GeneQuery: A General QA-based Framework for Spatial Gene Expression Predictions from Histology Images

Gene expression profiling provides profound insights into molecular mechanisms, but its time-consuming and costly nature often presents significant challenges. In contrast, whole-slide hematoxylin and eosin (H&E) stained histological images are readily accessible and allow for detailed examinations of tissue structure and composition at the microscopic level. Recent advancements have utilized these histological images to predict spatially resolved gene expression profiles. However, state-of-the-art works treat gene expression prediction as a multi-output regression problem, where each gene is learned independently with its own weights, failing to capture the shared dependencies and co-expression patterns between genes. Besides, existing works can only predict gene expression values for genes seen during training, limiting their ability to generalize to new, unseen genes. To address the above limitations, this paper presents GeneQuery, which aims to solve this gene expression prediction task in a question-answering (QA) manner for better generality and flexibility. Specifically, GeneQuery takes gene-related texts as queries and whole-slide images as contexts and then predicts the queried gene expression values. With such a transformation, GeneQuery can implicitly estimate the gene distribution by introducing the gene random variable. Besides, the proposed GeneQuery consists of two architecture implementations, i.e., spot-aware GeneQuery for capturing patterns between images and gene-aware GeneQuery for capturing patterns between genes. Comprehensive experiments on spatial transcriptomics datasets show that the proposed GeneQuery outperforms existing state-of-the-art methods on known and unseen genes. More results also demonstrate that GeneQuery can potentially analyze the tissue structure.

SHAP-CAT: A interpretable multi-modal framework enhancing WSI classification via virtual staining and shapley-value-based multimodal fusion

The multimodal model has demonstrated promise in histopathology. However, most multimodal models are based on H\&E and genomics, adopting increasingly complex yet black-box designs. In our paper, we propose a novel interpretable multimodal framework named SHAP-CAT, which uses a Shapley-value-based dimension reduction technique for effective multimodal fusion. Starting with two paired modalities -- H\&E and IHC images, we employ virtual staining techniques to enhance limited input data by generating a new clinical-related modality. Lightweight bag-level representations are extracted from image modalities and a Shapley-value-based mechanism is used for dimension reduction. For each dimension of the bag-level representation, attribution values are calculated to indicate how changes in the specific dimensions of the input affect the model output. In this way, we select a few top important dimensions of bag-level representation for each image modality to late fusion. Our experimental results demonstrate that the proposed SHAP-CAT framework incorporating synthetic modalities significantly enhances model performance, yielding a 5\% increase in accuracy for the BCI, an 8\% increase for IHC4BC-ER, and an 11\% increase for the IHC4BC-PR dataset.

CHESS: Optimizing LLM Inference via Channel-Wise Thresholding and Selective Sparsification

Deploying large language models (LLMs) on edge devices presents significant challenges due to the substantial computational overhead and memory requirements. Activation sparsification can mitigate these challenges by reducing the number of activated neurons during inference. Existing methods typically employ thresholding-based sparsification based on the statistics of activation tensors. However, these methods do not explicitly model the impact of activation sparsification on performance, leading to suboptimal performance degradation. To address this issue, this paper reformulates the activation sparsification problem by introducing a new objective that optimizes the sparsification decisions. Building on this reformulation, we propose CHESS, a general activation sparsification approach via CHannel-wise thrEsholding and Selective Sparsification. First, channel-wise thresholding assigns a unique threshold to each activation channel in the feed-forward network (FFN) layers. Then, selective sparsification involves applying thresholding-based activation sparsification to specific layers within the attention modules. Finally, we detail the implementation of sparse kernels to accelerate LLM inference. Experimental results demonstrate that the proposed CHESS achieves lower performance degradation over 8 downstream tasks while activating fewer parameters compared to existing methods, thus speeding up the LLM inference by up to 1.27x.

Advances in Multiple Instance Learning for Whole Slide Image Analysis: Techniques, Challenges, and Future Directions

Whole slide images (WSIs) are gigapixel-scale digital images of H\&E-stained tissue samples widely used in pathology. The substantial size and complexity of WSIs pose unique analytical challenges. Multiple Instance Learning (MIL) has emerged as a powerful approach for addressing these challenges, particularly in cancer classification and detection. This survey provides a comprehensive overview of the challenges and methodologies associated with applying MIL to WSI analysis, including attention mechanisms, pseudo-labeling, transformers, pooling functions, and graph neural networks. Additionally, it explores the potential of MIL in discovering cancer cell morphology, constructing interpretable machine learning models, and quantifying cancer grading. By summarizing the current challenges, methodologies, and potential applications of MIL in WSI analysis, this survey aims to inform researchers about the state of the field and inspire future research directions.

Retrieval-Augmented Generation for Natural Language Processing: A Survey

Large language models (LLMs) have demonstrated great success in various fields, benefiting from their huge amount of parameters that store knowledge. However, LLMs still suffer from several key issues, such as hallucination problems, knowledge update issues, and lacking domain-specific expertise. The appearance of retrieval-augmented generation (RAG), which leverages an external knowledge database to augment LLMs, makes up those drawbacks of LLMs. This paper reviews all significant techniques of RAG, especially in the retriever and the retrieval fusions. Besides, tutorial codes are provided for implementing the representative techniques in RAG. This paper further discusses the RAG training, including RAG with/without datastore update. Then, we introduce the application of RAG in representative natural language processing tasks and industrial scenarios. Finally, this paper discusses the future directions and challenges of RAG for promoting its development.

