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.

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.

Large Language Model for Verilog Generation with Golden Code Feedback

Recent advancements in large language models (LLMs) have catalyzed significant interest in the automatic generation of Register-Transfer Level (RTL) code, particularly Verilog, from natural language instructions. While commercial LLMs like ChatGPT have dominated this domain, open-source alternatives have lagged considerably in performance, limiting the flexibility and data privacy of this emerging technology. This study introduces a novel approach utilizing reinforcement learning with golden code feedback to enhance the performance of pre-trained models. Leveraging open-source data and base models, we have achieved state-of-the-art (SOTA) results with a substantial margin. Notably, our 6.7B parameter model \ours{} demonstrates superior performance compared to current best-in-class 13B and 16B models. Furthermore, through a comprehensive analysis of the limitations in direct fine-tuning and the training dynamics of reinforcement learning, we posit that the development of comprehensive supervisory signals, which are align with the inherent parallel semantics of Verilog code, is critical to effective generation. The code and data associated with this research are publicly available at \url{https://github.com/CatIIIIIIII/veriseek}. The model weights can be accessed at \url{https://huggingface.co/WANGNingroci/VeriSeek}.

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.

On the Compressibility of Quantized Large Language Models

Deploying Large Language Models (LLMs) on edge or mobile devices offers significant benefits, such as enhanced data privacy and real-time processing capabilities. However, it also faces critical challenges due to the substantial memory requirement of LLMs. Quantization is an effective way of reducing the model size while maintaining good performance. However, even after quantization, LLMs may still be too big to fit entirely into the limited memory of edge or mobile devices and have to be partially loaded from the storage to complete the inference. In this case, the I/O latency of model loading becomes the bottleneck of the LLM inference latency. In this work, we take a preliminary step of studying applying data compression techniques to reduce data movement and thus speed up the inference of quantized LLM on memory-constrained devices. In particular, we discussed the compressibility of quantized LLMs, the trade-off between the compressibility and performance of quantized LLMs, and opportunities to optimize both of them jointly.