Impact of Stain Variation and Color Normalization for Prognostic Predictions in Pathology

In recent years, deep neural networks (DNNs) have demonstrated remarkable performance in pathology applications, potentially even outperforming expert pathologists due to their ability to learn subtle features from large datasets. One complication in preparing digital pathology datasets for DNN tasks is variation in tinctorial qualities. A common way to address this is to perform stain normalization on the images. In this study, we show that a well-trained DNN model trained on one batch of histological slides failed to generalize to another batch prepared at a different time from the same tissue blocks, even when stain normalization methods were applied. This study used sample data from a previously reported DNN that was able to identify patients with early stage non-small cell lung cancer (NSCLC) whose tumors did and did not metastasize, with high accuracy, based on training and then testing of digital images from H&E stained primary tumor tissue sections processed at the same time. In this study we obtained a new series of histologic slides from the adjacent recuts of same tissue blocks processed in the same lab but at a different time. We found that the DNN trained on the either batch of slides/images was unable to generalize and failed to predict progression in the other batch of slides/images (AUC_cross-batch = 0.52 - 0.53 compared to AUC_same-batch = 0.74 - 0.81). The failure to generalize did not improve even when the tinctorial difference correction were made through either traditional color-tuning or stain normalization with the help of a Cycle Generative Adversarial Network (CycleGAN) process. This highlights the need to develop an entirely new way to process and collect consistent microscopy images from histologic slides that can be used to both train and allow for the general application of predictive DNN algorithms.

MG-Verilog: Multi-grained Dataset Towards Enhanced LLM-assisted Verilog Generation

Large Language Models (LLMs) have recently shown promise in streamlining hardware design processes by encapsulating vast amounts of domain-specific data. In addition, they allow users to interact with the design processes through natural language instructions, thus making hardware design more accessible to developers. However, effectively leveraging LLMs in hardware design necessitates providing domain-specific data during inference (e.g., through in-context learning), fine-tuning, or pre-training. Unfortunately, existing publicly available hardware datasets are often limited in size, complexity, or detail, which hinders the effectiveness of LLMs in hardware design tasks. To address this issue, we first propose a set of criteria for creating high-quality hardware datasets that can effectively enhance LLM-assisted hardware design. Based on these criteria, we propose a Multi-Grained-Verilog (MG-Verilog) dataset, which encompasses descriptions at various levels of detail and corresponding code samples. To benefit the broader hardware design community, we have developed an open-source infrastructure that facilitates easy access, integration, and extension of the dataset to meet specific project needs. Furthermore, to fully exploit the potential of the MG-Verilog dataset, which varies in complexity and detail, we introduce a balanced fine-tuning scheme. This scheme serves as a unique use case to leverage the diverse levels of detail provided by the dataset. Extensive experiments demonstrate that the proposed dataset and fine-tuning scheme consistently improve the performance of LLMs in hardware design tasks.

When Linear Attention Meets Autoregressive Decoding: Towards More Effective and Efficient Linearized Large Language Models

Autoregressive Large Language Models (LLMs) have achieved impressive performance in language tasks but face two significant bottlenecks: (1) quadratic complexity in the attention module as the number of tokens increases, and (2) limited efficiency due to the sequential processing nature of autoregressive LLMs during generation. While linear attention and speculative decoding offer potential solutions, their applicability and synergistic potential for enhancing autoregressive LLMs remain uncertain. We conduct the first comprehensive study on the efficacy of existing linear attention methods for autoregressive LLMs, integrating them with speculative decoding. We introduce an augmentation technique for linear attention that ensures compatibility with speculative decoding, enabling more efficient training and serving of LLMs. Extensive experiments and ablation studies involving seven existing linear attention models and five encoder/decoder-based LLMs consistently validate the effectiveness of our augmented linearized LLMs. Notably, our approach achieves up to a 6.67 reduction in perplexity on the LLaMA model and up to a 2$\times$ speedup during generation compared to prior linear attention methods. Codes and models are available at https://github.com/GATECH-EIC/Linearized-LLM.

