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Gene Incremental Learning for Single-Cell Transcriptomics
Qi, Jiaxin, Cui, Yan, Huang, Jianqiang, Xie, Gaogang
Classes, as fundamental elements of Computer Vision, have been extensively studied within incremental learning frameworks. In contrast, tokens, which play essential roles in many research fields, exhibit similar characteristics of growth, yet investigations into their incremental learning remain significantly scarce. This research gap primarily stems from the holistic nature of tokens in language, which imposes significant challenges on the design of incremental learning frameworks for them. To overcome this obstacle, in this work, we turn to a type of token, gene, for a large-scale biological dataset--single-cell transcriptomics--to formulate a pipeline for gene incremental learning and establish corresponding evaluations. We found that the forgetting problem also exists in gene incremental learning, thus we adapted existing class incremental learning methods to mitigate the forgetting of genes. Through extensive experiments, we demonstrated the soundness of our framework design and evaluations, as well as the effectiveness of our method adaptations. Finally, we provide a complete benchmark for gene incremental learning in single-cell transcriptomics.
MoETTA: Test-Time Adaptation Under Mixed Distribution Shifts with MoE-LayerNorm
Fan, Xiao, Jiang, Jingyan, Chen, Zhaoru, Huang, Fanding, Chen, Xiao, Jiang, Qinting, Zhang, Bowen, Tang, Xing, Wang, Zhi
Test-Time adaptation (TTA) has proven effective in mitigating performance drops under single-domain distribution shifts by updating model parameters during inference. However, real-world deployments often involve mixed distribution shifts, where test samples are affected by diverse and potentially conflicting domain factors, posing significant challenges even for SOTA TTA methods. A key limitation in existing approaches is their reliance on a unified adaptation path, which fails to account for the fact that optimal gradient directions can vary significantly across different domains. Moreover, current benchmarks focus only on synthetic or homogeneous shifts, failing to capture the complexity of real-world heterogeneous mixed distribution shifts. To address this, we propose MoETTA, a novel entropy-based TTA framework that integrates the Mixture-of-Experts (MoE) architecture. Rather than enforcing a single parameter update rule for all test samples, MoETTA introduces a set of structurally decoupled experts, enabling adaptation along diverse gradient directions. This design allows the model to better accommodate heterogeneous shifts through flexible and disentangled parameter updates. To simulate realistic deployment conditions, we introduce two new benchmarks: potpourri and potpourri+. While classical settings focus solely on synthetic corruptions, potpourri encompasses a broader range of domain shifts--including natural, artistic, and adversarial distortions--capturing more realistic deployment challenges. Additionally, potpourri+ further includes source-domain samples to evaluate robustness against catastrophic forgetting. Extensive experiments across three mixed distribution shifts settings show that MoETTA consistently outperforms strong baselines, establishing SOTA performance and highlighting the benefit of modeling multiple adaptation directions via expert-level diversity.
Multi-Agent VLMs Guided Self-Training with PNU Loss for Low-Resource Offensive Content Detection
Wang, Han, Ji, Deyi, Lu, Junyu, Zhu, Lanyun, Zhang, Hailong, Wu, Haiyang, Liu, Liqun, Shu, Peng, Lee, Roy Ka-Wei
Accurate detection of offensive content on social media demands high-quality labeled data; however, such data is often scarce due to the low prevalence of offensive instances and the high cost of manual annotation. To address this low-resource challenge, we propose a self-training framework that leverages abundant unlabeled data through collaborative pseudo-labeling. Starting with a lightweight classifier trained on limited labeled data, our method iteratively assigns pseudo-labels to unlabeled instances with the support of Multi-Agent Vision-Language Models (MA-VLMs). Unlabeled data on which the classifier and MA-VLMs agree are designated as the Agreed-Unknown set, while conflicting samples form the Disagreed-Unknown set. To enhance label reliability, MA-VLMs simulate dual perspectives, moderator and user, capturing both regulatory and subjective viewpoints. The classifier is optimized using a novel Positive-Negative-Unlabeled (PNU) loss, which jointly exploits labeled, Agreed-Unknown, and Disagreed-Unknown data while mitigating pseudo-label noise. Experiments on benchmark datasets demonstrate that our framework substantially outperforms baselines under limited supervision and approaches the performance of large-scale models.
