Three mechanistically different variability and noise sources in the trial-to-trial fluctuations of responses to brain stimulation

Motor-evoked potentials (MEPs) are among the few directly observable responses to external brain stimulation and serve a variety of applications, often in the form of input-output (IO) curves. Previous statistical models with two variability sources inherently consider the small MEPs at the low-side plateau as part of the neural recruitment properties. However, recent studies demonstrated that small MEP responses under resting conditions are contaminated and over-shadowed by background noise of mostly technical quality, e.g., caused by the amplifier, and suggested that the neural recruitment curve should continue below this noise level. This work intends to separate physiological variability from background noise and improve the description of recruitment behaviour. We developed a triple-variability-source model around a logarithmic logistic function without a lower plateau and incorporated an additional source for background noise. Compared to models with two or fewer variability sources, our approach better described IO characteristics, evidenced by lower Bayesian Information Criterion scores across all subjects and pulse shapes. The model independently extracted hidden variability information across the stimulated neural system and isolated it from background noise, which led to an accurate estimation of the IO curve parameters. This new model offers a robust tool to analyse brain stimulation IO curves in clinical and experimental neuroscience and reduces the risk of spurious results from inappropriate statistical methods. The presented model together with the corresponding calibration method provides a more accurate representation of MEP responses and variability sources, advances our understanding of cortical excitability, and may improve the assessment of neuromodulation effects.

SGAC: A Graph Neural Network Framework for Imbalanced and Structure-Aware AMP Classification

Classifying antimicrobial peptides(AMPs) from the vast array of peptides mined from metagenomic sequencing data is a significant approach to addressing the issue of antibiotic resistance. However, current AMP classification methods, primarily relying on sequence-based data, neglect the spatial structure of peptides, thereby limiting the accurate classification of AMPs. Additionally, the number of known AMPs is significantly lower than that of non-AMPs, leading to imbalanced datasets that reduce predictive accuracy for AMPs. To alleviate these two limitations, we first employ Omegafold to predict the three-dimensional spatial structures of AMPs and non-AMPs, constructing peptide graphs based on the amino acids' C$_\alpha$ positions. Building upon this, we propose a novel classification model named Spatial GNN-based AMP Classifier (SGAC). Our SGAC model employs a graph encoder based on Graph Neural Networks (GNNs) to process peptide graphs, generating high-dimensional representations that capture essential features from the three-dimensional spatial structure of amino acids. Then, to address the inherent imbalanced datasets, SGAC first incorporates Weight-enhanced Contrastive Learning, which clusters similar peptides while ensuring separation between dissimilar ones, using weighted contributions to emphasize AMP-specific features. Furthermore, SGAC employs Weight-enhanced Pseudo-label Distillation to dynamically generate high-confidence pseudo labels for ambiguous peptides, further refining predictions and promoting balanced learning between AMPs and non-AMPs. Experiments on publicly available AMP and non-AMP datasets demonstrate that SGAC significantly outperforms traditional sequence-based methods and achieves state-of-the-art performance among graph-based models, validating its effectiveness in AMP classification.

On the Structural Memory of LLM Agents

Memory plays a pivotal role in enabling large language model~(LLM)-based agents to engage in complex and long-term interactions, such as question answering (QA) and dialogue systems. While various memory modules have been proposed for these tasks, the impact of different memory structures across tasks remains insufficiently explored. This paper investigates how memory structures and memory retrieval methods affect the performance of LLM-based agents. Specifically, we evaluate four types of memory structures, including chunks, knowledge triples, atomic facts, and summaries, along with mixed memory that combines these components. In addition, we evaluate three widely used memory retrieval methods: single-step retrieval, reranking, and iterative retrieval. Extensive experiments conducted across four tasks and six datasets yield the following key insights: (1) Different memory structures offer distinct advantages, enabling them to be tailored to specific tasks; (2) Mixed memory structures demonstrate remarkable resilience in noisy environments; (3) Iterative retrieval consistently outperforms other methods across various scenarios. Our investigation aims to inspire further research into the design of memory systems for LLM-based agents.

