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arXiv2025

StackTrans: From Large Language Model to Large Pushdown Automata Model

The Transformer architecture has emerged as a landmark advancement within the broad field of artificial intelligence, effectively catalyzing the advent of large language models (LLMs). However, despite its remarkable capabilities and the substantial progress it has facilitated, the Transformer architecture still has some limitations. One such intrinsic limitation is its inability to effectively capture the Chomsky hierarchy, such as regular expressions or deterministic context-free grammars. Drawing inspiration from pushdown automata, which efficiently resolve deterministic context-free grammars using stacks, we propose StackTrans to address the aforementioned issue within LLMs. Unlike previous approaches that modify the attention computation, StackTrans explicitly incorporates hidden state stacks between Transformer layers. This design maintains compatibility with existing frameworks like flash-attention. Specifically, our design features stack operations -- such as pushing and popping hidden states -- that are differentiable and can be learned in an end-to-end manner. Our comprehensive evaluation spans benchmarks for both Chomsky hierarchies and large-scale natural languages. Across these diverse tasks, StackTrans consistently outperforms standard Transformer models and other baselines. We have successfully scaled StackTrans up from 360M to 7B parameters. In particular, our from-scratch pretrained model StackTrans-360M outperforms several larger open-source LLMs with 2-3x more parameters, showcasing its superior efficiency and reasoning capability.

cs.SE↗

arXiv2021

BERTology Meets Biology: Interpreting Attention in Protein Language Models

Transformer architectures have proven to learn useful representations for protein classification and generation tasks. However, these representations present challenges in interpretability. In this work, we demonstrate a set of methods for analyzing protein Transformer models through the lens of attention. We show that attention: (1) captures the folding structure of proteins, connecting amino acids that are far apart in the underlying sequence, but spatially close in the three-dimensional structure, (2) targets binding sites, a key functional component of proteins, and (3) focuses on progressively more complex biophysical properties with increasing layer depth. We find this behavior to be consistent across three Transformer architectures (BERT, ALBERT, XLNet) and two distinct protein datasets. We also present a three-dimensional visualization of the interaction between attention and protein structure. Code for visualization and analysis is available at https://github.com/salesforce/provis.

cs.CL↗

arXiv2020

Information Extraction from Swedish Medical Prescriptions with Sig-Transformer Encoder

Relying on large pretrained language models such as Bidirectional Encoder Representations from Transformers (BERT) for encoding and adding a simple prediction layer has led to impressive performance in many clinical natural language processing (NLP) tasks. In this work, we present a novel extension to the Transformer architecture, by incorporating signature transform with the self-attention model. This architecture is added between embedding and prediction layers. Experiments on a new Swedish prescription data show the proposed architecture to be superior in two of the three information extraction tasks, comparing to baseline models. Finally, we evaluate two different embedding approaches between applying Multilingual BERT and translating the Swedish text to English then encode with a BERT model pretrained on clinical notes.

cs.CL↗

arXiv2025

Transformers Applied to Short-term Solar PV Power Output Forecasting

Reliable forecasts of the power output from variable renewable energy generators like solar photovoltaic systems are important to balancing load on real-time electricity markets and ensuring electricity supply reliability. However, solar PV power output is highly uncertain, with significant variations occurring over both longer (daily or seasonally) and shorter (within minutes) timescales due to weather conditions, especially cloud cover. This paper builds on existing work that uses convolutional neural networks in the computer vision task of predicting (in a Nowcast model) and forecasting (in a Forecast model) solar PV power output (Stanford EAO SUNSET Model). A pure transformer architecture followed by a fully-connected layer is applied to one year of image data with experiments run on various combinations of learning rate and batch size. We find that the transformer architecture performs almost as well as the baseline model in the PV output prediction task. However, it performs worse on sunny days.

cs.CE↗

arXiv2021

Explaining Documents' Relevance to Search Queries

We present GenEx, a generative model to explain search results to users beyond just showing matches between query and document words. Adding GenEx explanations to search results greatly impacts user satisfaction and search performance. Search engines mostly provide document titles, URLs, and snippets for each result. Existing model-agnostic explanation methods similarly focus on word matching or content-based features. However, a recent user study shows that word matching features are quite obvious to users and thus of slight value. GenEx explains a search result by providing a terse description for the query aspect covered by that result. We cast the task as a sequence transduction problem and propose a novel model based on the Transformer architecture. To represent documents with respect to the given queries and yet not generate the queries themselves as explanations, two query-attention layers and masked-query decoding are added to the Transformer architecture. The model is trained without using any human-generated explanations. Training data are instead automatically constructed to ensure a tolerable noise level and a generalizable learned model. Experimental evaluation shows that our explanation models significantly outperform the baseline models. Evaluation through user studies also demonstrates that our explanation model generates short yet useful explanations.

