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 Deep Learning


Deep Learning-Driven Peptide Classification in Biological Nanopores

arXiv.org Artificial Intelligence

A device capable of performing real time classification of proteins in a clinical setting would allow for inexpensive and rapid disease diagnosis. One such candidate for this technology are nanopore devices. These devices work by measuring a current signal that arises when a protein or peptide enters a nanometer-length-scale pore. Should this current be uniquely related to the structure of the peptide and its interactions with the pore, the signals can be used to perform identification. While such a method would allow for real time identification of peptides and proteins in a clinical setting, to date, the complexities of these signals limit their accuracy. In this work, we tackle the issue of classification by converting the current signals into scaleogram images via wavelet transforms, capturing amplitude, frequency, and time information in a modality well-suited to machine learning algorithms. When tested on 42 peptides, our method achieved a classification accuracy of ~$81\,\%$, setting a new state-of-the-art in the field and taking a step toward practical peptide/protein diagnostics at the point of care. In addition, we demonstrate model transfer techniques that will be critical when deploying these models into real hardware, paving the way to a new method for real-time disease diagnosis.


Quantum Variational Activation Functions Empower Kolmogorov-Arnold Networks

arXiv.org Artificial Intelligence

Variational quantum circuits (VQCs) are central to quantum machine learning, while recent progress in Kolmogorov-Arnold networks (KANs) highlights the power of learnable activation functions. We unify these directions by introducing quantum variational activation functions (QVAFs), realized through single-qubit data re-uploading circuits called DatA Re-Uploading ActivatioNs (DARUANs). We show that DARUAN with trainable weights in data pre-processing possesses an exponentially growing frequency spectrum with data repetitions, enabling an exponential reduction in parameter size compared with Fourier-based activations without loss of expressivity. Embedding DARUAN into KANs yields quantum-inspired KANs (QKANs), which retain the interpretability of KANs while improving their parameter efficiency, expressivity, and generalization. We further introduce two novel techniques to enhance scalability, feasibility and computational efficiency, such as layer extension and hybrid QKANs (HQKANs) as drop-in replacements of multi-layer perceptrons (MLPs) for feed-forward networks in large-scale models. We provide theoretical analysis and extensive experiments on function regression, image classification, and autoregressive generative language modeling, demonstrating the efficiency and scalability of QKANs. DARUANs and QKANs offer a promising direction for advancing quantum machine learning on both noisy intermediate-scale quantum (NISQ) hardware and classical quantum simulators.


Artificial neural networks ensemble methodology to predict significant wave height

arXiv.org Artificial Intelligence

Institute of Mathematics and Statistics, Federal University of Rio Grande do Sul (UFRGS), Av. Center for Coastal and Oceanic Geology Studies (CECO), Federal University of Rio Grande do Sul (UFRGS), Av. Abstract The forecast of wave variables are important for several applications that depend on a better description of the ocean state. Due to the chaotic behaviour of the differential equations which model this problem, a well know strategy to overcome the difficulties is basically to run several simulations, by for instance, varying the initial condition, and averaging the result of each of these, creating an ensemble. Moreover, in the last few years, considering the amount of available data and the computational power increase, machine learning algorithms have been applied as surrogate to traditional numerical models, yielding comparative or better results. In this work, we present a methodology to create an ensemble of different artificial neural networks architectures, namely, MLP, RNN, LSTM, CNN and a hybrid CNN-LSTM, which aims to predict significant wave height on six different locations in the Brazilian coast. The networks are trained using NOAA's numerical reforecast data and target the residual between observational data and the numerical model output. A new strategy to create the training and target datasets is demonstrated. Introduction Numerical simulations of both weather and ocean parameters rely on the evolution of nonlinear dynamical systems that have a high sensitivity on initial conditions. Considering that errors in the observations and analysis are present, and therefore in the initial conditions, the concept of a unique deterministic solution of the governing equations becomes fragile [1, 2].