Grade Like a Human: Rethinking Automated Assessment with Large Language Models

While large language models (LLMs) have been used for automated grading, they have not yet achieved the same level of performance as humans, especially when it comes to grading complex questions. Existing research on this topic focuses on a particular step in the grading procedure: grading using predefined rubrics. However, grading is a multifaceted procedure that encompasses other crucial steps, such as grading rubrics design and post-grading review. There has been a lack of systematic research exploring the potential of LLMs to enhance the entire grading~process. In this paper, we propose an LLM-based grading system that addresses the entire grading procedure, including the following key components: 1) Developing grading rubrics that not only consider the questions but also the student answers, which can more accurately reflect students' performance. 2) Under the guidance of grading rubrics, providing accurate and consistent scores for each student, along with customized feedback. 3) Conducting post-grading review to better ensure accuracy and fairness. Additionally, we collected a new dataset named OS from a university operating system course and conducted extensive experiments on both our new dataset and the widely used Mohler dataset. Experiments demonstrate the effectiveness of our proposed approach, providing some new insights for developing automated grading systems based on LLMs.

BehaviorGPT: Smart Agent Simulation for Autonomous Driving with Next-Patch Prediction

Simulating realistic interactions among traffic agents is crucial for efficiently validating the safety of autonomous driving systems. Existing leading simulators primarily use an encoder-decoder structure to encode the historical trajectories for future simulation. However, such a paradigm complicates the model architecture, and the manual separation of history and future trajectories leads to low data utilization. To address these challenges, we propose Behavior Generative Pre-trained Transformers (BehaviorGPT), a decoder-only, autoregressive architecture designed to simulate the sequential motion of multiple agents. Crucially, our approach discards the traditional separation between "history" and "future," treating each time step as the "current" one, resulting in a simpler, more parameter- and data-efficient design that scales seamlessly with data and computation. Additionally, we introduce the Next-Patch Prediction Paradigm (NP3), which enables models to reason at the patch level of trajectories and capture long-range spatial-temporal interactions. BehaviorGPT ranks first across several metrics on the Waymo Sim Agents Benchmark, demonstrating its exceptional performance in multi-agent and agent-map interactions. We outperformed state-of-the-art models with a realism score of 0.741 and improved the minADE metric to 1.540, with an approximately 91.6% reduction in model parameters.

RAEE: A Training-Free Retrieval-Augmented Early Exiting Framework for Efficient Inference

Deploying large language model inference remains challenging due to their high computational overhead. Early exiting accelerates model inference by adaptively reducing the number of inference layers. Existing methods require training internal classifiers to determine whether to exit at each intermediate layer. However, such classifier-based early exiting frameworks require significant effort to design and train the classifiers. To address these limitations, this paper proposes RAEE, a training-free Retrieval-Augmented Early Exiting framework for efficient inference. First, this paper demonstrates that the early exiting problem can be modeled as a distribution prediction problem, where the distribution is approximated using similar data's existing information. Next, the paper details the process of collecting existing information to build the retrieval database. Finally, based on the pre-built retrieval database, RAEE leverages the retrieved similar data's exiting information to guide the backbone model to exit at the layer, which is predicted by the approximated distribution. Experimental results demonstrate that the proposed RAEE can significantly accelerate inference. RAEE also achieves state-of-the-art zero-shot performance on 8 classification tasks.

IHC Matters: Incorporating IHC analysis to H&E Whole Slide Image Analysis for Improved Cancer Grading via Two-stage Multimodal Bilinear Pooling Fusion

Immunohistochemistry (IHC) plays a crucial role in pathology as it detects the over-expression of protein in tissue samples. However, there are still fewer machine learning model studies on IHC's impact on accurate cancer grading. We discovered that IHC and H\&E possess distinct advantages and disadvantages while possessing certain complementary qualities. Building on this observation, we developed a two-stage multi-modal bilinear model with a feature pooling module. This model aims to maximize the potential of both IHC and HE's feature representation, resulting in improved performance compared to their individual use. Our experiments demonstrate that incorporating IHC data into machine learning models, alongside H\&E stained images, leads to superior predictive results for cancer grading. The proposed framework achieves an impressive ACC higher of 0.953 on the public dataset BCI.

Pre-processing matters: A segment search method for WSI classification

Pre-processing for whole slide images can affect classification performance both in the training and inference stages. Our study analyzes the impact of pre-processing parameters on inference and training across single- and multiple-domain datasets. However, searching for an optimal parameter set is time-consuming. To overcome this, we propose a novel Similarity-based Simulated Annealing approach for fast parameter tuning to enhance inference performance on single-domain data. Our method demonstrates significant performance improvements in accuracy, which raise accuracy from 0.512 to 0.847 in a single domain. We further extend our insight into training performance in multi-domain data by employing a novel Bayesian optimization to search optimal pre-processing parameters, resulting in a high AUC of 0.967. We highlight that better pre-processing for WSI can contribute to further accuracy improvement in the histology area.