cs.IR↗

arXiv2025

Training-Free ANN-to-SNN Conversion for High-Performance Spiking Transformer

Leveraging the event-driven paradigm, Spiking Neural Networks (SNNs) offer a promising approach for energy-efficient Transformer architectures.While ANN-to-SNN conversion avoids the high training cost of directly trained Spiking Transformers, existing approaches still struggle to handle the nonlinear operations within Transformer blocks, and often require additional fine-tuning of pretrained ANNs.To address these limitations, we propose a training-free and high-performance ANN-to-SNN conversion framework tailored for Transformer architectures. Specifically, we introduce a Multi-basis Exponential Decay (MBE) neuron that combines exponential decay with a multi-basis encoding strategy to effectively approximate nonlinear operations, eliminating the need for weight modifications in pretrained ANNs.Extensive experiments across diverse tasks (CV, NLU, NLG) and mainstream Transformer architectures (ViT, RoBERTa, GPT-2) demonstrate that our method achieves near-lossless conversion accuracy with significantly lower latency. This provides a promising pathway for the efficient and scalable deployment of Spiking Transformers in real-world applications.

cs.LG↗

arXiv2024

A Contrastive Learning Scheme with Transformer Innate Patches

This paper presents Contrastive Transformer, a contrastive learning scheme using the Transformer innate patches. Contrastive Transformer enables existing contrastive learning techniques, often used for image classification, to benefit dense downstream prediction tasks such as semantic segmentation. The scheme performs supervised patch-level contrastive learning, selecting the patches based on the ground truth mask, subsequently used for hard-negative and hard-positive sampling. The scheme applies to all vision-transformer architectures, is easy to implement, and introduces minimal additional memory footprint. Additionally, the scheme removes the need for huge batch sizes, as each patch is treated as an image. We apply and test Contrastive Transformer for the case of aerial image segmentation, known for low-resolution data, large class imbalance, and similar semantic classes. We perform extensive experiments to show the efficacy of the Contrastive Transformer scheme on the ISPRS Potsdam aerial image segmentation dataset. Additionally, we show the generalizability of our scheme by applying it to multiple inherently different Transformer architectures. Ultimately, the results show a consistent increase in mean IoU across all classes.

cs.CV↗

arXiv2025

Permutation-Invariant Transformer Neural Architectures for Set-Based Indoor Localization Using Learned RSSI Embeddings

We propose a permutation-invariant neural architecture for indoor localization using RSSI scans from Wi-Fi access points. Each scan is modeled as an unordered set of (BSSID, RSSI) pairs, where BSSIDs are mapped to learned embeddings and concatenated with signal strength. These are processed by a Set Transformer, enabling the model to handle variable-length, sparse inputs while learning attention-based representations over access point relationships. We evaluate the model on a dataset collected across a campus environment consisting of six buildings. Results show that the model accurately recovers fine-grained spatial structure and maintains performance across physically distinct domains. In our experiments, a simple LSTM consistently outperformed all other models, achieving the lowest mean localization error across three tasks (E1 - E3), with average errors as low as 2.23 m. The Set Transformer performed competitively, ranking second in every experiment and outperforming the MLP, RNN, and basic attention models, particularly in scenarios involving multiple buildings (E2) and multiple floors (E3). Performance degraded most in E2, where signal conditions varied substantially across buildings, highlighting the importance of architectural robustness to domain diversity. This work demonstrates that set-based neural models are a natural fit for signal-based localization, offering a principled approach to handling sparse, unordered inputs in real-world positioning tasks.

cs.LG↗

arXiv2025

Model Hemorrhage and the Robustness Limits of Large Language Models

Large language models (LLMs) demonstrate strong performance across natural language processing tasks, yet undergo significant performance degradation when modified for deployment through quantization, pruning, or decoding strategy adjustments. We define this phenomenon as model hemorrhage - performance decline caused by parameter alterations and architectural changes. Through systematic analysis of various LLM frameworks, we identify key vulnerability patterns: layer expansion frequently disrupts attention mechanisms, compression techniques induce information loss cascades, and decoding adjustments amplify prediction divergences. Our investigation reveals transformer architectures exhibit inherent robustness thresholds that determine hemorrhage severity across modification types. We propose three mitigation strategies: gradient-aware pruning preserves critical weight pathways, dynamic quantization scaling maintains activation integrity, and decoding calibration aligns generation trajectories with original model distributions. This work establishes foundational metrics for evaluating model stability during adaptation, providing practical guidelines for maintaining performance while enabling efficient LLM deployment. Our findings advance understanding of neural network resilience under architectural transformations, particularly for large-scale language models.

