Cryo-electron microscopy (cryo-EM) is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. As this technique can capture dynamic biomolecular complexes, 3D reconstruction methods are increasingly being developed to resolve this intrinsic structural heterogeneity. However, the absence of standardized benchmarks with ground truth structures and validation metrics limits the advancement of the field. Here, we propose CryoBench, a suite of datasets, metrics, and performance benchmarks for heterogeneous reconstruction in cryo-EM. We propose five datasets representing different sources of heterogeneity and degrees of difficulty. These include conformational heterogeneity generated from simple motions and random configurations of antibody complexes and from tens of thousands of structures sampled from a molecular dynamics simulation. We also design datasets containing compositional heterogeneity from mixtures of ribosome assembly states and 100 common complexes present in cells. We then perform a comprehensive analysis of state-of-the-art heterogeneous reconstruction tools including neural and non-neural methods and their sensitivity to noise, and propose new metrics for quantitative comparison of methods. We hope that this benchmark will be a foundational resource for analyzing existing methods and new algorithmic development in both the cryo-EM and machine learning communities.

IVISIT is a generic interactive visual simulation tool that is based on Python/Numpy and can be used for system simulation, parameter optimization, parameter management, and visualization of system dynamics as required, for example,for developing neural network simulations, machine learning applications, or computer vision systems. It provides classes for rapid prototyping of applications and visualization and manipulation of system properties using interactive GUI elements like sliders, images, textboxes, option lists, checkboxes and buttons based on Tkinter and Matplotlib. Parameters and simulation configurations can be stored and managed based on SQLite database functions. This technical report describes the main architecture and functions of IVISIT, and provides easy examples how to rapidly implement interactive applications and manage parameter settings.

In the face of complex natural images, existing deep clustering algorithms fall significantly short in terms of clustering accuracy when compared to supervised classification methods, making them less practical. This paper introduces an image clustering algorithm based on self-supervised pretrained models and latent feature distribution optimization, substantially enhancing clustering performance. It is found that: (1) For complex natural images, we effectively enhance the discriminative power of latent features by leveraging self-supervised pretrained models and their fine-tuning, resulting in improved clustering performance. (2) In the latent feature space, by searching for k-nearest neighbor images for each training sample and shortening the distance between the training sample and its nearest neighbor, the discriminative power of latent features can be further enhanced, and clustering performance can be improved. (3) In the latent feature space, reducing the distance between sample features and the nearest predefined cluster centroids can optimize the distribution of latent features, therefore further improving clustering performance. Through experiments on multiple datasets, our approach outperforms the latest clustering algorithms and achieves state-of-the-art clustering results. When the number of categories in the datasets is small, such as CIFAR-10 and STL-10, and there are significant differences between categories, our clustering algorithm has similar accuracy to supervised methods without using pretrained models, slightly lower than supervised methods using pre-trained models. The code linked algorithm is https://github.com/LihengHu/semi.

The widespread use of Deep Neural Networks (DNNs) has recently resulted in their application to challenging scientific visualization tasks. While advanced DNNs demonstrate impressive generalization abilities, understanding factors like prediction quality, confidence, robustness, and uncertainty is crucial. These insights aid application scientists in making informed decisions. However, DNNs lack inherent mechanisms to measure prediction uncertainty, prompting the creation of distinct frameworks for constructing robust uncertainty-aware models tailored to various visualization tasks. In this work, we develop uncertainty-aware implicit neural representations to model steady-state vector fields effectively. We comprehensively evaluate the efficacy of two principled deep uncertainty estimation techniques: (1) Deep Ensemble and (2) Monte Carlo Dropout, aimed at enabling uncertainty-informed visual analysis of features within steady vector field data. Our detailed exploration using several vector data sets indicate that uncertainty-aware models generate informative visualization results of vector field features. Furthermore, incorporating prediction uncertainty improves the resilience and interpretability of our DNN model, rendering it applicable for the analysis of non-trivial vector field data sets.

Traditional categorical data, often collected in psychological tests and educational assessments, are typically single-layer and gathered only once.This paper considers a more general case, multi-layer categorical data with polytomous responses. To model such data, we present a novel statistical model, the multi-layer latent class model (multi-layer LCM). This model assumes that all layers share common subjects and items. To discover subjects' latent classes and other model parameters under this model, we develop three efficient spectral methods based on the sum of response matrices, the sum of Gram matrices, and the debiased sum of Gram matrices, respectively. Within the framework of multi-layer LCM, we demonstrate the estimation consistency of these methods under mild conditions regarding data sparsity. Our theoretical findings reveal two key insights: (1) increasing the number of layers can enhance the performance of the proposed methods, highlighting the advantages of considering multiple layers in latent class analysis; (2) we theoretically show that the algorithm based on the debiased sum of Gram matrices usually performs best. Additionally, we propose an approach that combines the averaged modularity metric with our methods to determine the number of latent classes. Extensive experiments are conducted to support our theoretical results and show the powerfulness of our methods in the task of learning latent classes and estimating the number of latent classes in multi-layer categorical data with polytomous responses.