ChemFixer: Correcting Invalid Molecules to Unlock Previously Unseen Chemical Space
Park, Jun-Hyoung, Song, Ho-Jun, Lee, Seong-Whan
Deep learning-based molecular generation models have shown great potential in efficiently exploring vast chemical spaces by generating potential drug candidates with desired properties. However, these models often produce chemically invalid molecules, which limits the usable scope of the learned chemical space and poses significant challenges for practical applications. To address this issue, we propose ChemFixer, a framework designed to correct invalid molecules into valid ones. ChemFixer is built on a transformer architecture, pre-trained using masking techniques, and fine-tuned on a large-scale dataset of valid/invalid molecular pairs that we constructed. Through comprehensive evaluations across diverse generative models, ChemFixer improved molecular validity while effectively preserving the chemical and biological distributional properties of the original outputs. This indicates that ChemFixer can recover molecules that could not be previously generated, thereby expanding the diversity of potential drug candidates. Furthermore, ChemFixer was effectively applied to a drug-target interaction (DTI) prediction task using limited data, improving the validity of generated ligands and discovering promising ligand-protein pairs. These results suggest that ChemFixer is not only effective in data-limited scenarios, but also extensible to a wide range of downstream tasks. Taken together, ChemFixer shows promise as a practical tool for various stages of deep learning-based drug discovery, enhancing molecular validity and expanding accessible chemical space.
VitalBench: A Rigorous Multi-Center Benchmark for Long-Term Vital Sign Prediction in Intraoperative Care
Cai, Xiuding, Wang, Xueyao, Wang, Sen, Zhu, Yaoyao, Chen, Jiao, Yao, Yu
Intraoperative monitoring and prediction of vital signs are critical for ensuring patient safety and improving surgical outcomes. Despite recent advances in deep learning models for medical time-series forecasting, several challenges persist, including the lack of standardized benchmarks, incomplete data, and limited cross-center validation. To address these challenges, we introduce VitalBench, a novel benchmark specifically designed for intraoperative vital sign prediction. VitalBench includes data from over 4,000 surgeries across two independent medical centers, offering three evaluation tracks: complete data, incomplete data, and cross-center generalization. This framework reflects the real-world complexities of clinical practice, minimizing reliance on extensive preprocessing and incorporating masked loss techniques for robust and unbiased model evaluation. By providing a standardized and unified platform for model development and comparison, VitalBench enables researchers to focus on architectural innovation while ensuring consistency in data handling. This work lays the foundation for advancing predictive models for intraoperative vital sign forecasting, ensuring that these models are not only accurate but also robust and adaptable across diverse clinical environments. Our code and data are available at https://github.com/XiudingCai/VitalBench.
Multi-Horizon Time Series Forecasting of non-parametric CDFs with Deep Lattice Networks
Erdmann, Niklas, Bentsen, Lars, Stenbro, Roy, Riise, Heine Nygard, Warakagoda, Narada Dilp, Engelstad, Paal E.
Probabilistic forecasting is not only a way to add more information to a prediction of the future, but it also builds on weaknesses in point prediction. Sudden changes in a time series can still be captured by a cumulative distribution function (CDF), while a point prediction is likely to miss it entirely. The modeling of CDFs within forecasts has historically been limited to parametric approaches, but due to recent advances, this no longer has to be the case. We aim to advance the fields of probabilistic forecasting and monotonic networks by connecting them and propose an approach that permits the forecasting of implicit, complete, and nonparametric CDFs. For this purpose, we propose an adaptation to deep lattice networks (DLN) for monotonically constrained simultaneous/implicit quantile regression in time series forecasting. Quantile regression usually produces quantile crossovers, which need to be prevented to achieve a legitimate CDF. By leveraging long short term memory units (LSTM) as the embedding layer, and spreading quantile inputs to all sub-lattices of a DLN with an extended output size, we can produce a multi-horizon forecast of an implicit CDF due to the monotonic constraintability of DLNs that prevent quantile crossovers. We compare and evaluate our approach's performance to relevant state of the art within the context of a highly relevant application of time series forecasting: Day-ahead, hourly forecasts of solar irradiance observations. Our experiments show that the adaptation of a DLN performs just as well or even better than an unconstrained approach. Further comparison of the adapted DLN against a scalable monotonic neural network shows that our approach performs better. With this adaptation of DLNs, we intend to create more interest and crossover investigations in techniques of monotonic neural networks and probabilistic forecasting.
Adaptive Redundancy Regulation for Balanced Multimodal Information Refinement
Yang, Zhe, Li, Wenrui, Chen, Hongtao, Wang, Penghong, Xiong, Ruiqin, Fan, Xiaopeng
Abstract--Multimodal learning aims to improve performance by leveraging data from multiple sources. During joint multi-modal training, due to modality bias, the advantaged modality often dominates backpropagation, leading to imbalanced optimization. Existing methods still face two problems: First, the long-term dominance of the dominant modality weakens representation-output coupling in the late stages of training, resulting in the accumulation of redundant information. Second, previous methods often directly and uniformly adjust the gradients of the advantaged modality, ignoring the semantics and directionality between modalities. T o address these limitations, we propose Adaptive Redundancy Regulation for Balanced Multimodal Information Refinement (RedReg), which is inspired by information bottleneck principle. Specifically, we construct a redundancy phase monitor that uses a joint criterion of effective gain growth rate and redundancy to trigger intervention only when redundancy is high. Furthermore, we design a co-information gating mechanism to estimate the contribution of the current dominant modality based on cross-modal semantics. When the task primarily relies on a single modality, the suppression term is automatically disabled to preserve modality-specific information. Finally, we project the gradient of the dominant modality onto the orthogonal complement of the joint multi-modal gradient subspace and suppress the gradient according to redundancy. Experiments show that our method demonstrates superiority among current major methods in most scenarios. Ablation experiments verify the effectiveness of our method. The code is available at https://github.com/xia-zhe/RedReg.git Index T erms--Multimodal learning, modality imbalance, information bottleneck This work was supported in part by the National Key R&D Program of China (2023YFA1008501) and the National Natural Science Foundation of China (NSFC) under grant 624B2049 and U22B2035. Wenrui Li, Penghong Wang, and Xiaopeng Fan are with the Department of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China, and also with Harbin Institute of Technology Suzhou Research Institute, Suzhou 215104, China. Hongtao Chen is with the School of Mathematical Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China (e-mail: ht166chen@163.com).