A Decade of Deep Learning: A Survey on The Magnificent Seven

Deep learning has fundamentally reshaped the landscape of artificial intelligence over the past decade, enabling remarkable achievements across diverse domains. At the heart of these developments lie multi-layered neural network architectures that excel at automatic feature extraction, leading to significant improvements in machine learning tasks. To demystify these advances and offer accessible guidance, we present a comprehensive overview of the most influential deep learning algorithms selected through a broad-based survey of the field. Our discussion centers on pivotal architectures, including Residual Networks, Transformers, Generative Adversarial Networks, Variational Autoencoders, Graph Neural Networks, Contrastive Language-Image Pre-training, and Diffusion models. We detail their historical context, highlight their mathematical foundations and algorithmic principles, and examine subsequent variants, extensions, and practical considerations such as training methodologies, normalization techniques, and learning rate schedules. Beyond historical and technical insights, we also address their applications, challenges, and potential research directions. This survey aims to serve as a practical manual for both newcomers seeking an entry point into cutting-edge deep learning methods and experienced researchers transitioning into this rapidly evolving domain.

DuSEGO: Dual Second-order Equivariant Graph Ordinary Differential Equation

Graph Neural Networks (GNNs) with equivariant properties have achieved significant success in modeling complex dynamic systems and molecular properties. However, their expressiveness ability is limited by: (1) Existing methods often overlook the over-smoothing issue caused by traditional GNN models, as well as the gradient explosion or vanishing problems in deep GNNs. (2) Most models operate on first-order information, neglecting that the real world often consists of second-order systems, which further limits the model's representation capabilities. To address these issues, we propose the \textbf{Du}al \textbf{S}econd-order \textbf{E}quivariant \textbf{G}raph \textbf{O}rdinary Differential Equation (\method{}) for equivariant representation. Specifically, \method{} apply the dual second-order equivariant graph ordinary differential equations (Graph ODEs) on graph embeddings and node coordinates, simultaneously. Theoretically, we first prove that \method{} maintains the equivariant property. Furthermore, we provide theoretical insights showing that \method{} effectively alleviates the over-smoothing problem in both feature representation and coordinate update. Additionally, we demonstrate that the proposed \method{} mitigates the exploding and vanishing gradients problem, facilitating the training of deep multi-layer GNNs. Extensive experiments on benchmark datasets validate the superiority of the proposed \method{} compared to baselines.

Degree Distribution based Spiking Graph Networks for Domain Adaptation

Spiking Graph Networks (SGNs) have garnered significant attraction from both researchers and industry due to their ability to address energy consumption challenges in graph classification. However, SGNs are only effective for in-distribution data and cannot tackle out-of-distribution data. In this paper, we first propose the domain adaptation problem in SGNs, and introduce a novel framework named Degree-aware Spiking Graph Domain Adaptation for Classification. The proposed DeSGDA addresses the spiking graph domain adaptation problem by three aspects: node degree-aware personalized spiking representation, adversarial feature distribution alignment, and pseudo-label distillation. First, we introduce the personalized spiking representation method for generating degree-dependent spiking signals. Specifically, the threshold of triggering a spike is determined by the node degree, allowing this personalized approach to capture more expressive information for classification. Then, we propose the graph feature distribution alignment module that is adversarially trained using membrane potential against a domain discriminator. Such an alignment module can efficiently maintain high performance and low energy consumption in the case of inconsistent distribution. Additionally, we extract consistent predictions across two spaces to create reliable pseudo-labels, effectively leveraging unlabeled data to enhance graph classification performance. Extensive experiments on benchmark datasets validate the superiority of the proposed DeSGDA compared with competitive baselines.

Revolutionizing Disease Diagnosis with simultaneous functional PET/MR and Deeply Integrated Brain Metabolic, Hemodynamic, and Perfusion Networks

