Real-world event sequences are often generated by different temporal point processes (TPPs) and thus have clustering structures. Nonetheless, in the modeling and prediction of event sequences, most existing TPPs ignore the inherent clustering structures of the event sequences, leading to the models with unsatisfactory interpretability. In this study, we learn structure-enhanced TPPs with the help of Gromov-Wasserstein (GW) regularization, which imposes clustering structures on the sequence-level embeddings of the TPPs in the maximum likelihood estimation framework.In the training phase, the proposed method leverages a nonparametric TPP kernel to regularize the similarity matrix derived based on the sequence embeddings. In large-scale applications, we sample the kernel matrix and implement the regularization as a Gromov-Wasserstein (GW) discrepancy term, which achieves a trade-off between regularity and computational efficiency.The TPPs learned through this method result in clustered sequence embeddings and demonstrate competitive predictive and clustering performance, significantly improving the model interpretability without compromising prediction accuracy.

Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the nucleotide sequences, especially specific motifs known as transcription factor binding sites (TFBSs). Designing high-fitness CREs is crucial for therapeutic and bioengineering applications. Current CRE design methods are limited by two major drawbacks: (1) they typically rely on iterative optimization strategies that modify existing sequences and are prone to local optima, and (2) they lack the guidance of biological prior knowledge in sequence optimization. In this paper, we address these limitations by proposing a generative approach that leverages reinforcement learning (RL) to fine-tune a pre-trained autoregressive (AR) model. Our method incorporates data-driven biological priors by deriving computational inference-based rewards that simulate the addition of activator TFBSs and removal of repressor TFBSs, which are then integrated into the RL process. We evaluate our method on promoter design tasks in two yeast media conditions and enhancer design tasks for three human cell types, demonstrating its ability to generate high-fitness CREs while maintaining sequence diversity. The code is available at https://github.com/yangzhao1230/TACO.

Accurately predicting 3D structures and dynamics of physical systems is crucial in scientific applications. Existing approaches that rely on geometric Graph Neural Networks (GNNs) effectively enforce $\mathrm{E}(3)$-equivariance, but they often fall in leveraging extensive broader information. While direct application of Large Language Models (LLMs) can incorporate external knowledge, they lack the capability for spatial reasoning with guaranteed equivariance. In this paper, we propose EquiLLM, a novel framework for representing 3D physical systems that seamlessly integrates E(3)-equivariance with LLM capabilities. Specifically, EquiLLM comprises four key components: geometry-aware prompting, an equivariant encoder, an LLM, and an equivariant adaptor. Essentially, the LLM guided by the instructive prompt serves as a sophisticated invariant feature processor, while 3D directional information is exclusively handled by the equivariant encoder and adaptor modules. Experimental results demonstrate that EquiLLM delivers significant improvements over previous methods across molecular dynamics simulation, human motion simulation, and antibody design, highlighting its promising generalizability.

Long-tailed learning has garnered increasing attention due to its practical significance. Among the various approaches, the fine-tuning paradigm has gained considerable interest with the advent of foundation models. However, most existing methods primarily focus on leveraging knowledge from these models, overlooking the inherent biases introduced by the imbalanced training data they rely on. In this paper, we examine how such imbalances from pre-training affect long-tailed downstream tasks. Specifically, we find the imbalance biases inherited in foundation models on downstream task as parameter imbalance and data imbalance. During fine-tuning, we observe that parameter imbalance plays a more critical role, while data imbalance can be mitigated using existing re-balancing strategies. Moreover, we find that parameter imbalance cannot be effectively addressed by current re-balancing techniques, such as adjusting the logits, during training, unlike data imbalance. To tackle both imbalances simultaneously, we build our method on causal learning and view the incomplete semantic factor as the confounder, which brings spurious correlations between input samples and labels. To resolve the negative effects of this, we propose a novel backdoor adjustment method that learns the true causal effect between input samples and labels, rather than merely fitting the correlations in the data. Notably, we achieve an average performance increase of about $1.67\%$ on each dataset.

Single image defocus deblurring (SIDD) aims to restore an all-in-focus image from a defocused one. Distribution shifts in defocused images generally lead to performance degradation of existing methods during out-of-distribution inferences. In this work, we gauge the intrinsic reason behind the performance degradation, which is identified as the heterogeneity of lens-specific point spread functions. Empirical evidence supports this finding, motivating us to employ a continual test-time adaptation (CTTA) paradigm for SIDD. However, traditional CTTA methods, which primarily rely on entropy minimization, cannot sufficiently explore task-dependent information for pixel-level regression tasks like SIDD. To address this issue, we propose a novel Siamese networks-based continual test-time adaptation framework, which adapts source models to continuously changing target domains only requiring unlabeled target data in an online manner. To further mitigate semantically erroneous textures introduced by source SIDD models under severe degradation, we revisit the learning paradigm through a structural causal model and propose Causal Siamese networks (CauSiam). Our method leverages large-scale pre-trained vision-language models to derive discriminative universal semantic priors and integrates these priors into Siamese networks, ensuring causal identifiability between blurry inputs and restored images. Extensive experiments demonstrate that CauSiam effectively improves the generalization performance of existing SIDD methods in continuously changing domains.

