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.

Transtreaming: Adaptive Delay-aware Transformer for Real-time Streaming Perception

Real-time object detection is critical for the decision-making process for many real-world applications, such as collision avoidance and path planning in autonomous driving. This work presents an innovative real-time streaming perception method, Transtreaming, which addresses the challenge of real-time object detection with dynamic computational delay. The core innovation of Transtreaming lies in its adaptive delay-aware transformer, which can concurrently predict multiple future frames and select the output that best matches the real-world present time, compensating for any system-induced computation delays. The proposed model outperforms the existing state-of-the-art methods, even in single-frame detection scenarios, by leveraging a transformer-based methodology. It demonstrates robust performance across a range of devices, from powerful V100 to modest 2080Ti, achieving the highest level of perceptual accuracy on all platforms. Unlike most state-of-the-art methods that struggle to complete computation within a single frame on less powerful devices, Transtreaming meets the stringent real-time processing requirements on all kinds of devices. The experimental results emphasize the system's adaptability and its potential to significantly improve the safety and reliability for many real-world systems, such as autonomous driving.

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.

Large Language Model (LLM) for Telecommunications: A Comprehensive Survey on Principles, Key Techniques, and Opportunities

Large language models (LLMs) have received considerable attention recently due to their outstanding comprehension and reasoning capabilities, leading to great progress in many fields. The advancement of LLM techniques also offers promising opportunities to automate many tasks in the telecommunication (telecom) field. After pre-training and fine-tuning, LLMs can perform diverse downstream tasks based on human instructions, paving the way to artificial general intelligence (AGI)-enabled 6G. Given the great potential of LLM technologies, this work aims to provide a comprehensive overview of LLM-enabled telecom networks. In particular, we first present LLM fundamentals, including model architecture, pre-training, fine-tuning, inference and utilization, model evaluation, and telecom deployment. Then, we introduce LLM-enabled key techniques and telecom applications in terms of generation, classification, optimization, and prediction problems. Specifically, the LLM-enabled generation applications include telecom domain knowledge, code, and network configuration generation. After that, the LLM-based classification applications involve network security, text, image, and traffic classification problems. Moreover, multiple LLM-enabled optimization techniques are introduced, such as automated reward function design for reinforcement learning and verbal reinforcement learning. Furthermore, for LLM-aided prediction problems, we discussed time-series prediction models and multi-modality prediction problems for telecom. Finally, we highlight the challenges and identify the future directions of LLM-enabled telecom networks.

The Pitfalls and Promise of Conformal Inference Under Adversarial Attacks

In safety-critical applications such as medical imaging and autonomous driving, where decisions have profound implications for patient health and road safety, it is imperative to maintain both high adversarial robustness to protect against potential adversarial attacks and reliable uncertainty quantification in decision-making. With extensive research focused on enhancing adversarial robustness through various forms of adversarial training (AT), a notable knowledge gap remains concerning the uncertainty inherent in adversarially trained models. To address this gap, this study investigates the uncertainty of deep learning models by examining the performance of conformal prediction (CP) in the context of standard adversarial attacks within the adversarial defense community. It is first unveiled that existing CP methods do not produce informative prediction sets under the commonly used $l_{\infty}$-norm bounded attack if the model is not adversarially trained, which underpins the importance of adversarial training for CP. Our paper next demonstrates that the prediction set size (PSS) of CP using adversarially trained models with AT variants is often worse than using standard AT, inspiring us to research into CP-efficient AT for improved PSS. We propose to optimize a Beta-weighting loss with an entropy minimization regularizer during AT to improve CP-efficiency, where the Beta-weighting loss is shown to be an upper bound of PSS at the population level by our theoretical analysis. Moreover, our empirical study on four image classification datasets across three popular AT baselines validates the effectiveness of the proposed Uncertainty-Reducing AT (AT-UR).

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.

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.