Daily Papers

Single-nucleus RNA sequencing (snRNA-seq) has significantly advanced our understanding of the disease etiology of neurodegenerative disorders. However, the low quality of specimens derived from postmortem brain tissues, combined with the high variability caused by disease heterogeneity, makes it challenging to integrate snRNA-seq data from multiple sources for precise analyses. To address these challenges, we present scMamba, a pre-trained model designed to improve the quality and utility of snRNA-seq analysis, with a particular focus on neurodegenerative diseases. Inspired by the recent Mamba model, scMamba introduces a novel architecture that incorporates a linear adapter layer, gene embeddings, and bidirectional Mamba blocks, enabling efficient processing of snRNA-seq data while preserving information from the raw input. Notably, scMamba learns generalizable features of cells and genes through pre-training on snRNA-seq data, without relying on dimension reduction or selection of highly variable genes. We demonstrate that scMamba outperforms benchmark methods in various downstream tasks, including cell type annotation, doublet detection, imputation, and the identification of differentially expressed genes.

Work in psychology has highlighted that the geometric model of similarity standard in deep learning is not psychologically plausible because its metric properties such as symmetry do not align with human perception. In contrast, Tversky (1977) proposed an axiomatic theory of similarity based on a representation of objects as sets of features, and their similarity as a function of common and distinctive features. However, this model has not been used in deep learning before, partly due to the challenge of incorporating discrete set operations. We develop a differentiable parameterization of Tversky's similarity that is learnable through gradient descent, and derive neural network building blocks such as the Tversky projection layer, which unlike the linear projection layer can model non-linear functions such as XOR. Through experiments with image recognition and language modeling, we show that the Tversky projection layer is a beneficial replacement for the linear projection layer, which employs geometric similarity. On the NABirds image classification task, a frozen ResNet-50 adapted with a Tversky projection layer achieves a 24.7% relative accuracy improvement over the linear layer adapter baseline. With Tversky projection layers, GPT-2's perplexity on PTB decreases by 7.5%, and its parameter count by 34.8%. Finally, we propose a unified interpretation of both projection layers as computing similarities of input stimuli to learned prototypes, for which we also propose a novel visualization technique highlighting the interpretability of Tversky projection layers. Our work offers a new paradigm for thinking about the similarity model implicit in deep learning, and designing networks that are interpretable under an established theory of psychological similarity.

Low-rank adaptation (LoRA) has emerged as a leading parameter-efficient fine-tuning technique for adapting large foundation models, yet it often locks adapters into suboptimal minima near their initialization. This hampers model generalization and limits downstream operators such as adapter merging and pruning. Here, we propose CoTo, a progressive training strategy that gradually increases adapters' activation probability over the course of fine-tuning. By stochastically deactivating adapters, CoTo encourages more balanced optimization and broader exploration of the loss landscape. We provide a theoretical analysis showing that CoTo promotes layer-wise dropout stability and linear mode connectivity, and we adopt a cooperative-game approach to quantify each adapter's marginal contribution. Extensive experiments demonstrate that CoTo consistently boosts single-task performance, enhances multi-task merging accuracy, improves pruning robustness, and reduces training overhead, all while remaining compatible with diverse LoRA variants. Code is available at https://github.com/zwebzone/coto.

Large Multimodal Models encode extensive factual knowledge in their pre-trained weights. However, its knowledge remains static and limited, unable to keep pace with real-world developments, which hinders continuous knowledge acquisition. Effective knowledge injection thus becomes critical, involving two goals: knowledge adaptation (injecting new knowledge) and knowledge retention (preserving old knowledge). Existing methods often struggle to learn new knowledge and suffer from catastrophic forgetting. To address this, we propose KORE, a synergistic method of KnOwledge-oRientEd augmentations and constraints for injecting new knowledge into large multimodal models while preserving old knowledge. Unlike general text or image data augmentation, KORE automatically converts individual knowledge items into structured and comprehensive knowledge to ensure that the model accurately learns new knowledge, enabling accurate adaptation. Meanwhile, KORE stores previous knowledge in the covariance matrix of LMM's linear layer activations and initializes the adapter by projecting the original weights into the matrix's null space, defining a fine-tuning direction that minimizes interference with previous knowledge, enabling powerful retention. Extensive experiments on various LMMs, including LLaVA-v1.5-7B, LLaVA-v1.5-13B, and Qwen2.5-VL-7B, show that KORE achieves superior new knowledge injection performance and effectively mitigates catastrophic forgetting.

While diffusion models show extraordinary talents in text-to-image generation, they may still fail to generate highly aesthetic images. More specifically, there is still a gap between the generated images and the real-world aesthetic images in finer-grained dimensions including color, lighting, composition, etc. In this paper, we propose Cross-Attention Value Mixing Control (VMix) Adapter, a plug-and-play aesthetics adapter, to upgrade the quality of generated images while maintaining generality across visual concepts by (1) disentangling the input text prompt into the content description and aesthetic description by the initialization of aesthetic embedding, and (2) integrating aesthetic conditions into the denoising process through value-mixed cross-attention, with the network connected by zero-initialized linear layers. Our key insight is to enhance the aesthetic presentation of existing diffusion models by designing a superior condition control method, all while preserving the image-text alignment. Through our meticulous design, VMix is flexible enough to be applied to community models for better visual performance without retraining. To validate the effectiveness of our method, we conducted extensive experiments, showing that VMix outperforms other state-of-the-art methods and is compatible with other community modules (e.g., LoRA, ControlNet, and IPAdapter) for image generation. The project page is https://vmix-diffusion.github.io/VMix/.

Transformer-based pre-trained models with millions of parameters require large storage. Recent approaches tackle this shortcoming by training adapters, but these approaches still require a relatively large number of parameters. In this study, AdapterBias, a surprisingly simple yet effective adapter architecture, is proposed. AdapterBias adds a token-dependent shift to the hidden output of transformer layers to adapt to downstream tasks with only a vector and a linear layer. Extensive experiments are conducted to demonstrate the effectiveness of AdapterBias. The experiments show that our proposed method can dramatically reduce the trainable parameters compared to the previous works with a minimal decrease in task performances compared with fine-tuned pre-trained models. We further find that AdapterBias automatically learns to assign more significant representation shifts to the tokens related to the task in consideration.