Simultaneous functional PET/MR (sf-PET/MR) presents a cutting-edge multimodal neuroimaging technique. It provides an unprecedented opportunity for concurrently monitoring and integrating multifaceted brain networks built by spatiotemporally covaried metabolic activity, neural activity, and cerebral blood flow (perfusion). Albeit high scientific/clinical values, short in hardware accessibility of PET/MR hinders its applications, let alone modern AI-based PET/MR fusion models. Our objective is to develop a clinically feasible AI-based disease diagnosis model trained on comprehensive sf-PET/MR data with the power of, during inferencing, allowing single modality input (e.g., PET only) as well as enforcing multimodal-based accuracy. To this end, we propose MX-ARM, a multimodal MiXture-of-experts Alignment and Reconstruction Model. It is modality detachable and exchangeable, allocating different multi-layer perceptrons dynamically ("mixture of experts") through learnable weights to learn respective representations from different modalities. Such design will not sacrifice model performance in uni-modal situation. To fully exploit the inherent complex and nonlinear relation among modalities while producing fine-grained representations for uni-modal inference, we subsequently add a modal alignment module to line up a dominant modality (e.g., PET) with representations of auxiliary modalities (MR). We further adopt multimodal reconstruction to promote the quality of learned features. Experiments on precious multimodal sf-PET/MR data for Mild Cognitive Impairment diagnosis showcase the efficacy of our model toward clinically feasible precision medicine.

PASCL: Supervised Contrastive Learning with Perturbative Augmentation for Particle Decay Reconstruction

In high-energy physics, particles produced in collision events decay in a format of a hierarchical tree structure, where only the final decay products can be observed using detectors. However, the large combinatorial space of possible tree structures makes it challenging to recover the actual decay process given a set of final particles. To better analyse the hierarchical tree structure, we propose a graph-based deep learning model to infer the tree structure to reconstruct collision events. In particular, we use a compact matrix representation termed as lowest common ancestor generations (LCAG) matrix, to encode the particle decay tree structure. Then, we introduce a perturbative augmentation technique applied to node features, aiming to mimic experimental uncertainties and increase data diversity. We further propose a supervised graph contrastive learning algorithm to utilize the information of inter-particle relations from multiple decay processes. Extensive experiments show that our proposed supervised graph contrastive learning with perturbative augmentation (PASCL) method outperforms state-of-the-art baseline models on an existing physics-based dataset, significantly improving the reconstruction accuracy. This method provides a more effective training strategy for models with the same parameters and makes way for more accurate and efficient high-energy particle physics data analysis.

A Robbins--Monro Sequence That Can Exploit Prior Information For Faster Convergence

We propose a new method to improve the convergence speed of the Robbins-Monro algorithm by introducing prior information about the target point into the Robbins-Monro iteration. We achieve the incorporation of prior information without the need of a -- potentially wrong -- regression model, which would also entail additional constraints. We show that this prior-information Robbins-Monro sequence is convergent for a wide range of prior distributions, even wrong ones, such as Gaussian, weighted sum of Gaussians, e.g., in a kernel density estimate, as well as bounded arbitrary distribution functions greater than zero. We furthermore analyse the sequence numerically to understand its performance and the influence of parameters. The results demonstrate that the prior-information Robbins-Monro sequence converges faster than the standard one, especially during the first steps, which are particularly important for applications where the number of function measurements is limited, and when the noise of observing the underlying function is large. We finally propose a rule to select the parameters of the sequence.

A Social-aware Gaussian Pre-trained Model for Effective Cold-start Recommendation

The use of pre-training is an emerging technique to enhance a neural model's performance, which has been shown to be effective for many neural language models such as BERT. This technique has also been used to enhance the performance of recommender systems. In such recommender systems, pre-training models are used to learn a better initialisation for both users and items. However, recent existing pre-trained recommender systems tend to only incorporate the user interaction data at the pre-training stage, making it difficult to deliver good recommendations, especially when the interaction data is sparse. To alleviate this common data sparsity issue, we propose to pre-train the recommendation model not only with the interaction data but also with other available information such as the social relations among users, thereby providing the recommender system with a better initialisation compared with solely relying on the user interaction data. We propose a novel recommendation model, the Social-aware Gaussian Pre-trained model (SGP), which encodes the user social relations and interaction data at the pre-training stage in a Graph Neural Network (GNN). Afterwards, in the subsequent fine-tuning stage, our SGP model adopts a Gaussian Mixture Model (GMM) to factorise these pre-trained embeddings for further training, thereby benefiting the cold-start users from these pre-built social relations. Our extensive experiments on three public datasets show that, in comparison to 16 competitive baselines, our SGP model significantly outperforms the best baseline by upto 7.7% in terms of NDCG@10. In addition, we show that SGP permits to effectively alleviate the cold-start problem, especially when users newly register to the system through their friends' suggestions.