Hala Technical Report: Building Arabic-Centric Instruction & Translation Models at Scale

arXiv.org Artificial Intelligence

We present Hala, a family of Arabic-centric instruction and translation models built with our translate-and-tune pipeline. We first compress a strong AR$\leftrightarrow$EN teacher to FP8 (yielding $\sim$2$\times$ higher throughput with no quality loss) and use it to create high-fidelity bilingual supervision. A lightweight language model LFM2-1.2B is then fine-tuned on this data and used to translate high-quality English instruction sets into Arabic, producing a million-scale corpus tailored to instruction following. We train Hala models at 350M, 700M, 1.2B, and 9B parameters, and apply slerp merging to balance Arabic specialization with base-model strengths. On Arabic-centric benchmarks, Hala achieves state-of-the-art results within both the "nano" ($\leq$2B) and "small" (7-9B) categories, outperforming their bases. We release models, data, evaluation, and recipes to accelerate research in Arabic NLP.


Slim-SC: Thought Pruning for Efficient Scaling with Self-Consistency

arXiv.org Artificial Intelligence

Recently, Test-Time Scaling (TTS) has gained increasing attention for improving LLM reasoning performance at test time without retraining the model. A notable TTS technique is Self-Consistency (SC), which generates multiple reasoning chains in parallel and selects the final answer via majority voting. While effective, the order-of-magnitude computational overhead limits its broad deployment. Prior attempts to accelerate SC mainly rely on model-based confidence scores or heuristics with limited empirical support. For the first time, we theoretically and empirically analyze the inefficiencies of SC and reveal actionable opportunities for improvement. Building on these insights, we propose Slim-SC, a step-wise pruning strategy that identifies and removes redundant chains using inter-chain similarity at the thought level. Experiments on three STEM reasoning datasets and two recent LLM architectures show that Slim-SC reduces inference latency and KVC usage by up to 45% and 26%, respectively, with R1-Distill, while maintaining or improving accuracy, thus offering a simple yet efficient TTS alternative for SC.


Personalization on a Budget: Minimally-Labeled Continual Learning for Resource-Efficient Seizure Detection

arXiv.org Artificial Intelligence

Seizure detection remains challenging, as current clinical practice relies on expert analysis of electroencephalogra-phy, which is a time-consuming process and requires specialized knowledge. Addressing this challenge, this paper explores automated epileptic seizure detection using deep learning, focusing on personalized continual learning models that adapt to each patient's unique electroencephalog-raphy signal features, which evolve over time. Methods: In this context, our approach addresses the challenge of integrating new data into existing models without catastrophic forgetting, a common issue in static deep learning models. We propose EpiSMART, a continual learning framework for seizure detection that uses a size-constrained replay buffer and an informed sample selection strategy to incrementally adapt to patient-specific electroencephalog-raphy signals. By selectively retaining high-entropy and seizure-predicted samples, our method preserves critical past information while maintaining high performance with minimal memory and computational requirements. Results: Validation on the CHB-MIT dataset, shows that EpiSMART achieves a 21% improvement in the F1 score over a trained baseline without updates in all other patients. On average, EpiSMART requires only 6.46 minutes of labeled data and 6.28 updates per day, making it suitable for real-time deployment in wearable systems. Conclusion: EpiSMART enables robust and personalized seizure detection under realistic and resource-constrained conditions by effectively integrating new data into existing models without degrading past knowledge. Significanc: This framework advances automated seizure detection by providing a continual learning approach that supports patient-specific adaptation and practical deployment in wearable healthcare systems.


