex interconnections is crucial, especially in contexts where comorbidities…

Machine Learning · Computer Science 2025-10-13 Xihan Qin , Li Liao

We identify intrinsic limitations of Rotary Positional Embeddings (RoPE) in Transformer-based long-context language models. Our theoretical analysis abstracts away from the specific content of the context and depends only on its length. We…

Computation and Language · Computer Science 2026-05-18 Yufeng Du , Phillip Harris , Minyang Tian , Eliu A Huerta , Srikanth Ronanki , Subendhu Rongali , Aram Galstyan , Hao Peng

Despite the remarkable capabilities of Multimodal Large Language Models (MLLMs), they still suffer from visual fading in long-context scenarios. Specifically, the attention to visual tokens diminishes as the text sequence lengthens, leading…

Computer Vision and Pattern Recognition · Computer Science 2026-03-12 Lin Chen , Bolin Ni , Qi Yang , Zili Wang , Kun Ding , Ying Wang , Houwen Peng , Shiming Xiang

The attention mechanism is a fundamental component of the Transformer model, contributing to interactions among distinct tokens, in contrast to earlier feed-forward neural networks. In general, the attention scores are determined simply by…

Computation and Language · Computer Science 2024-10-11 Chuanyang Zheng , Yihang Gao , Han Shi , Jing Xiong , Jiankai Sun , Jingyao Li , Minbin Huang , Xiaozhe Ren , Michael Ng , Xin Jiang , Zhenguo Li , Yu Li

We introduce a new way of learning to encode position information for non-recurrent models, such as Transformer models. Unlike RNN and LSTM, which contain inductive bias by loading the input tokens sequentially, non-recurrent models are…

Machine Learning · Computer Science 2020-03-23 Xuanqing Liu , Hsiang-Fu Yu , Inderjit Dhillon , Cho-Jui Hsieh

Vision Transformers have demonstrated remarkable success in computer vision tasks, yet their reliance on learnable one-dimensional positional embeddings fundamentally disrupts the inherent two-dimensional spatial structure of images through…

Computer Vision and Pattern Recognition · Computer Science 2025-08-27 Zhihang Xin , Xitong Hu , Rui Wang

Despite the success of Transformers on language understanding, code generation, and logical reasoning, they still fail to generalize over length on basic arithmetic tasks such as addition and multiplication. A major reason behind this…

Machine Learning · Computer Science 2024-06-05 Mahdi Sabbaghi , George Pappas , Hamed Hassani , Surbhi Goel

Existing positional encoding methods in transformers are fundamentally signal-agnostic, deriving positional information solely from sequence indices while ignoring the underlying signal characteristics. This limitation is particularly…

Machine Learning · Computer Science 2026-05-07 Habib Irani , Vangelis Metsis

Multivariate long-term time series forecasting is of great application across many domains, such as energy consumption and weather forecasting. With the development of transformer-based methods, the performance of multivariate long-term…

Machine Learning · Computer Science 2023-05-29 Zheng Sun , Yi Wei , Wenxiao Jia , Long Yu

Unsupervised pre-training on vast amounts of graph data is critical in real-world applications wherein labeled data is limited, such as molecule properties prediction or materials science. Existing approaches pre-train models for specific…

Machine Learning · Computer Science 2024-10-01 Viet Anh Nguyen , Nhat Khang Ngo , Truong Son Hy

Transformers, central to the successes in modern Natural Language Processing, often falter on arithmetic tasks despite their vast capabilities --which paradoxically include remarkable coding abilities. We observe that a crucial challenge is…

Computation and Language · Computer Science 2023-11-28 Ruoqi Shen , Sébastien Bubeck , Ronen Eldan , Yin Tat Lee , Yuanzhi Li , Yi Zhang

Multivariate time series (MTS) forecasting is vital in fields like weather, energy, and finance. However, despite deep learning advancements, traditional Transformer-based models often diminish the effect of crucial inter-variable…

Machine Learning · Computer Science 2025-03-03 Yanhong Li , David C. Anastasiu

Electroencephalography (EEG) is a widely used non-invasive technique for measuring brain activity in brain-computer interface (BCI) applications. Supervised EEG decoding models often struggle to generalize across tasks, subjects, and…

Artificial Intelligence · Computer Science 2026-05-29 Ayse Betul Yuce , Sebastian Stober

A key module in neural transformer-based deep architectures is positional encoding. This module enables a suitable way to encode positional information as input for transformer neural layers. This success has been rooted in the use of…

Machine Learning · Computer Science 2025-12-23 Ezequiel Lopez-Rubio , Macoris Decena-Gimenez , Rafael Marcos Luque-Baena