cs.CL↗

arXiv2023

Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs

Despite their widespread success in various domains, Transformer networks have yet to perform well across datasets in the domain of 3D atomistic graphs such as molecules even when 3D-related inductive biases like translational invariance and rotational equivariance are considered. In this paper, we demonstrate that Transformers can generalize well to 3D atomistic graphs and present Equiformer, a graph neural network leveraging the strength of Transformer architectures and incorporating SE(3)/E(3)-equivariant features based on irreducible representations (irreps). First, we propose a simple and effective architecture by only replacing original operations in Transformers with their equivariant counterparts and including tensor products. Using equivariant operations enables encoding equivariant information in channels of irreps features without complicating graph structures. With minimal modifications to Transformers, this architecture has already achieved strong empirical results. Second, we propose a novel attention mechanism called equivariant graph attention, which improves upon typical attention in Transformers through replacing dot product attention with multi-layer perceptron attention and including non-linear message passing. With these two innovations, Equiformer achieves competitive results to previous models on QM9, MD17 and OC20 datasets.

cs.LG↗

arXiv2022

Temporal Attention for Language Models

Pretrained language models based on the transformer architecture have shown great success in NLP. Textual training data often comes from the web and is thus tagged with time-specific information, but most language models ignore this information. They are trained on the textual data alone, limiting their ability to generalize temporally. In this work, we extend the key component of the transformer architecture, i.e., the self-attention mechanism, and propose temporal attention - a time-aware self-attention mechanism. Temporal attention can be applied to any transformer model and requires the input texts to be accompanied with their relevant time points. It allows the transformer to capture this temporal information and create time-specific contextualized word representations. We leverage these representations for the task of semantic change detection; we apply our proposed mechanism to BERT and experiment on three datasets in different languages (English, German, and Latin) that also vary in time, size, and genre. Our proposed model achieves state-of-the-art results on all the datasets.

cs.CL↗

arXiv2024

Gasformer: A Transformer-based Architecture for Segmenting Methane Emissions from Livestock in Optical Gas Imaging

Methane emissions from livestock, particularly cattle, significantly contribute to climate change. Effective methane emission mitigation strategies are crucial as the global population and demand for livestock products increase. We introduce Gasformer, a novel semantic segmentation architecture for detecting low-flow rate methane emissions from livestock, and controlled release experiments using optical gas imaging. We present two unique datasets captured with a FLIR GF77 OGI camera. Gasformer leverages a Mix Vision Transformer encoder and a Light-Ham decoder to generate multi-scale features and refine segmentation maps. Gasformer outperforms other state-of-the-art models on both datasets, demonstrating its effectiveness in detecting and segmenting methane plumes in controlled and real-world scenarios. On the livestock dataset, Gasformer achieves mIoU of 88.56%, surpassing other state-of-the-art models. Materials are available at: github.com/toqitahamid/Gasformer.

cs.CV↗

arXiv2021

Open-Domain Conversational Search Assistant with Transformers

Open-domain conversational search assistants aim at answering user questions about open topics in a conversational manner. In this paper we show how the Transformer architecture achieves state-of-the-art results in key IR tasks, leveraging the creation of conversational assistants that engage in open-domain conversational search with single, yet informative, answers. In particular, we propose an open-domain abstractive conversational search agent pipeline to address two major challenges: first, conversation context-aware search and second, abstractive search-answers generation. To address the first challenge, the conversation context is modeled with a query rewriting method that unfolds the context of the conversation up to a specific moment to search for the correct answers. These answers are then passed to a Transformer-based re-ranker to further improve retrieval performance. The second challenge, is tackled with recent Abstractive Transformer architectures to generate a digest of the top most relevant passages. Experiments show that Transformers deliver a solid performance across all tasks in conversational search, outperforming the best TREC CAsT 2019 baseline.

cs.IR↗

arXiv2023

Transformers are Universal Predictors

We find limits to the Transformer architecture for language modeling and show it has a universal prediction property in an information-theoretic sense. We further analyze performance in non-asymptotic data regimes to understand the role of various components of the Transformer architecture, especially in the context of data-efficient training. We validate our theoretical analysis with experiments on both synthetic and real datasets.

cs.LG↗

arXiv2025

Bypassing the Exponential Dependency: Looped Transformers Efficiently Learn In-context by Multi-step Gradient Descent

