Mixture of neural fields for heterogeneous reconstruction in cryo-EM

Cryo-electron microscopy (cryo-EM) is an experimental technique for protein structure determination that images an ensemble of macromolecules in near-physiological contexts. While recent advances enable the reconstruction of dynamic conformations of a single biomolecular complex, current methods do not adequately model samples with mixed conformational and compositional heterogeneity. In particular, datasets containing mixtures of multiple proteins require the joint inference of structure, pose, compositional class, and conformational states for 3D reconstruction. Here, we present Hydra, an approach that models both conformational and compositional heterogeneity fully ab initio by parameterizing structures as arising from one of K neural fields. We employ a new likelihood-based loss function and demonstrate the effectiveness of our approach on synthetic datasets composed of mixtures of proteins with large degrees of conformational variability. We additionally demonstrate Hydra on an experimental dataset of a cellular lysate containing a mixture of different protein complexes. Hydra expands the expressivity of heterogeneous reconstruction methods and thus broadens the scope of cryo-EM to increasingly complex samples.

Convergence Rate Analysis of LION

The LION (evoLved sIgn mOmeNtum) optimizer for deep neural network training was found by Google via program search, with the simple sign update yet showing impressive performance in training large scale networks. Although previous studies have investigated its convergence properties, a comprehensive analysis, especially the convergence rate, is still desirable. Recognizing that LION can be regarded as solving a specific constrained problem, this paper focuses on demonstrating its convergence to the Karush-Kuhn-Tucker (KKT) point at the rate of $\cal O(\sqrt{d}K^{-1/4})$ measured by gradient $\ell_1$ norm, where $d$ is the problem dimension and $K$ is the number of iteration steps. Step further, we remove the constraint and establish that LION converges to the critical point of the general unconstrained problem at the same rate. This rate not only delivers the currently optimal dependence on the problem dimension $d$ but also tightly matches the theoretical lower bound for nonconvex stochastic optimization algorithms, which is typically measured using the gradient $\ell_2$ norm, with respect to the number of iterations $K$. Through extensive experiments, we not only demonstrate that LION achieves lower loss and higher performance compared to standard SGD, but also empirically confirm that the gradient $\ell_1/\ell_2$ norm ratio aligns with $\Theta(\sqrt{d})$, thus proving that our convergence rate matches the theoretical lower bound with respect to $d$ in the empirical sense.

KcMF: A Knowledge-compliant Framework for Schema and Entity Matching with Fine-tuning-free LLMs

Schema and entity matching tasks are crucial for data integration and management. While large language models (LLMs) have shown promising results in these tasks, they suffer from hallucinations and confusion about task instructions. In this paper, we present the Knowledge-Compliant Matching Framework (KcMF), an LLM-based approach that addresses these issues without the need for domain-specific fine-tuning. KcMF employs a pseudo-code-based task decomposition strategy to adopt task-specific natural language statements that guide LLM reasoning and reduce confusion. We also propose two mechanisms, Dataset as Knowledge (DaK) and Example as Knowledge (EaK), to build domain knowledge sets when unstructured domain knowledge is lacking. Additionally, we introduce a result-ensembling strategy to leverage multiple knowledge sources and suppress poorly formatted outputs. Comprehensive evaluations on schema and entity matching tasks demonstrate that KcMF outperforms previous non-LLM state-of-the-art (SOTA) methods by an average F1 score of 22.9% and competes effectively with SOTA fine-tuned LLMs. Moreover, KcMF generalizes well across different LLMs.

An End-to-End Model for Time Series Classification In the Presence of Missing Values

Time series classification with missing data is a prevalent issue in time series analysis, as temporal data often contain missing values in practical applications. The traditional two-stage approach, which handles imputation and classification separately, can result in sub-optimal performance as label information is not utilized in the imputation process. On the other hand, a one-stage approach can learn features under missing information, but feature representation is limited as imputed errors are propagated in the classification process. To overcome these challenges, this study proposes an end-to-end neural network that unifies data imputation and representation learning within a single framework, allowing the imputation process to take advantage of label information. Differing from previous methods, our approach places less emphasis on the accuracy of imputation data and instead prioritizes classification performance. A specifically designed multi-scale feature learning module is implemented to extract useful information from the noise-imputation data. The proposed model is evaluated on 68 univariate time series datasets from the UCR archive, as well as a multivariate time series dataset with various missing data ratios and 4 real-world datasets with missing information. The results indicate that the proposed model outperforms state-of-the-art approaches for incomplete time series classification, particularly in scenarios with high levels of missing data.

Tabular Data Augmentation for Machine Learning: Progress and Prospects of Embracing Generative AI

Machine learning (ML) on tabular data is ubiquitous, yet obtaining abundant high-quality tabular data for model training remains a significant obstacle. Numerous works have focused on tabular data augmentation (TDA) to enhance the original table with additional data, thereby improving downstream ML tasks. Recently, there has been a growing interest in leveraging the capabilities of generative AI for TDA. Therefore, we believe it is time to provide a comprehensive review of the progress and future prospects of TDA, with a particular emphasis on the trending generative AI. Specifically, we present an architectural view of the TDA pipeline, comprising three main procedures: pre-augmentation, augmentation, and post-augmentation. Pre-augmentation encompasses preparation tasks that facilitate subsequent TDA, including error handling, table annotation, table simplification, table representation, table indexing, table navigation, schema matching, and entity matching. Augmentation systematically analyzes current TDA methods, categorized into retrieval-based methods, which retrieve external data, and generation-based methods, which generate synthetic data. We further subdivide these methods based on the granularity of the augmentation process at the row, column, cell, and table levels. Post-augmentation focuses on the datasets, evaluation and optimization aspects of TDA. We also summarize current trends and future directions for TDA, highlighting promising opportunities in the era of generative AI. In addition, the accompanying papers and related resources are continuously updated and maintained in the GitHub repository at https://github.com/SuDIS-ZJU/awesome-tabular-data-augmentation to reflect ongoing advancements in the field.

