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Harnessing the robust capabilities of Large Language Models (LLMs) for narrative generation, logical reasoning, and common-sense knowledge integration, this study delves into utilizing LLMs to enhance automated radiology report generation (R2Gen). Despite the wealth of knowledge within LLMs, efficiently triggering relevant knowledge within these large models for specific tasks like R2Gen poses a critical research challenge. This paper presents KARGEN, a Knowledge-enhanced Automated radiology Report GENeration framework based on LLMs. Utilizing a frozen LLM to generate reports, the framework integrates a knowledge graph to unlock chest disease-related knowledge within the LLM to enhance the clinical utility of generated reports. This is achieved by leveraging the knowledge graph to distill disease-related features in a designed way. Since a radiology report encompasses both normal and disease-related findings, the extracted graph-enhanced disease-related features are integrated with regional image features, attending to both aspects. We explore two fusion methods to automatically prioritize and select the most relevant features. The fused features are employed by LLM to generate reports that are more sensitive to diseases and of improved quality. Our approach demonstrates promising results on the MIMIC-CXR and IU-Xray datasets.

In recent years, automated radiology report generation has experienced significant growth. This paper introduces MRScore, an automatic evaluation metric tailored for radiology report generation by leveraging Large Language Models (LLMs). Conventional NLG (natural language generation) metrics like BLEU are inadequate for accurately assessing the generated radiology reports, as systematically demonstrated by our observations within this paper. To address this challenge, we collaborated with radiologists to develop a framework that guides LLMs for radiology report evaluation, ensuring alignment with human analysis. Our framework includes two key components: i) utilizing GPT to generate large amounts of training data, i.e., reports with different qualities, and ii) pairing GPT-generated reports as accepted and rejected samples and training LLMs to produce MRScore as the model reward. Our experiments demonstrate MRScore's higher correlation with human judgments and superior performance in model selection compared to traditional metrics. Our code and datasets will be available on GitHub.

Multimodal Large Language Models (MLLMs) have shown success in various general image processing tasks, yet their application in medical imaging is nascent, lacking tailored models. This study investigates the potential of MLLMs in improving the understanding and generation of Chest X-Rays (CXRs). We introduce MedXChat, a unified framework facilitating seamless interactions between medical assistants and users for diverse CXR tasks, including text report generation, visual question-answering (VQA), and Text-to-CXR generation. Our MLLMs using natural language as the input breaks task boundaries, maximally simplifying medical professional training by allowing diverse tasks within a single environment. For CXR understanding, we leverage powerful off-the-shelf visual encoders (e.g., ViT) and LLMs (e.g., mPLUG-Owl) to convert medical imagery into language-like features, and subsequently fine-tune our large pre-trained models for medical applications using a visual adapter network and a delta-tuning approach. For CXR generation, we introduce an innovative synthesis approach that utilizes instruction-following capabilities within the Stable Diffusion (SD) architecture. This technique integrates smoothly with the existing model framework, requiring no extra parameters, thereby maintaining the SD's generative strength while also bestowing upon it the capacity to render fine-grained medical images with high fidelity. Through comprehensive experiments, our model demonstrates exceptional cross-task adaptability, displaying adeptness across all three defined tasks. Our MedXChat model and the instruction dataset utilized in this research will be made publicly available to encourage further exploration in the field.

The advancement of Large Language Models (LLMs) has brought substantial attention to the Chain of Thought (CoT) approach, primarily due to its ability to enhance the capability of LLMs on complex reasoning tasks. Moreover, the significance of CoT approaches extends to the application of LLMs for multi-modal tasks. However, the selection of optimal CoT demonstration examples in multi-modal reasoning remains less explored for LLMs due to the inherent complexity of multi-modal examples. In this paper, we introduce a novel approach that addresses this challenge by using retrieval mechanisms to dynamically and automatically select demonstration examples based on cross-modal and intra-modal similarities. Furthermore, we employ a Stratified Sampling method of categorising demonstration examples into groups based on their types and then retrieving examples from different groups respectively to promote the diversity of demonstration examples. Through a series of experiments on two popular benchmark datasets: ScienceQA and MathVista, we demonstrate that our approach significantly improves the performance of GPT-4 by 6% on ScienceQA and 12.9% on MathVista, and enhances the performance of GPT-4V on two datasets by 2.7%, substantially improving the performance of the most advanced LLMs and LMMs for complex multi-modal reasoning tasks., Comment: Work in progress

This work conducts an evaluation of GPT-4V's multimodal capability for medical image analysis, with a focus on three representative tasks of radiology report generation, medical visual question answering, and medical visual grounding. For the evaluation, a set of prompts is designed for each task to induce the corresponding capability of GPT-4V to produce sufficiently good outputs. Three evaluation ways including quantitative analysis, human evaluation, and case study are employed to achieve an in-depth and extensive evaluation. Our evaluation shows that GPT-4V excels in understanding medical images and is able to generate high-quality radiology reports and effectively answer questions about medical images. Meanwhile, it is found that its performance for medical visual grounding needs to be substantially improved. In addition, we observe the discrepancy between the evaluation outcome from quantitative analysis and that from human evaluation. This discrepancy suggests the limitations of conventional metrics in assessing the performance of large language models like GPT-4V and the necessity of developing new metrics for automatic quantitative analysis.

Large Language Models (LLMs) have consistently showcased remarkable generalization capabilities when applied to various language tasks. Nonetheless, harnessing the full potential of LLMs for Radiology Report Generation (R2Gen) still presents a challenge, stemming from the inherent disparity in modality between LLMs and the R2Gen task. To bridge this gap effectively, we propose R2GenGPT, which is a novel solution that aligns visual features with the word embedding space of LLMs using an efficient visual alignment module. This innovative approach empowers the previously static LLM to seamlessly integrate and process image information, marking a step forward in optimizing R2Gen performance. R2GenGPT offers the following benefits. First, it attains state-of-the-art (SOTA) performance by training only the lightweight visual alignment module while freezing all the parameters of LLM. Second, it exhibits high training efficiency, as it requires the training of an exceptionally minimal number of parameters while achieving rapid convergence. By employing delta tuning, our model only trains 5M parameters (which constitute just 0.07\% of the total parameter count) to achieve performance close to the SOTA levels. Our code is available at https://github.com/wang-zhanyu/R2GenGPT., Comment: Accepted by meta-radiology

In clinical scenarios, multi-specialist consultation could significantly benefit the diagnosis, especially for intricate cases. This inspires us to explore a "multi-expert joint diagnosis" mechanism to upgrade the existing "single expert" framework commonly seen in the current literature. To this end, we propose METransformer, a method to realize this idea with a transformer-based backbone. The key design of our method is the introduction of multiple learnable "expert" tokens into both the transformer encoder and decoder. In the encoder, each expert token interacts with both vision tokens and other expert tokens to learn to attend different image regions for image representation. These expert tokens are encouraged to capture complementary information by an orthogonal loss that minimizes their overlap. In the decoder, each attended expert token guides the cross-attention between input words and visual tokens, thus influencing the generated report. A metrics-based expert voting strategy is further developed to generate the final report. By the multi-experts concept, our model enjoys the merits of an ensemble-based approach but through a manner that is computationally more efficient and supports more sophisticated interactions among experts. Experimental results demonstrate the promising performance of our proposed model on two widely used benchmarks. Last but not least, the framework-level innovation makes our work ready to incorporate advances on existing "single-expert" models to further improve its performance., Comment: Accepted by CVPR2023

Medical Visual Question Answering (VQA) systems play a supporting role to understand clinic-relevant information carried by medical images. The questions to a medical image include two categories: close-end (such as Yes/No question) and open-end. To obtain answers, the majority of the existing medical VQA methods relies on classification approaches, while a few works attempt to use generation approaches or a mixture of the two. The classification approaches are relatively simple but perform poorly on long open-end questions. To bridge this gap, in this paper, we propose a new Transformer based framework for medical VQA (named as Q2ATransformer), which integrates the advantages of both the classification and the generation approaches and provides a unified treatment for the close-end and open-end questions. Specifically, we introduce an additional Transformer decoder with a set of learnable candidate answer embeddings to query the existence of each answer class to a given image-question pair. Through the Transformer attention, the candidate answer embeddings interact with the fused features of the image-question pair to make the decision. In this way, despite being a classification-based approach, our method provides a mechanism to interact with the answer information for prediction like the generation-based approaches. On the other hand, by classification, we mitigate the task difficulty by reducing the search space of answers. Our method achieves new state-of-the-art performance on two medical VQA benchmarks. Especially, for the open-end questions, we achieve 79.19% on VQA-RAD and 54.85% on PathVQA, with 16.09% and 41.45% absolute improvements, respectively.

Privacy protection methods, such as differentially private mechanisms, introduce noise into resulting statistics which often produces complex and intractable sampling distributions. In this paper, we propose a simulation-based "repro sample" approach to produce statistically valid confidence intervals and hypothesis tests, which builds on the work of Xie and Wang (2022). We show that this methodology is applicable to a wide variety of private inference problems, appropriately accounts for biases introduced by privacy mechanisms (such as by clamping), and improves over other state-of-the-art inference methods such as the parametric bootstrap in terms of the coverage and type I error of the private inference. We also develop significant improvements and extensions for the repro sample methodology for general models (not necessarily related to privacy), including 1) modifying the procedure to ensure guaranteed coverage and type I errors, even accounting for Monte Carlo error, and 2) proposing efficient numerical algorithms to implement the confidence intervals and $p$-values., Comment: 25 pages before references and appendices, 42 pages total, 10 figures, 9 tables

Differentially private (DP) mechanisms protect individual-level information by introducing randomness into the statistical analysis procedure. Despite the availability of numerous DP tools, there remains a lack of general techniques for conducting statistical inference under DP. We examine a DP bootstrap procedure that releases multiple private bootstrap estimates to infer the sampling distribution and construct confidence intervals (CIs). Our privacy analysis presents new results on the privacy cost of a single DP bootstrap estimate, applicable to any DP mechanism, and identifies some misapplications of the bootstrap in the existing literature. For the composition of the DP bootstrap, we present a numerical method to compute the exact privacy cost of releasing multiple DP bootstrap estimates, and using the Gaussian-DP (GDP) framework (Dong et al., 2022), we show that the release of $B$ DP bootstrap estimates from mechanisms satisfying $(\mu/\sqrt{(2-2/\mathrm{e})B})$-GDP asymptotically satisfies $\mu$-GDP as $B$ goes to infinity. Then, we perform private statistical inference by post-processing the DP bootstrap estimates. We prove that our point estimates are consistent, our standard CIs are asymptotically valid, and both enjoy optimal convergence rates. To further improve the finite performance, we use deconvolution with DP bootstrap estimates to accurately infer the sampling distribution. We derive CIs for tasks such as population mean estimation, logistic regression, and quantile regression, and we compare them to existing methods using simulations and real-world experiments on 2016 Canada Census data. Our private CIs achieve the nominal coverage level and offer the first approach to private inference for quantile regression.

In contrast to traditional exhaustive search, selective search first clusters documents into several groups before all the documents are searched exhaustively by a query, to limit the search executed within one group or only a few groups. Selective search is designed to reduce the latency and computation in modern large-scale search systems. In this study, we propose MICO, a Mutual Information CO-training framework for selective search with minimal supervision using the search logs. After training, MICO does not only cluster the documents, but also routes unseen queries to the relevant clusters for efficient retrieval. In our empirical experiments, MICO significantly improves the performance on multiple metrics of selective search and outperforms a number of existing competitive baselines.

Automated radiographic report generation is a challenging cross-domain task that aims to automatically generate accurate and semantic-coherence reports to describe medical images. Despite the recent progress in this field, there are still many challenges at least in the following aspects. First, radiographic images are very similar to each other, and thus it is difficult to capture the fine-grained visual differences using CNN as the visual feature extractor like many existing methods. Further, semantic information has been widely applied to boost the performance of generation tasks (e.g. image captioning), but existing methods often fail to provide effective medical semantic features. Toward solving those problems, in this paper, we propose a memory-augmented sparse attention block utilizing bilinear pooling to capture the higher-order interactions between the input fine-grained image features while producing sparse attention. Moreover, we introduce a novel Medical Concepts Generation Network (MCGN) to predict fine-grained semantic concepts and incorporate them into the report generation process as guidance. Our proposed method shows promising performance on the recently released largest benchmark MIMIC-CXR. It outperforms multiple state-of-the-art methods in image captioning and medical report generation., Comment: MICCAI 2022

Video captioning is a challenging task since it requires generating sentences describing various diverse and complex videos. Existing video captioning models lack adequate visual representation due to the neglect of the existence of gaps between videos and texts. To bridge this gap, in this paper, we propose a CLIP4Caption framework that improves video captioning based on a CLIP-enhanced video-text matching network (VTM). This framework is taking full advantage of the information from both vision and language and enforcing the model to learn strongly text-correlated video features for text generation. Besides, unlike most existing models using LSTM or GRU as the sentence decoder, we adopt a Transformer structured decoder network to effectively learn the long-range visual and language dependency. Additionally, we introduce a novel ensemble strategy for captioning tasks. Experimental results demonstrate the effectiveness of our method on two datasets: 1) on MSR-VTT dataset, our method achieved a new state-of-the-art result with a significant gain of up to 10% in CIDEr; 2) on the private test data, our method ranking 2nd place in the ACM MM multimedia grand challenge 2021: Pre-training for Video Understanding Challenge. It is noted that our model is only trained on the MSR-VTT dataset.

This report describes our solution to the VALUE Challenge 2021 in the captioning task. Our solution, named CLIP4Caption++, is built on X-Linear/X-Transformer, which is an advanced model with encoder-decoder architecture. We make the following improvements on the proposed CLIP4Caption++: We employ an advanced encoder-decoder model architecture X-Transformer as our main framework and make the following improvements: 1) we utilize three strong pre-trained CLIP models to extract the text-related appearance visual features. 2) we adopt the TSN sampling strategy for data enhancement. 3) we involve the video subtitle information to provide richer semantic information. 3) we introduce the subtitle information, which fuses with the visual features as guidance. 4) we design word-level and sentence-level ensemble strategies. Our proposed method achieves 86.5, 148.4, 64.5 CIDEr scores on VATEX, YC2C, and TVC datasets, respectively, which shows the superior performance of our proposed CLIP4Caption++ on all three datasets., Comment: 4 pages, VALUE Challenge 2021 captioning task chamionship solution

In this work, we investigate the idea of variance reduction by studying its properties with general adaptive mirror descent algorithms in nonsmooth nonconvex finite-sum optimization problems. We propose a simple yet generalized framework for variance reduced adaptive mirror descent algorithms named SVRAMD and provide its convergence analysis in both the nonsmooth nonconvex problem and the P-L conditioned problem. We prove that variance reduction reduces the SFO complexity of adaptive mirror descent algorithms and thus accelerates their convergence. In particular, our general theory implies that variance reduction can be applied to algorithms using time-varying step sizes and self-adaptive algorithms such as AdaGrad and RMSProp. Moreover, the convergence rates of SVRAMD recover the best existing rates of non-adaptive variance reduced mirror descent algorithms without complicated algorithmic components. Extensive experiments in deep learning validate our theoretical findings., Comment: NeurIPS 2020 OPT workshop

Devising dynamic pricing policy with always valid online statistical learning procedure is an important and as yet unresolved problem. Most existing dynamic pricing policy, which focus on the faithfulness of adopted customer choice models, exhibit a limited capability for adapting the online uncertainty of learned statistical model during pricing process. In this paper, we propose a novel approach for designing dynamic pricing policy based regularized online statistical learning with theoretical guarantees. The new approach overcomes the challenge of continuous monitoring of online Lasso procedure and possesses several appealing properties. In particular, we make the decisive observation that the always-validity of pricing decisions builds and thrives on the online regularization scheme. Our proposed online regularization scheme equips the proposed optimistic online regularized maximum likelihood pricing (OORMLP) pricing policy with three major advantages: encode market noise knowledge into pricing process optimism; empower online statistical learning with always-validity over all decision points; envelop prediction error process with time-uniform non-asymptotic oracle inequalities. This type of non-asymptotic inference results allows us to design more sample-efficient and robust dynamic pricing algorithms in practice. In theory, the proposed OORMLP algorithm exploits the sparsity structure of high-dimensional models and secures a logarithmic regret in a decision horizon. These theoretical advances are made possible by proposing an optimistic online Lasso procedure that resolves dynamic pricing problems at the process level, based on a novel use of non-asymptotic martingale concentration. In experiments, we evaluate OORMLP in different synthetic and real pricing problem settings, and demonstrate that OORMLP advances the state-of-the-art methods., Comment: The following article has been accepted by JASA; see https://www.tandfonline.com/doi/full/10.1080/01621459.2023.2284979

In the light of the fact that the stochastic gradient descent (SGD) often finds a flat minimum valley in the training loss, we propose a novel directional pruning method which searches for a sparse minimizer in or close to that flat region. The proposed pruning method does not require retraining or the expert knowledge on the sparsity level. To overcome the computational formidability of estimating the flat directions, we propose to use a carefully tuned $\ell_1$ proximal gradient algorithm which can provably achieve the directional pruning with a small learning rate after sufficient training. The empirical results demonstrate the promising results of our solution in highly sparse regime (92% sparsity) among many existing pruning methods on the ResNet50 with the ImageNet, while using only a slightly higher wall time and memory footprint than the SGD. Using the VGG16 and the wide ResNet 28x10 on the CIFAR-10 and CIFAR-100, we demonstrate that our solution reaches the same minima valley as the SGD, and the minima found by our solution and the SGD do not deviate in directions that impact the training loss. The code that reproduces the results of this paper is available at https://github.com/donlan2710/gRDA-Optimizer/tree/master/directional_pruning., Comment: Camera-ready version for the NeurIPS 2020. 29 pages

This paper addresses the meta-learning problem in sparse linear regression with infinite tasks. We assume that the learner can access several similar tasks. The goal of the learner is to transfer knowledge from the prior tasks to a similar but novel task. For p parameters, size of the support set k , and l samples per task, we show that T \in O (( k log(p) ) /l ) tasks are sufficient in order to recover the common support of all tasks. With the recovered support, we can greatly reduce the sample complexity for estimating the parameter of the novel task, i.e., l \in O (1) with respect to T and p . We also prove that our rates are minimax optimal. A key difference between meta-learning and the classical multi-task learning, is that meta-learning focuses only on the recovery of the parameters of the novel task, while multi-task learning estimates the parameter of all tasks, which requires l to grow with T . Instead, our efficient meta-learning estimator allows for l to be constant with respect to T (i.e., few-shot learning).

Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the uncertainty using the notion of uniquely mapped (UM) reads, which motivated the design of a new assembler BAUM. It mainly consists of two types of iterations. The first type of iterations constructs initial contigs from a reference, say a genome of a species that could be quite distant, by adaptive read mapping, filtration by the reference's unique regions, and reference updating. A statistical test is proposed to split the layouts at possible structural variation sites. The second type of iterations includes mapping, scaffolding/contig-extension, and contig merging. We extend each contig by locally assembling the reads whose mates are uniquely mapped to an end of the contig. Instead of the de Bruijn graph method, we take the overlap-layout-consensus (OLC) paradigm. The OLC is implemented by parallel computation, and has linear complexity with respect to the number of contigs. The adjacent extended contigs are merged if their alignment is confirmed by the adjusted gap distance. Throughout the assembling, the mapping criterion is selected by probabilistic calculations. These innovations can be used complementary to the existing de novo assemblers. