Multimodal Large Language Models for Bioimage Analysis

Rapid advancements in imaging techniques and analytical methods over the past decade have revolutionized our ability to comprehensively probe the biological world at multiple scales, pinpointing the type, quantity, location, and even temporal dynamics of biomolecules. The surge in data complexity and volume presents significant challenges in translating this wealth of information into knowledge. The recently emerged Multimodal Large Language Models (MLLMs) exhibit strong emergent capacities, such as understanding, analyzing, reasoning, and generalization. With these capabilities, MLLMs hold promise to extract intricate information from biological images and data obtained through various modalities, thereby expediting our biological understanding and aiding in the development of novel computational frameworks. Previously, such capabilities were mostly attributed to humans for interpreting and summarizing meaningful conclusions from comprehensive observations and analysis of biological images. However, the current development of MLLMs shows increasing promise in serving as intelligent assistants or agents for augmenting human researchers in biology research

Implicit Neural Image Field for Biological Microscopy Image Compression

The rapid pace of innovation in biological microscopy imaging has led to large images, putting pressure on data storage and impeding efficient sharing, management, and visualization. This necessitates the development of efficient compression solutions. Traditional CODEC methods struggle to adapt to the diverse bioimaging data and often suffer from sub-optimal compression. In this study, we propose an adaptive compression workflow based on Implicit Neural Representation (INR). This approach permits application-specific compression objectives, capable of compressing images of any shape and arbitrary pixel-wise decompression. We demonstrated on a wide range of microscopy images from real applications that our workflow not only achieved high, controllable compression ratios (e.g., 512x) but also preserved detailed information critical for downstream analysis.

Decomposing the Neurons: Activation Sparsity via Mixture of Experts for Continual Test Time Adaptation

Continual Test-Time Adaptation (CTTA), which aims to adapt the pre-trained model to ever-evolving target domains, emerges as an important task for vision models. As current vision models appear to be heavily biased towards texture, continuously adapting the model from one domain distribution to another can result in serious catastrophic forgetting. Drawing inspiration from the human visual system's adeptness at processing both shape and texture according to the famous Trichromatic Theory, we explore the integration of a Mixture-of-Activation-Sparsity-Experts (MoASE) as an adapter for the CTTA task. Given the distinct reaction of neurons with low/high activation to domain-specific/agnostic features, MoASE decomposes the neural activation into high-activation and low-activation components with a non-differentiable Spatial Differentiate Dropout (SDD). Based on the decomposition, we devise a multi-gate structure comprising a Domain-Aware Gate (DAG) that utilizes domain information to adaptive combine experts that process the post-SDD sparse activations of different strengths, and the Activation Sparsity Gate (ASG) that adaptively assigned feature selection threshold of the SDD for different experts for more precise feature decomposition. Finally, we introduce a Homeostatic-Proximal (HP) loss to bypass the error accumulation problem when continuously adapting the model. Extensive experiments on four prominent benchmarks substantiate that our methodology achieves state-of-the-art performance in both classification and segmentation CTTA tasks. Our code is now available at https://github.com/RoyZry98/MoASE-Pytorch.

SpikeNVS: Enhancing Novel View Synthesis from Blurry Images via Spike Camera

One of the most critical factors in achieving sharp Novel View Synthesis (NVS) using neural field methods like Neural Radiance Fields (NeRF) and 3D Gaussian Splatting (3DGS) is the quality of the training images. However, Conventional RGB cameras are susceptible to motion blur. In contrast, neuromorphic cameras like event and spike cameras inherently capture more comprehensive temporal information, which can provide a sharp representation of the scene as additional training data. Recent methods have explored the integration of event cameras to improve the quality of NVS. The event-RGB approaches have some limitations, such as high training costs and the inability to work effectively in the background. Instead, our study introduces a new method that uses the spike camera to overcome these limitations. By considering texture reconstruction from spike streams as ground truth, we design the Texture from Spike (TfS) loss. Since the spike camera relies on temporal integration instead of temporal differentiation used by event cameras, our proposed TfS loss maintains manageable training costs. It handles foreground objects with backgrounds simultaneously. We also provide a real-world dataset captured with our spike-RGB camera system to facilitate future research endeavors. We conduct extensive experiments using synthetic and real-world datasets to demonstrate that our design can enhance novel view synthesis across NeRF and 3DGS. The code and dataset will be made available for public access.

HUB: Guiding Learned Optimizers with Continuous Prompt Tuning

Learned optimizers are a crucial component of meta-learning. Recent advancements in scalable learned optimizers have demonstrated their superior performance over hand-designed optimizers in various tasks. However, certain characteristics of these models, such as an unstable learning curve, limited ability to handle unseen tasks and network architectures, difficult-to-control behaviours, and poor performance in fine-tuning tasks impede their widespread adoption. To tackle the issue of generalization in scalable learned optimizers, we propose a hybrid-update-based (HUB) optimization strategy inspired by recent advancements in hard prompt tuning and result selection techniques used in large language and vision models. This approach can be easily applied to any task that involves hand-designed or learned optimizer. By incorporating hand-designed optimizers as the second component in our hybrid approach, we are able to retain the benefits of learned optimizers while stabilizing the training process and, more importantly, improving testing performance. We validate our design through a total of 17 tasks, consisting of thirteen training from scratch and four fine-tuning settings. These tasks vary in model sizes, architectures, or dataset sizes, and the competing optimizers are hyperparameter-tuned. We outperform all competitors in 94% of the tasks with better testing performance. Furthermore, we conduct a theoretical analysis to examine the potential impact of our hybrid strategy on the behaviours and inherited traits of learned optimizers.