A Unified Shape-Aware Foundation Model for Time Series Classification

Foundation models pre-trained on large-scale source datasets are reshaping the traditional training paradigm for time series classification. However, existing time series foundation models primarily focus on forecasting tasks and often overlook classification-specific challenges, such as modeling interpretable shapelets that capture class-discriminative temporal features. To bridge this gap, we propose UniShape, a unified shape-aware foundation model designed for time series classification. UniShape incorporates a shape-aware adapter that adaptively aggregates multiscale discriminative subsequences (shapes) into class tokens, effectively selecting the most relevant subsequence scales to enhance model interpretability. Meanwhile, a prototype-based pretraining module is introduced to jointly learn instance- and shape-level representations, enabling the capture of transferable shape patterns. Pre-trained on a large-scale multi-domain time series dataset comprising 1.89 million samples, UniShape exhibits superior generalization across diverse target domains. Experiments on 128 UCR datasets and 30 additional time series datasets demonstrate that UniShape achieves state-of-the-art classification performance, with interpretability and ablation analyses further validating its effectiveness.

Exposing Vulnerabilities in Counterfeit Prevention Systems Utilizing Physically Unclonable Surface Features

Counterfeit products pose significant risks to public health and safety through infiltrating untrusted supply chains. Among numerous anti-counterfeiting techniques, leveraging inherent, unclonable microscopic irregularities of paper surfaces is an accurate and cost-effective solution. Prior work of this approach has focused on enabling ubiquitous acquisition of these physically unclonable features (PUFs). However, we will show that existing authentication methods relying on paper surface PUFs may be vulnerable to adversaries, resulting in a gap between technological feasibility and secure real-world deployment. This gap is investigated through formalizing an operational framework for paper-PUF-based authentication. Informed by this framework, we reveal system-level vulnerabilities across both physical and digital domains, designing physical denial-of-service and digital forgery attacks to disrupt proper authentication. The effectiveness of the designed attacks underscores the strong need for security countermeasures for reliable and resilient authentication based on paper PUFs. The proposed framework further facilitates a comprehensive, stage-by-stage security analysis, guiding the design of future counterfeit prevention systems. This analysis delves into potential attack strategies, offering a foundational understanding of how various system components, such as physical features and verification processes, might be exploited by adversaries.

Tighter Truncated Rectangular Prism Approximation for RNN Robustness Verification

Robustness verification is a promising technique for rigorously proving Recurrent Neural Networks (RNNs) robustly. A key challenge is to over-approximate the nonlinear activation functions with linear constraints, which can transform the verification problem into an efficiently solvable linear programming problem. Existing methods over-approximate the nonlinear parts with linear bounding planes individually, which may cause significant over-estimation and lead to lower verification accuracy. In this paper, in order to tightly enclose the three-dimensional nonlinear surface generated by the Hadamard product, we propose a novel truncated rectangular prism formed by two linear relaxation planes and a refinement-driven method to minimize both its volume and surface area for tighter over-approximation. Based on this approximation, we implement a prototype DeepPrism for RNN robustness verification. The experimental results demonstrate that \emph{DeepPrism} has significant improvement compared with the state-of-the-art approaches in various tasks of image classification, speech recognition and sentiment analysis.

Hierarchical Structure-Property Alignment for Data-Efficient Molecular Generation and Editing

Property-constrained molecular generation and editing are crucial in AI-driven drug discovery but remain hindered by two factors: (i) capturing the complex relationships between molecular structures and multiple properties remains challenging, and (ii) the narrow coverage and incomplete annotations of molecular properties weaken the effectiveness of property-based models. To tackle these limitations, we propose HSPAG, a data-efficient framework featuring hierarchical structure-property alignment. By treating SMILES and molecular properties as complementary modalities, the model learns their relationships at atom, substructure, and whole-molecule levels. Moreover, we select representative samples through scaffold clustering and hard samples via an auxiliary variational auto-encoder (VAE), substantially reducing the required pre-training data. In addition, we incorporate a property relevance-aware masking mechanism and diversified perturbation strategies to enhance generation quality under sparse annotations. Experiments demonstrate that HSPAG captures fine-grained structure-property relationships and supports controllable generation under multiple property constraints. Two real-world case studies further validate the editing capabilities of HSPAG.

Unified Molecule Pre-training with Flexible 2D and 3D Modalities: Single and Paired Modality Integration

Molecular representation learning plays a crucial role in advancing applications such as drug discovery and material design. Existing work leverages 2D and 3D modalities of molecular information for pre-training, aiming to capture comprehensive structural and geometric insights. However, these methods require paired 2D and 3D molecular data to train the model effectively and prevent it from collapsing into a single modality, posing limitations in scenarios where a certain modality is unavailable or computationally expensive to generate. To overcome this limitation, we propose FlexMol, a flexible molecule pre-training framework that learns unified molecular representations while supporting single-modality input. Specifically, inspired by the unified structure in vision-language models, our approach employs separate models for 2D and 3D molecular data, leverages parameter sharing to improve computational efficiency, and utilizes a decoder to generate features for the missing modality. This enables a multistage continuous learning process where both modalities contribute collaboratively during training, while ensuring robustness when only one modality is available during inference. Extensive experiments demonstrate that FlexMol achieves superior performance across a wide range of molecular property prediction tasks, and we also empirically demonstrate its effectiveness with incomplete data. Our code and data are available at https://github.com/tewiSong/FlexMol.