Modern vehicles rely on a myriad of electronic control units (ECUs) interconnected via controller area networks (CANs) for critical operations. Despite their ubiquitous use and reliability, CANs are susceptible to sophisticated cyberattacks, particularly masquerade attacks, which inject false data that mimic legitimate messages at the expected frequency. These attacks pose severe risks such as unintended acceleration, brake deactivation, and rogue steering. Traditional intrusion detection systems (IDS) often struggle to detect these subtle intrusions due to their seamless integration into normal traffic. This paper introduces a novel framework for detecting masquerade attacks in the CAN bus using graph machine learning (ML). We hypothesize that the integration of shallow graph embeddings with time series features derived from CAN frames enhances the detection of masquerade attacks. We show that by representing CAN bus frames as message sequence graphs (MSGs) and enriching each node with contextual statistical attributes from time series, we can enhance detection capabilities across various attack patterns compared to using only graph-based features. Our method ensures a comprehensive and dynamic analysis of CAN frame interactions, improving robustness and efficiency. Extensive experiments on the ROAD dataset validate the effectiveness of our approach, demonstrating statistically significant improvements in the detection rates of masquerade attacks compared to a baseline that uses only graph-based features, as confirmed by Mann-Whitney U and Kolmogorov-Smirnov tests (p < 0.05).

In this work, we present a transformer-based framework for predicting future pedestrian states based on clustered historical trajectory data. In previous studies, researchers propose enhancing pedestrian trajectory predictions by using manually crafted labels to categorize pedestrian behaviors and intentions. However, these approaches often only capture a limited range of pedestrian behaviors and introduce human bias into the predictions. To alleviate the dependency on manually crafted labels, we utilize a transformer encoder coupled with hierarchical density-based clustering to automatically identify diverse behavior patterns, and use these clusters in data-driven reachability analysis. By using a transformer-based approach, we seek to enhance the representation of pedestrian trajectories and uncover characteristics or features that are subsequently used to group trajectories into different "behavior" clusters. We show that these behavior clusters can be used with data-driven reachability analysis, yielding an end-to-end data-driven approach to predicting the future motion of pedestrians. We train and evaluate our approach on a real pedestrian dataset, showcasing its effectiveness in forecasting pedestrian movements.

Episodic structures are inherently interpretable and adaptable to evolving large-scale key events. However, state-of-the-art automatic event detection methods overlook event episodes and, therefore, struggle with these crucial characteristics. This paper introduces a novel task, episode detection, aimed at identifying episodes from a news corpus containing key event articles. An episode describes a cohesive cluster of core entities (e.g., "protesters", "police") performing actions at a specific time and location. Furthermore, an episode is a significant part of a larger group of episodes under a particular key event. Automatically detecting episodes is challenging because, unlike key events and atomic actions, we cannot rely on explicit mentions of times and locations to distinguish between episodes or use semantic similarity to merge inconsistent episode co-references. To address these challenges, we introduce EpiMine, an unsupervised episode detection framework that (1) automatically identifies the most salient, key-event-relevant terms and segments, (2) determines candidate episodes in an article based on natural episodic partitions estimated through shifts in discriminative term combinations, and (3) refines and forms final episode clusters using large language model-based reasoning on the candidate episodes. We construct three diverse, real-world event datasets annotated at the episode level. EpiMine outperforms all baselines on these datasets by an average 59.2% increase across all metrics.

Recently, representation learning with contrastive learning algorithms has been successfully applied to challenging unlabeled datasets. However, these methods are unable to distinguish important features from unimportant ones under simply unsupervised settings, and definitions of importance vary according to the type of downstream task or analysis goal, such as the identification of objects or backgrounds. In this paper, we focus on unsupervised image clustering as the downstream task and propose a representation learning method that enhances features critical to the clustering task. We extend a clustering-friendly contrastive learning method and incorporate a contrastive analysis approach, which utilizes a reference dataset to separate important features from unimportant ones, into the design of loss functions. Conducting an experimental evaluation of image clustering for three datasets with characteristic backgrounds, we show that for all datasets, our method achieves higher clustering scores compared with conventional contrastive analysis and deep clustering methods.

Active learning (AL) aims to enhance model performance by selectively collecting highly informative data, thereby minimizing annotation costs. However, in practical scenarios, unlabeled data may contain out-of-distribution (OOD) samples, leading to wasted annotation costs if data is incorrectly selected. Recent research has explored methods to apply AL to open-set data, but these methods often require or incur unavoidable cost losses to minimize them. To address these challenges, we propose a novel selection strategy, CLIPN for AL (CLIPNAL), which minimizes cost losses without requiring OOD samples. CLIPNAL sequentially evaluates the purity and informativeness of data. First, it utilizes a pre-trained vision-language model to detect and exclude OOD data by leveraging linguistic and visual information of in-distribution (ID) data without additional training. Second, it selects highly informative data from the remaining ID data, and then the selected samples are annotated by human experts. Experimental results on datasets with various open-set conditions demonstrate that CLIPNAL achieves the lowest cost loss and highest performance across all scenarios. Code is available at https://github.com/DSBA-Lab/OpenAL.