DeepDefense: Layer-Wise Gradient-Feature Alignment for Building Robust Neural Networks
Lin, Ci, Yeap, Tet, Kiringa, Iluju, Zhang, Biwei
Deep neural networks are known to be vulnerable to adversarial perturbations, which are small and carefully crafted inputs that lead to incorrect predictions. In this paper, we propose DeepDefense, a novel defense framework that applies Gradient-Feature Alignment (GFA) regularization across multiple layers to suppress adversarial vulnerability. By aligning input gradients with internal feature representations, DeepDefense promotes a smoother loss landscape in tangential directions, thereby reducing the model's sensitivity to adversarial noise. We provide theoretical insights into how adversarial perturbation can be decomposed into radial and tangential components and demonstrate that alignment suppresses loss variation in tangential directions, where most attacks are effective. Empirically, our method achieves significant improvements in robustness across both gradient-based and optimization-based attacks. For example, on CIFAR-10, CNN models trained with DeepDefense outperform standard adversarial training by up to 15.2% under APGD attacks and 24.7% under FGSM attacks. Against optimization-based attacks such as DeepFool and EADEN, DeepDefense requires 20 to 30 times higher perturbation magnitudes to cause misclassification, indicating stronger decision boundaries and a flatter loss landscape. Our approach is architecture-agnostic, simple to implement, and highly effective, offering a promising direction for improving the adversarial robustness of deep learning models.
nuCarla: A nuScenes-Style Bird's-Eye View Perception Dataset for CARLA Simulation
Qiao, Zhijie, Cao, Zhong, Liu, Henry X.
End-to-end (E2E) autonomous driving heavily relies on closed-loop simulation, where perception, planning, and control are jointly trained and evaluated in interactive environments. Yet, most existing datasets are collected from the real world under non-interactive conditions, primarily supporting open-loop learning while offering limited value for closed-loop testing. Due to the lack of standardized, large-scale, and thoroughly verified datasets to facilitate learning of meaningful intermediate representations, such as bird's-eye-view (BEV) features, closed-loop E2E models remain far behind even simple rule-based baselines. To address this challenge, we introduce nuCarla, a large-scale, nuScenes-style BEV perception dataset built within the CARLA simulator. nuCarla features (1) full compatibility with the nuScenes format, enabling seamless transfer of real-world perception models; (2) a dataset scale comparable to nuScenes, but with more balanced class distributions; (3) direct usability for closed-loop simulation deployment; and (4) high-performance BEV backbones that achieve state-of-the-art detection results. By providing both data and models as open benchmarks, nuCarla substantially accelerates closed-loop E2E development, paving the way toward reliable and safety-aware research in autonomous driving.
Blurred Encoding for Trajectory Representation Learning
Zhou, Silin, Chen, Yao, Shang, Shuo, Chen, Lisi, He, Bingsheng, Shibasaki, Ryosuke
Trajectory representation learning (TRL) maps trajectories to vector embeddings and facilitates tasks such as trajectory classification and similarity search. State-of-the-art (SOTA) TRL methods transform raw GPS trajectories to grid or road trajectories to capture high-level travel semantics, i.e., regions and roads. However, they lose fine-grained spatial-temporal details as multiple GPS points are grouped into a single grid cell or road segment. To tackle this problem, we propose the BLUrred Encoding method, dubbed BLUE, which gradually reduces the precision of GPS coordinates to create hierarchical patches with multiple levels. The low-level patches are small and preserve fine-grained spatial-temporal details, while the high-level patches are large and capture overall travel patterns. To complement different patch levels with each other, our BLUE is an encoder-decoder model with a pyramid structure. At each patch level, a Transformer is used to learn the trajectory embedding at the current level, while pooling prepares inputs for the higher level in the encoder, and up-resolution provides guidance for the lower level in the decoder. BLUE is trained using the trajectory reconstruction task with the MSE loss. We compare BLUE with 8 SOTA TRL methods for 3 downstream tasks, the results show that BLUE consistently achieves higher accuracy than all baselines, outperforming the best-performing baselines by an average of 30.90%. Our code is available at https://github.com/slzhou-xy/BLUE.