Adapting LLMs to Time Series Forecasting via Temporal Heterogeneity Modeling and Semantic Alignment

Large Language Models (LLMs) have recently demonstrated impressive capabilities in natural language processing due to their strong generalization and sequence modeling capabilities. However, their direct application to time series forecasting remains challenging due to two fundamental issues: the inherent heterogeneity of temporal patterns and the modality gap between continuous numerical signals and discrete language representations. In this work, we propose TALON, a unified framework that enhances LLM-based forecasting by modeling temporal heterogeneity and enforcing semantic alignment. Specifically, we design a Heterogeneous Temporal Encoder that partitions multivariate time series into structurally coherent segments, enabling localized expert modeling across diverse temporal patterns. To bridge the modality gap, we introduce a Semantic Alignment Module that aligns temporal features with LLM-compatible representations, enabling effective integration of time series into language-based models while eliminating the need for handcrafted prompts during inference. Extensive experiments on seven real-world benchmarks demonstrate that TALON achieves superior performance across all datasets, with average MSE improvements of up to 11\% over recent state-of-the-art methods. These results underscore the effectiveness of incorporating both pattern-aware and semantic-aware designs when adapting LLMs for time series forecasting. The code is available at: https://github.com/syrGitHub/TALON.

Learning Soft Sparse Shapes for Efficient Time-Series Classification

Shapelets are discriminative subsequences (or shapes) with high interpretability in time series classification. Due to the time-intensive nature of shapelet discovery, existing shapelet-based methods mainly focus on selecting discriminative shapes while discarding others to achieve candidate subsequence sparsification. However, this approach may exclude beneficial shapes and overlook the varying contributions of shapelets to classification performance. To this end, we propose a \textbf{Soft} sparse \textbf{Shape}s (\textbf{SoftShape}) model for efficient time series classification. Our approach mainly introduces soft shape sparsification and soft shape learning blocks. The former transforms shapes into soft representations based on classification contribution scores, merging lower-scored ones into a single shape to retain and differentiate all subsequence information. The latter facilitates intra- and inter-shape temporal pattern learning, improving model efficiency by using sparsified soft shapes as inputs. Specifically, we employ a learnable router to activate a subset of class-specific expert networks for intra-shape pattern learning. Meanwhile, a shared expert network learns inter-shape patterns by converting sparsified shapes into sequences. Extensive experiments show that SoftShape outperforms state-of-the-art methods and produces interpretable results.

Collaborative Multi-Agent Reinforcement Learning for Automated Feature Transformation with Graph-Driven Path Optimization

Feature transformation methods aim to find an optimal mathematical feature-feature crossing process that generates high-value features and improves the performance of downstream machine learning tasks. Existing frameworks, though designed to mitigate manual costs, often treat feature transformations as isolated operations, ignoring dynamic dependencies between transformation steps. To address the limitations, we propose TCTO, a collaborative multi-agent reinforcement learning framework that automates feature engineering through graph-driven path optimization. The framework's core innovation lies in an evolving interaction graph that models features as nodes and transformations as edges. Through graph pruning and backtracking, it dynamically eliminates low-impact edges, reduces redundant operations, and enhances exploration stability. This graph also provides full traceability to empower TCTO to reuse high-utility subgraphs from historical transformations. To demonstrate the efficacy and adaptability of our approach, we conduct comprehensive experiments and case studies, which show superior performance across a range of datasets.

Subset-Contrastive Multi-Omics Network Embedding

Motivation: Network-based analyses of omics data are widely used, and while many of these methods have been adapted to single-cell scenarios, they often remain memory- and space-intensive. As a result, they are better suited to batch data or smaller datasets. Furthermore, the application of network-based methods in multi-omics often relies on similarity-based networks, which lack structurally-discrete topologies. This limitation may reduce the effectiveness of graph-based methods that were initially designed for topologies with better defined structures. Results: We propose Subset-Contrastive multi-Omics Network Embedding (SCONE), a method that employs contrastive learning techniques on large datasets through a scalable subgraph contrastive approach. By exploiting the pairwise similarity basis of many network-based omics methods, we transformed this characteristic into a strength, developing an approach that aims to achieve scalable and effective analysis. Our method demonstrates synergistic omics integration for cell type clustering in single-cell data. Additionally, we evaluate its performance in a bulk multi-omics integration scenario, where SCONE performs comparable to the state-of-the-art despite utilising limited views of the original data. We anticipate that our findings will motivate further research into the use of subset contrastive methods for omics data.

Bridging Distribution Gaps in Time Series Foundation Model Pretraining with Prototype-Guided Normalization

Foundation models have achieved remarkable success across diverse machine-learning domains through large-scale pretraining on large, diverse datasets. However, pretraining on such datasets introduces significant challenges due to substantial mismatches in data distributions, a problem particularly pronounced with time series data. In this paper, we tackle this issue by proposing a domain-aware adaptive normalization strategy within the Transformer architecture. Specifically, we replace the traditional LayerNorm with a prototype-guided dynamic normalization mechanism (ProtoNorm), where learned prototypes encapsulate distinct data distributions, and sample-to-prototype affinity determines the appropriate normalization layer. This mechanism effectively captures the heterogeneity of time series characteristics, aligning pretrained representations with downstream tasks. Through comprehensive empirical evaluation, we demonstrate that our method significantly outperforms conventional pretraining techniques across both classification and forecasting tasks, while effectively mitigating the adverse effects of distribution shifts during pretraining. Incorporating ProtoNorm is as simple as replacing a single line of code. Extensive experiments on diverse real-world time series benchmarks validate the robustness and generalizability of our approach, advancing the development of more versatile time series foundation models.