In-context learning has been recognized as a key factor in the success of Large Language Models (LLMs). It refers to the model's ability to learn patterns on the fly from provided in-context examples in the prompt during inference. Previous studies have demonstrated that the Transformer architecture used in LLMs can implement a single-step gradient descent update by processing in-context examples in a single forward pass. Recent work has further shown that, during in-context learning, a looped Transformer can implement multi-step gradient descent updates in forward passes. However, their theoretical results require an exponential number of in-context examples, $n = \exp(Ω(T))$, where $T$ is the number of loops or passes, to achieve a reasonably low error. In this paper, we study linear looped Transformers in-context learning on linear vector generation tasks. We show that linear looped Transformers can implement multi-step gradient descent efficiently for in-context learning. Our results demonstrate that as long as the input data has a constant condition number, e.g., $n = O(d)$, the linear looped Transformers can achieve a small error by multi-step gradient descent during in-context learning. Furthermore, our preliminary experiments validate our theoretical analysis. Our findings reveal that the Transformer architecture possesses a stronger in-context learning capability than previously understood, offering new insights into the mechanisms behind LLMs and potentially guiding the better design of efficient inference algorithms for LLMs.

cs.LG↗

arXiv2026

Dynamic Windowing in Transformers via Regime Incorporation for Financial Time Series

Financial time series exhibit non-stationary behavior, where the strength and extent of temporal dependencies vary across market regimes. Trending, low-volatility phases typically require long-range contextual information, whereas mean-reverting, high-volatility periods rely more heavily on short-term dynamics. Standard Transformer architectures, with fixed attention windows and static positional encodings, are therefore unable to adapt to such variations. In this work, we propose a regime-aware dynamic windowing framework that incorporates market regime information directly into the Transformer. We construct four generic regime signals from price series: volatility ratio, trend strength, local predictability ratio (LPR), and rolling autocorrelation. We incorporate these signals into the model through two mechanisms: (i) regime-augmented inputs to a standard Transformer architecture, and (ii) a modified attention layer that modulates attention weights using regime embeddings. Experiments on five S&P 500 stocks show consistent improvements across five evaluation metrics, demonstrating that regime-aware dynamic windowing enhances both interpretability and predictive performance in financial forecasting tasks.

cs.CE↗

arXiv2024

Sparse-VQ Transformer: An FFN-Free Framework with Vector Quantization for Enhanced Time Series Forecasting

Time series analysis is vital for numerous applications, and transformers have become increasingly prominent in this domain. Leading methods customize the transformer architecture from NLP and CV, utilizing a patching technique to convert continuous signals into segments. Yet, time series data are uniquely challenging due to significant distribution shifts and intrinsic noise levels. To address these two challenges,we introduce the Sparse Vector Quantized FFN-Free Transformer (Sparse-VQ). Our methodology capitalizes on a sparse vector quantization technique coupled with Reverse Instance Normalization (RevIN) to reduce noise impact and capture sufficient statistics for forecasting, serving as an alternative to the Feed-Forward layer (FFN) in the transformer architecture. Our FFN-free approach trims the parameter count, enhancing computational efficiency and reducing overfitting. Through evaluations across ten benchmark datasets, including the newly introduced CAISO dataset, Sparse-VQ surpasses leading models with a 7.84% and 4.17% decrease in MAE for univariate and multivariate time series forecasting, respectively. Moreover, it can be seamlessly integrated with existing transformer-based models to elevate their performance.

cs.LG↗

arXiv2026

Multi-source Transfer Learning of Time Series with a Shapelet-based Distance Measure

Transfer learning is an effective technique for addressing data scarcity in deep learning for time series classification, but its success depends on the selection of source datasets. Conventional transferability estimation methods are often computationally expensive, as they require fully pre-training a model on each potential source dataset to assess its suitability. This paper introduces a novel, training-free source selection method named Shapelet Matching. Our approach first identifies discriminative shapelets from the target and potential source datasets. Then, Shapelet Matching quantifies dataset similarity by comparing the extracted sets of shapelets. To mitigate the risk of negative transfer from selecting an unsuitable single source, we introduce a multi-source transfer learning method. We select several source datasets based on their shapelet-based similarity scores, combine them into a single multi-source dataset, and use this aggregated dataset for pre-training. The model is then fine-tuned on the target task. We evaluated our method on 128 datasets from the UCR Archive using both temporal CNN and Transformer architectures. The empirical results demonstrate that our multi-source pre-training reduces the risk of negative transfer on average. Shapelet Matching achieves the strongest performance for the CNN backbone and remains competitive for patch-based Transformer architectures, while avoiding the cost of pre-training a separate model for every candidate source.

cs.LG↗