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.

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.

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.

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.

Improving Natural Language Understanding with Computation-Efficient Retrieval Representation Fusion

Retrieval-based augmentations that aim to incorporate knowledge from an external database into language models have achieved great success in various knowledge-intensive (KI) tasks, such as question-answering and text generation. However, integrating retrievals in non-knowledge-intensive (NKI) tasks, such as text classification, is still challenging. Existing works focus on concatenating retrievals to inputs as context to form the prompt-based inputs. Unfortunately, such methods require language models to have the capability to handle long texts. Besides, inferring such concatenated data would also consume a significant amount of computational resources. To solve these challenges, we propose \textbf{ReFusion} in this paper, a computation-efficient \textbf{Re}trieval representation \textbf{Fusion} with neural architecture search. The main idea is to directly fuse the retrieval representations into the language models. Specifically, we first propose an online retrieval module that retrieves representations of similar sentences. Then, we present a retrieval fusion module including two effective ranking schemes, i.e., reranker-based scheme and ordered-mask-based scheme, to fuse the retrieval representations with hidden states. Furthermore, we use Neural Architecture Search (NAS) to seek the optimal fusion structure across different layers. Finally, we conduct comprehensive experiments, and the results demonstrate our ReFusion can achieve superior and robust performance on various NKI tasks.

NFL: Robust Learned Index via Distribution Transformation

Recent works on learned index open a new direction for the indexing field. The key insight of the learned index is to approximate the mapping between keys and positions with piece-wise linear functions. Such methods require partitioning key space for a better approximation. Although lots of heuristics are proposed to improve the approximation quality, the bottleneck is that the segmentation overheads could hinder the overall performance. This paper tackles the approximation problem by applying a \textit{distribution transformation} to the keys before constructing the learned index. A two-stage Normalizing-Flow-based Learned index framework (NFL) is proposed, which first transforms the original complex key distribution into a near-uniform distribution, then builds a learned index leveraging the transformed keys. For effective distribution transformation, we propose a Numerical Normalizing Flow (Numerical NF). Based on the characteristics of the transformed keys, we propose a robust After-Flow Learned Index (AFLI). To validate the performance, comprehensive evaluations are conducted on both synthetic and real-world workloads, which shows that the proposed NFL produces the highest throughput and the lowest tail latency compared to the state-of-the-art learned indexes.