SEG-Parking: Towards Safe, Efficient, and Generalizable Autonomous Parking via End-to-End Offline Reinforcement Learning

arXiv.org Artificial Intelligence

Autonomous parking is a critical component for achieving safe and efficient urban autonomous driving. However, unstructured environments and dynamic interactions pose significant challenges to autonomous parking tasks. To address this problem, we propose SEG-Parking, a novel end-to-end offline reinforcement learning (RL) framework to achieve interaction-aware autonomous parking. Notably, a specialized parking dataset is constructed for parking scenarios, which include those without interference from the opposite vehicle (OV) and complex ones involving interactions with the OV. Based on this dataset, a goal-conditioned state encoder is pretrained to map the fused perception information into the latent space. Then, an offline RL policy is optimized with a conservative regularizer that penalizes out-of-distribution actions. Extensive closed-loop experiments are conducted in the high-fidelity CARLA simulator. Comparative results demonstrate the superior performance of our framework with the highest success rate and robust generalization to out-of-distribution parking scenarios. The related dataset and source code will be made publicly available after the paper is accepted.


Ensemble of Pre-Trained Models for Long-Tailed Trajectory Prediction

arXiv.org Artificial Intelligence

This work explores the application of ensemble modeling to the multidimensional regression problem of trajectory prediction for vehicles in urban environments. As newer and bigger state-of-the-art prediction models for autonomous driving continue to emerge, an important open challenge is the problem of how to combine the strengths of these big models without the need for costly re-training. We show how, perhaps surprisingly, combining state-of-the-art deep learning models out-of-the-box (without retraining or fine-tuning) with a simple confidence-weighted average method can enhance the overall prediction. Indeed, while combining trajectory prediction models is not straightforward, this simple approach enhances performance by 10% over the best prediction model, especially in the long-tailed metrics. We show that this performance improvement holds on both the NuScenes and Argoverse datasets, and that these improvements are made across the dataset distribution. The code for our work is open source.


TFMAdapter: Lightweight Instance-Level Adaptation of Foundation Models for Forecasting with Covariates

arXiv.org Artificial Intelligence

Time Series Foundation Models (TSFMs) have recently achieved state-of-the-art performance in univariate forecasting on new time series simply by conditioned on a brief history of past values. Their success demonstrates that large-scale pretraining across diverse domains can acquire the inductive bias to generalize from temporal patterns in a brief history. However, most TSFMs are unable to leverage covariates -- future-available exogenous variables critical for accurate forecasting in many applications -- due to their domain-specific nature and the lack of associated inductive bias. We propose TFMAdapter, a lightweight, instance-level adapter that augments TSFMs with covariate information without fine-tuning. Instead of retraining, TFMAdapter operates on the limited history provided during a single model call, learning a non-parametric cascade that combines covariates with univariate TSFM forecasts. However, such learning would require univariate forecasts at all steps in the history, requiring too many calls to the TSFM. To enable training on the full historical context while limiting TSFM invocations, TFMAdapter uses a two-stage method: (1) generating pseudo-forecasts with a simple regression model, and (2) training a Gaussian Process regressor to refine predictions using both pseudo- and TSFM forecasts alongside covariates. Extensive experiments on real-world datasets demonstrate that TFMAdapter consistently outperforms both foundation models and supervised baselines, achieving a 24-27\% improvement over base foundation models with minimal data and computational overhead. Our results highlight the potential of lightweight adapters to bridge the gap between generic foundation models and domain-specific forecasting needs.


Do Large Language Models Understand Word Senses?

arXiv.org Artificial Intelligence

Understanding the meaning of words in context is a fundamental capability for Large Language Models (LLMs). Despite extensive evaluation efforts, the extent to which LLMs show evidence that they truly grasp word senses remains underexplored. In this paper, we address this gap by evaluating both i) the Word Sense Disambiguation (WSD) capabilities of instruction-tuned LLMs, comparing their performance to state-of-the-art systems specifically designed for the task, and ii) the ability of two top-performing open- and closed-source LLMs to understand word senses in three generative settings: definition generation, free-form explanation, and example generation. Notably, we find that, in the WSD task, leading models such as GPT-4o and DeepSeek-V3 achieve performance on par with specialized WSD systems, while also demonstrating greater robustness across domains and levels of difficulty. In the generation tasks, results reveal that LLMs can explain the meaning of words in context up to 98\% accuracy, with the highest performance observed in the free-form explanation task, which best aligns with their generative capabilities.