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Neural methods of molecule property prediction require efficient encoding of structure and property relationship to be accurate. Recent work using graph algorithms shows limited generalization in the latent molecule encoding space. We build…

Quantitative Methods · Quantitative Biology 2020-11-26 Prateeth Nayak , Andrew Silberfarb , Ran Chen , Tulay Muezzinoglu , John Byrnes

Recurrent models have been dominating the field of neural machine translation (NMT) for the past few years. Transformers \citep{vaswani2017attention}, have radically changed it by proposing a novel architecture that relies on a feed-forward…

Computation and Language · Computer Science 2022-10-25 Joyce Zheng , Mehdi Rezagholizadeh , Peyman Passban

In order to preserve word-order information in a non-autoregressive setting, transformer architectures tend to include positional knowledge, by (for instance) adding positional encodings to token embeddings. Several modifications have been…

Computation and Language · Computer Science 2021-09-14 Vinit Ravishankar , Anders Søgaard

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

The self-attention mechanism in Transformer architecture, invariant to sequence order, necessitates positional embeddings to encode temporal order in time series prediction. We argue that this reliance on positional embeddings restricts the…

Machine Learning · Computer Science 2024-08-21 Yongbo Yu , Weizhong Yu , Feiping Nie , Xuelong Li

We propose a novel positional encoding for learning graph on Transformer architecture. Existing approaches either linearize a graph to encode absolute position in the sequence of nodes, or encode relative position with another node using…

Machine Learning · Computer Science 2022-10-17 Wonpyo Park , Woonggi Chang , Donggeon Lee , Juntae Kim , Seung-won Hwang

Several recent works use positional encodings to extend the receptive fields of graph neural network (GNN) layers equipped with attention mechanisms. These techniques, however, extend receptive fields to the complete graph, at substantial…

Machine Learning · Computer Science 2023-12-14 Rickard Brüel-Gabrielsson , Mikhail Yurochkin , Justin Solomon

Most approaches for semantic segmentation use only information from color cameras to parse the scenes, yet recent advancements show that using depth data allows to further improve performances. In this work, we focus on transformer-based…

Computer Vision and Pattern Recognition · Computer Science 2023-03-28 Francesco Barbato , Giulia Rizzoli , Pietro Zanuttigh

We conducted empirical experiments to assess the transferability of a light curve transformer to datasets with different cadences and magnitude distributions using various positional encodings (PEs). We proposed a new approach to…

Position encoding is the primary mechanism which induces notion of sequential order for input tokens in transformer architectures. Even though this formulation in the original transformer paper has yielded plausible performance for general…

Computation and Language · Computer Science 2023-10-10 Eren Unlu

Predictive process monitoring is a process mining task aimed at forecasting information about a running process trace, such as the most correct next activity to be executed. In medical domains, predictive process monitoring can provide…

Machine Learning · Computer Science 2026-02-18 Christopher Irwin , Marco Dossena , Giorgio Leonardi , Stefania Montani

A recent variation of Transformer, Performer, scales Transformer to longer sequences with a linear attention mechanism. However, it is not compatible with relative position encoding, which has advantages over absolute position encoding. In…

Computation and Language · Computer Science 2021-09-09 Peng Chen

We introduce Spline-based Transformers, a novel class of Transformer models that eliminate the need for positional encoding. Inspired by workflows using splines in computer animation, our Spline-based Transformers embed an input sequence of…

Machine Learning · Computer Science 2025-04-04 Prashanth Chandran , Agon Serifi , Markus Gross , Moritz Bächer

As we show in this paper, the prediction for output token $n+1$ of Transformer architectures without one of the mechanisms of positional encodings and causal attention is invariant to permutations of input tokens $1, 2, ..., n-1$. Usually,…

Machine Learning · Computer Science 2024-06-18 Chunsheng Zuo , Michael Guerzhoy

Recurrent Neural Networks were, until recently, one of the best ways to capture the timely dependencies in sequences. However, with the introduction of the Transformer, it has been proven that an architecture with only attention-mechanisms…

Machine Learning · Computer Science 2021-08-19 Radostin Cholakov , Todor Kolev

With the development of Internet of Things (IoT) systems, precise long-term forecasting method is requisite for decision makers to evaluate current statuses and formulate future policies. Currently, Transformer and MLP are two paradigms for…

Machine Learning · Computer Science 2023-12-12 Li Shen , Yuning Wei , Yangzhu Wang , Hongguang Li

Transformers have revolutionized the world of deep learning, specially in the field of natural language processing. Recently, the Audio Spectrogram Transformer (AST) was proposed for audio classification, leading to state of the art results…

Sound · Computer Science 2023-10-09 Leonardo Pepino , Pablo Riera , Luciana Ferrer

Transformers rely on both content-based and position-based addressing mechanisms to make predictions, but existing positional encoding techniques often diminish the effectiveness of position-based addressing. Many current methods enforce…

Computation and Language · Computer Science 2025-08-22 Jiajun Zhu , Peihao Wang , Ruisi Cai , Jason D. Lee , Pan Li , Zhangyang Wang

This paper addresses the task of anomaly diagnosis when the underlying data generation process has a complex spatio-temporal (ST) dependency. The key technical challenge is to extract actionable insights from the dependency tensor…

Machine Learning · Computer Science 2023-05-30 Jokin Labaien , Tsuyoshi Idé , Pin-Yu Chen , Ekhi Zugasti , Xabier De Carlos

Transformers have transformed modern machine learning, driving breakthroughs in computer vision, natural language processing, and robotics. At the core of their success lies the attention mechanism, which enables the modeling of global…

Computer Vision and Pattern Recognition · Computer Science 2025-10-07 Hemanth Saratchandran , Simon Lucey