Daily Papers

Unlike color photography images, which are consistently encoded into RGB channels, biological images encompass various modalities, where the type of microscopy and the meaning of each channel varies with each experiment. Importantly, the number of channels can range from one to a dozen and their correlation is often comparatively much lower than RGB, as each of them brings specific information content. This aspect is largely overlooked by methods designed out of the bioimage field, and current solutions mostly focus on intra-channel spatial attention, often ignoring the relationship between channels, yet crucial in most biological applications. Importantly, the variable channel type and count prevent the projection of several experiments to a unified representation for large scale pre-training. In this study, we propose ChAda-ViT, a novel Channel Adaptive Vision Transformer architecture employing an Inter-Channel Attention mechanism on images with an arbitrary number, order and type of channels. We also introduce IDRCell100k, a bioimage dataset with a rich set of 79 experiments covering 7 microscope modalities, with a multitude of channel types, and channel counts varying from 1 to 10 per experiment. Our proposed architecture, trained in a self-supervised manner, outperforms existing approaches in several biologically relevant downstream tasks. Additionally, it can be used to bridge the gap for the first time between assays with different microscopes, channel numbers or types by embedding various image and experimental modalities into a unified biological image representation. The latter should facilitate interdisciplinary studies and pave the way for better adoption of deep learning in biological image-based analyses. Code and Data to be released soon.

Feature reuse has been a key technique in light-weight convolutional neural networks (CNNs) design. Current methods usually utilize a concatenation operator to keep large channel numbers cheaply (thus large network capacity) by reusing feature maps from other layers. Although concatenation is parameters- and FLOPs-free, its computational cost on hardware devices is non-negligible. To address this, this paper provides a new perspective to realize feature reuse via structural re-parameterization technique. A novel hardware-efficient RepGhost module is proposed for implicit feature reuse via re-parameterization, instead of using concatenation operator. Based on the RepGhost module, we develop our efficient RepGhost bottleneck and RepGhostNet. Experiments on ImageNet and COCO benchmarks demonstrate that the proposed RepGhostNet is much more effective and efficient than GhostNet and MobileNetV3 on mobile devices. Specially, our RepGhostNet surpasses GhostNet 0.5x by 2.5% Top-1 accuracy on ImageNet dataset with less parameters and comparable latency on an ARM-based mobile phone.

Scaling up model and data size has been quite successful for the evolution of LLMs. However, the scaling law for the diffusion based text-to-image (T2I) models is not fully explored. It is also unclear how to efficiently scale the model for better performance at reduced cost. The different training settings and expensive training cost make a fair model comparison extremely difficult. In this work, we empirically study the scaling properties of diffusion based T2I models by performing extensive and rigours ablations on scaling both denoising backbones and training set, including training scaled UNet and Transformer variants ranging from 0.4B to 4B parameters on datasets upto 600M images. For model scaling, we find the location and amount of cross attention distinguishes the performance of existing UNet designs. And increasing the transformer blocks is more parameter-efficient for improving text-image alignment than increasing channel numbers. We then identify an efficient UNet variant, which is 45% smaller and 28% faster than SDXL's UNet. On the data scaling side, we show the quality and diversity of the training set matters more than simply dataset size. Increasing caption density and diversity improves text-image alignment performance and the learning efficiency. Finally, we provide scaling functions to predict the text-image alignment performance as functions of the scale of model size, compute and dataset size.

Transformer neural operators have recently become an effective approach for surrogate modeling of systems governed by partial differential equations (PDEs). In this paper, we introduce a modified implicit factorized transformer (IFactFormer-m) model which replaces the original chained factorized attention with parallel factorized attention. The IFactFormer-m model successfully performs long-term predictions for turbulent channel flow, whereas the original IFactFormer (IFactFormer-o), Fourier neural operator (FNO), and implicit Fourier neural operator (IFNO) exhibit a poor performance. Turbulent channel flows are simulated by direct numerical simulation using fine grids at friction Reynolds numbers Re_{tau}approx 180,395,590, and filtered to coarse grids for training neural operator. The neural operator takes the current flow field as input and predicts the flow field at the next time step, and long-term prediction is achieved in the posterior through an autoregressive approach. The results show that IFactFormer-m, compared to other neural operators and the traditional large eddy simulation (LES) methods including dynamic Smagorinsky model (DSM) and the wall-adapted local eddy-viscosity (WALE) model, reduces prediction errors in the short term, and achieves stable and accurate long-term prediction of various statistical properties and flow structures, including the energy spectrum, mean streamwise velocity, root mean square (rms) values of fluctuating velocities, Reynolds shear stress, and spatial structures of instantaneous velocity. Moreover, the trained IFactFormer-m is much faster than traditional LES methods. By analyzing the attention kernels, we elucidate the reasons why IFactFormer-m converges faster and achieves a stable and accurate long-term prediction compared to IFactFormer-o. Code and data are available at: https://github.com/huiyu-2002/IFactFormer-m.

Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spanning millions of images. This work explores the scaling properties of weakly supervised classifiers and self-supervised masked autoencoders (MAEs) when training with increasingly larger model backbones and microscopy datasets. Our results show that ViT-based MAEs outperform weakly supervised classifiers on a variety of tasks, achieving as much as a 11.5% relative improvement when recalling known biological relationships curated from public databases. Additionally, we develop a new channel-agnostic MAE architecture (CA-MAE) that allows for inputting images of different numbers and orders of channels at inference time. We demonstrate that CA-MAEs effectively generalize by inferring and evaluating on a microscopy image dataset (JUMP-CP) generated under different experimental conditions with a different channel structure than our pretraining data (RPI-93M). Our findings motivate continued research into scaling self-supervised learning on microscopy data in order to create powerful foundation models of cellular biology that have the potential to catalyze advancements in drug discovery and beyond.

Large Language Models (LLMs) excel in NLP, but their demands hinder their widespread deployment. While Quantization-Aware Training (QAT) offers a solution, its extensive training costs make Post-Training Quantization (PTQ) a more practical approach for LLMs. In existing studies, activation outliers in particular channels are identified as the bottleneck to PTQ accuracy. They propose to transform the magnitudes from activations to weights, which however offers limited alleviation or suffers from unstable gradients, resulting in a severe performance drop at low-bitwidth. In this paper, we propose QLLM, an accurate and efficient low-bitwidth PTQ method designed for LLMs. QLLM introduces an adaptive channel reassembly technique that reallocates the magnitude of outliers to other channels, thereby mitigating their impact on the quantization range. This is achieved by channel disassembly and channel assembly, which first breaks down the outlier channels into several sub-channels to ensure a more balanced distribution of activation magnitudes. Then similar channels are merged to maintain the original channel number for efficiency. Additionally, an adaptive strategy is designed to autonomously determine the optimal number of sub-channels for channel disassembly. To further compensate for the performance loss caused by quantization, we propose an efficient tuning method that only learns a small number of low-rank weights while freezing the pre-trained quantized model. After training, these low-rank parameters can be fused into the frozen weights without affecting inference. Extensive experiments on LLaMA-1 and LLaMA-2 show that QLLM can obtain accurate quantized models efficiently. For example, QLLM quantizes the 4-bit LLaMA-2-70B within 10 hours on a single A100-80G GPU, outperforming the previous state-of-the-art method by 7.89% on the average accuracy across five zero-shot tasks.