Predicting multiple functions labeled with Enzyme Commission (EC) numbers from the enzyme sequence is of great significance but remains a challenge due to its sparse multi-label classification nature, i.e., each enzyme is typically associated with only a few labels out of more than 6000 possible EC numbers. However, existing machine learning algorithms generally learn a fixed global representation for each enzyme to classify all functions, thereby they lack interpretability and the fine-grained information of some function-specific local residue fragments may be overwhelmed. Here we present an attention-based framework, namely ProtDETR (Protein Detection Transformer), by casting enzyme function prediction as a detection problem. It uses a set of learnable functional queries to adaptatively extract different local representations from the sequence of residue-level features for predicting different EC numbers. ProtDETR not only significantly outperforms existing deep learning-based enzyme function prediction methods, but also provides a new interpretable perspective on automatically detecting different local regions for identifying different functions through cross-attentions between queries and residue-level features. The development of genome sequencing technologies has unveiled a vast collection of protein sequences, but detailed functional annotations are only available for a very small number of them [2]. Evaluating the functions of protein sequences via wet experiments is time-consuming, labor-intensive, and expensive, underscoring the critical need for computational methods to predict protein functions. This is particularly acute in the study of enzymes, which catalyze various biological reactions and are central to understanding metabolic processes. For the most widely-used EC number classification scheme, each class of enzyme function is assigned an EC number, which is a four-level hierarchy reflecting the intricate organization of enzyme functions.

An event sequence generated by a temporal point process is often associated with a hidden and structured event branching process that captures the triggering relations between its historical and current events. In this study, we design a new plug-and-play module based on the Bregman ADMM (BADMM) algorithm, which infers event branches associated with event sequences in the maximum likelihood estimation framework of temporal point processes (TPPs). Specifically, we formulate the inference of event branches as an optimization problem for the event transition matrix under sparse and low-rank constraints, which is embedded in existing TPP models or their learning paradigms. We can implement this optimization problem based on subspace clustering and sparse group-lasso, respectively, and solve it using the Bregman ADMM algorithm, whose unrolling leads to the proposed BADMM module. When learning a classic TPP (e.g., Hawkes process) by the expectation-maximization algorithm, the BADMM module helps derive structured responsibility matrices in the E-step. Similarly, the BADMM module helps derive low-rank and sparse attention maps for the neural TPPs with self-attention layers. The structured responsibility matrices and attention maps, which work as learned event transition matrices, indicate event branches, e.g., inferring isolated events and those key events triggering many subsequent events. Experiments on both synthetic and real-world data show that plugging our BADMM module into existing TPP models and learning paradigms can improve model performance and provide us with interpretable structured event branches.

Human motion prediction (HMP) involves forecasting future human motion based on historical data. Graph Convolutional Networks (GCNs) have garnered widespread attention in this field for their proficiency in capturing relationships among joints in human motion. However, existing GCN-based methods tend to focus on either temporal-domain or spatial-domain features, or they combine spatio-temporal features without fully leveraging the complementarity and cross-dependency of these two features. In this paper, we propose the Spatial-Temporal Multi-Subgraph Graph Convolutional Network (STMS-GCN) to capture complex spatio-temporal dependencies in human motion. Specifically, we decouple the modeling of temporal and spatial dependencies, enabling cross-domain knowledge transfer at multiple scales through a spatio-temporal information consistency constraint mechanism. Besides, we utilize multiple subgraphs to extract richer motion information and enhance the learning associations of diverse subgraphs through a homogeneous information constraint mechanism. Extensive experiments on the standard HMP benchmarks demonstrate the superiority of our method.

Text-guided image generation and editing using diffusion models have achieved remarkable advancements. Among these, tuning-free methods have gained attention for their ability to perform edits without extensive model adjustments, offering simplicity and efficiency. However, existing tuning-free approaches often struggle with balancing fidelity and editing precision. Reconstruction errors in DDIM Inversion are partly attributed to the cross-attention mechanism in U-Net, which introduces misalignments during the inversion and reconstruction process. To address this, we analyze reconstruction from a structural perspective and propose a novel approach that replaces traditional cross-attention with uniform attention maps, significantly enhancing image reconstruction fidelity. Our method effectively minimizes distortions caused by varying text conditions during noise prediction. To complement this improvement, we introduce an adaptive mask-guided editing technique that integrates seamlessly with our reconstruction approach, ensuring consistency and accuracy in editing tasks. Experimental results demonstrate that our approach not only excels in achieving high-fidelity image reconstruction but also performs robustly in real image composition and editing scenarios. This study underscores the potential of uniform attention maps to enhance the fidelity and versatility of diffusion-based image processing methods. Code is available at https://github.com/Mowenyii/Uniform-Attention-Maps.

Medical vision-language pre-training methods mainly leverage the correspondence between paired medical images and radiological reports. Although multi-view spatial images and temporal sequences of image-report pairs are available in off-the-shelf multi-modal medical datasets, most existing methods have not thoroughly tapped into such extensive supervision signals. In this paper, we introduce the Med-ST framework for fine-grained spatial and temporal modeling to exploit information from multiple spatial views of chest radiographs and temporal historical records. For spatial modeling, Med-ST employs the Mixture of View Expert (MoVE) architecture to integrate different visual features from both frontal and lateral views. To achieve a more comprehensive alignment, Med-ST not only establishes the global alignment between whole images and texts but also introduces modality-weighted local alignment between text tokens and spatial regions of images. For temporal modeling, we propose a novel cross-modal bidirectional cycle consistency objective by forward mapping classification (FMC) and reverse mapping regression (RMR). By perceiving temporal information from simple to complex, Med-ST can learn temporal semantics. Experimental results across four distinct tasks demonstrate the effectiveness of Med-ST, especially in temporal classification tasks. Our code and model are available at https://github.com/SVT-Yang/MedST.