Revisiting CNNs for Trajectory Similarity Learning

Similarity search is a fundamental but expensive operator in querying trajectory data, due to its quadratic complexity of distance computation. To mitigate the computational burden for long trajectories, neural networks have been widely employed for similarity learning and each trajectory is encoded as a high-dimensional vector for similarity search with linear complexity. Given the sequential nature of trajectory data, previous efforts have been primarily devoted to the utilization of RNNs or Transformers. In this paper, we argue that the common practice of treating trajectory as sequential data results in excessive attention to capturing long-term global dependency between two sequences. Instead, our investigation reveals the pivotal role of local similarity, prompting a revisit of simple CNNs for trajectory similarity learning. We introduce ConvTraj, incorporating both 1D and 2D convolutions to capture sequential and geo-distribution features of trajectories, respectively. In addition, we conduct a series of theoretical analyses to justify the effectiveness of ConvTraj. Experimental results on three real-world large-scale datasets demonstrate that ConvTraj achieves state-of-the-art accuracy in trajectory similarity search. Owing to the simple network structure of ConvTraj, the training and inference speed on the Porto dataset with 1.6 million trajectories are increased by at least $240$x and $2.16$x, respectively. The source code and dataset can be found at \textit{\url{https://github.com/Proudc/ConvTraj}}.

LightTR: A Lightweight Framework for Federated Trajectory Recovery

With the proliferation of GPS-equipped edge devices, huge trajectory data is generated and accumulated in various domains, motivating a variety of urban applications. Due to the limited acquisition capabilities of edge devices, a lot of trajectories are recorded at a low sampling rate, which may lead to the effectiveness drop of urban applications. We aim to recover a high-sampled trajectory based on the low-sampled trajectory in free space, i.e., without road network information, to enhance the usability of trajectory data and support urban applications more effectively. Recent proposals targeting trajectory recovery often assume that trajectories are available at a central location, which fail to handle the decentralized trajectories and hurt privacy. To bridge the gap between decentralized training and trajectory recovery, we propose a lightweight framework, LightTR, for federated trajectory recovery based on a client-server architecture, while keeping the data decentralized and private in each client/platform center (e.g., each data center of a company). Specifically, considering the limited processing capabilities of edge devices, LightTR encompasses a light local trajectory embedding module that offers improved computational efficiency without compromising its feature extraction capabilities. LightTR also features a meta-knowledge enhanced local-global training scheme to reduce communication costs between the server and clients and thus further offer efficiency improvement. Extensive experiments demonstrate the effectiveness and efficiency of the proposed framework.

Task-Driven Exploration: Decoupling and Inter-Task Feedback for Joint Moment Retrieval and Highlight Detection

Video moment retrieval and highlight detection are two highly valuable tasks in video understanding, but until recently they have been jointly studied. Although existing studies have made impressive advancement recently, they predominantly follow the data-driven bottom-up paradigm. Such paradigm overlooks task-specific and inter-task effects, resulting in poor model performance. In this paper, we propose a novel task-driven top-down framework TaskWeave for joint moment retrieval and highlight detection. The framework introduces a task-decoupled unit to capture task-specific and common representations. To investigate the interplay between the two tasks, we propose an inter-task feedback mechanism, which transforms the results of one task as guiding masks to assist the other task. Different from existing methods, we present a task-dependent joint loss function to optimize the model. Comprehensive experiments and in-depth ablation studies on QVHighlights, TVSum, and Charades-STA datasets corroborate the effectiveness and flexibility of the proposed framework. Codes are available at https://github.com/EdenGabriel/TaskWeave.

E2USD: Efficient-yet-effective Unsupervised State Detection for Multivariate Time Series

We propose E2USD that enables efficient-yet-accurate unsupervised MTS state detection. E2USD exploits a Fast Fourier Transform-based Time Series Compressor (FFTCompress) and a Decomposed Dual-view Embedding Module (DDEM) that together encode input MTSs at low computational overhead. Additionally, we propose a False Negative Cancellation Contrastive Learning method (FNCCLearning) to counteract the effects of false negatives and to achieve more cluster-friendly embedding spaces. To reduce computational overhead further in streaming settings, we introduce Adaptive Threshold Detection (ADATD). Comprehensive experiments with six baselines and six datasets offer evidence that E2USD is capable of SOTA accuracy at significantly reduced computational overhead. Our code is available at https://github.com/AI4CTS/E2Usd.

On the $O$ Convergence Rate of RMSProp and Its Momentum Extension Measured by $\ell_1$ Norm: Better Dependence on the Dimension

Although adaptive gradient methods have been extensively used in deep learning, their convergence rates have not been thoroughly studied, particularly with respect to their dependence on the dimension. This paper considers the classical RMSProp and its momentum extension and establishes the convergence rate of $\frac{1}{T}\sum_{k=1}^TE\left[\|\nabla f(x^k)\|_1\right]\leq O(\frac{\sqrt{d}}{T^{1/4}})$ measured by $\ell_1$ norm without the bounded gradient assumption, where $d$ is the dimension of the optimization variable and $T$ is the iteration number. Since $\|x\|_2\ll\|x\|_1\leq\sqrt{d}\|x\|_2$ for problems with extremely large $d$, our convergence rate can be considered to be analogous to the $\frac{1}{T}\sum_{k=1}^TE\left[\|\nabla f(x^k)\|_2\right]\leq O(\frac{1}{T^{1/4}})$ one of SGD measured by $\ell_1$ norm.