ShiftAddLLM: Accelerating Pretrained LLMs via Post-Training Multiplication-Less Reparameterization

Large language models (LLMs) have shown impressive performance on language tasks but face challenges when deployed on resource-constrained devices due to their extensive parameters and reliance on dense multiplications, resulting in high memory demands and latency bottlenecks. Shift-and-add reparameterization offers a promising solution by replacing costly multiplications with hardware-friendly primitives in both the attention and multi-layer perceptron (MLP) layers of an LLM. However, current reparameterization techniques require training from scratch or full parameter fine-tuning to restore accuracy, which is resource-intensive for LLMs. To address this, we propose accelerating pretrained LLMs through post-training shift-and-add reparameterization, creating efficient multiplication-free models, dubbed ShiftAddLLM. Specifically, we quantize each weight matrix into binary matrices paired with group-wise scaling factors. The associated multiplications are reparameterized into (1) shifts between activations and scaling factors and (2) queries and adds according to the binary matrices. To reduce accuracy loss, we present a multi-objective optimization method to minimize both weight and output activation reparameterization errors. Additionally, based on varying sensitivity across layers to reparameterization, we develop an automated bit allocation strategy to further reduce memory usage and latency. Experiments on five LLM families and eight tasks consistently validate the effectiveness of ShiftAddLLM, achieving average perplexity improvements of 5.6 and 22.7 points at comparable or lower latency compared to the most competitive quantized LLMs at 3 and 2 bits, respectively, and more than 80% memory and energy reductions over the original LLMs. Codes and models are available at https://github.com/GATECH-EIC/ShiftAddLLM.

Length-scale study in deep learning prediction for non-small cell lung cancer brain metastasis

Deep learning assisted digital pathology has the potential to impact clinical practice in significant ways. In recent studies, deep neural network (DNN) enabled analysis outperforms human pathologists. Increasing sizes and complexity of the DNN architecture generally improves performance at the cost of DNN's explainability. For pathology, this lack of DNN explainability is particularly problematic as it hinders the broader clinical interpretation of the pathology features that may provide physiological disease insights. To better assess the features that DNN uses in developing predictive algorithms to interpret digital microscopic images, we sought to understand the role of resolution and tissue scale and here describe a novel method for studying the predictive feature length-scale that underpins a DNN's predictive power. We applied the method to study a DNN's predictive capability in the case example of brain metastasis prediction from early-stage non-small-cell lung cancer biopsy slides. The study highlights the DNN attention in the brain metastasis prediction targeting both cellular scale (resolution) and tissue scale features on H&E-stained histological whole slide images. At the cellular scale, we see that DNN's predictive power is progressively increased at higher resolution (i.e., lower resolvable feature length) and is largely lost when the resolvable feature length is longer than 5 microns. In addition, DNN uses more macro-scale features (maximal feature length) associated with tissue organization/architecture and is optimized when assessing visual fields larger than 41 microns. This study for the first time demonstrates the length-scale requirements necessary for optimal DNN learning on digital whole slide images.

Improving Cancer Imaging Diagnosis with Bayesian Networks and Deep Learning: A Bayesian Deep Learning Approach

With recent advancements in the development of artificial intelligence applications using theories and algorithms in machine learning, many accurate models can be created to train and predict on given datasets. With the realization of the importance of imaging interpretation in cancer diagnosis, this article aims to investigate the theory behind Deep Learning and Bayesian Network prediction models. Based on the advantages and drawbacks of each model, different approaches will be used to construct a Bayesian Deep Learning Model, combining the strengths while minimizing the weaknesses. Finally, the applications and accuracy of the resulting Bayesian Deep Learning approach in the health industry in classifying images will be analyzed.

MixRT: Mixed Neural Representations For Real-Time NeRF Rendering

Neural Radiance Field (NeRF) has emerged as a leading technique for novel view synthesis, owing to its impressive photorealistic reconstruction and rendering capability. Nevertheless, achieving real-time NeRF rendering in large-scale scenes has presented challenges, often leading to the adoption of either intricate baked mesh representations with a substantial number of triangles or resource-intensive ray marching in baked representations. We challenge these conventions, observing that high-quality geometry, represented by meshes with substantial triangles, is not necessary for achieving photorealistic rendering quality. Consequently, we propose MixRT, a novel NeRF representation that includes a low-quality mesh, a view-dependent displacement map, and a compressed NeRF model. This design effectively harnesses the capabilities of existing graphics hardware, thus enabling real-time NeRF rendering on edge devices. Leveraging a highly-optimized WebGL-based rendering framework, our proposed MixRT attains real-time rendering speeds on edge devices (over 30 FPS at a resolution of 1280 x 720 on a MacBook M1 Pro laptop), better rendering quality (0.2 PSNR higher in indoor scenes of the Unbounded-360 datasets), and a smaller storage size (less than 80% compared to state-of-the-art methods).

NetDistiller: Empowering Tiny Deep Learning via In-Situ Distillation

Boosting the task accuracy of tiny neural networks (TNNs) has become a fundamental challenge for enabling the deployments of TNNs on edge devices which are constrained by strict limitations in terms of memory, computation, bandwidth, and power supply. To this end, we propose a framework called NetDistiller to boost the achievable accuracy of TNNs by treating them as sub-networks of a weight-sharing teacher constructed by expanding the number of channels of the TNN. Specifically, the target TNN model is jointly trained with the weight-sharing teacher model via (1) gradient surgery to tackle the gradient conflicts between them and (2) uncertainty-aware distillation to mitigate the overfitting of the teacher model. Extensive experiments across diverse tasks validate NetDistiller's effectiveness in boosting TNNs' achievable accuracy over state-of-the-art methods. Our code is available at https://github.com/GATECH-EIC/NetDistiller.

A Survey on Graph Neural Network Acceleration: Algorithms, Systems, and Customized Hardware

Graph neural networks (GNNs) are emerging for machine learning research on graph-structured data. GNNs achieve state-of-the-art performance on many tasks, but they face scalability challenges when it comes to real-world applications that have numerous data and strict latency requirements. Many studies have been conducted on how to accelerate GNNs in an effort to address these challenges. These acceleration techniques touch on various aspects of the GNN pipeline, from smart training and inference algorithms to efficient systems and customized hardware. As the amount of research on GNN acceleration has grown rapidly, there lacks a systematic treatment to provide a unified view and address the complexity of relevant works. In this survey, we provide a taxonomy of GNN acceleration, review the existing approaches, and suggest future research directions. Our taxonomic treatment of GNN acceleration connects the existing works and sets the stage for further development in this area.

ShiftAddViT: Mixture of Multiplication Primitives Towards Efficient Vision Transformer

Vision Transformers (ViTs) have shown impressive performance and have become a unified backbone for multiple vision tasks. But both attention and multi-layer perceptions (MLPs) in ViTs are not efficient enough due to dense multiplications, resulting in costly training and inference. To this end, we propose to reparameterize the pre-trained ViT with a mixture of multiplication primitives, e.g., bitwise shifts and additions, towards a new type of multiplication-reduced model, dubbed $\textbf{ShiftAddViT}$, which aims for end-to-end inference speedups on GPUs without the need of training from scratch. Specifically, all $\texttt{MatMuls}$ among queries, keys, and values are reparameterized by additive kernels, after mapping queries and keys to binary codes in Hamming space. The remaining MLPs or linear layers are then reparameterized by shift kernels. We utilize TVM to implement and optimize those customized kernels for practical hardware deployment on GPUs. We find that such a reparameterization on (quadratic or linear) attention maintains model accuracy, while inevitably leading to accuracy drops when being applied to MLPs. To marry the best of both worlds, we further propose a new mixture of experts (MoE) framework to reparameterize MLPs by taking multiplication or its primitives as experts, e.g., multiplication and shift, and designing a new latency-aware load-balancing loss. Such a loss helps to train a generic router for assigning a dynamic amount of input tokens to different experts according to their latency. In principle, the faster experts run, the larger amount of input tokens are assigned. Extensive experiments consistently validate the effectiveness of our proposed ShiftAddViT, achieving up to $\textbf{5.18$\times$}$ latency reductions on GPUs and $\textbf{42.9%}$ energy savings, while maintaining comparable accuracy as original or efficient ViTs.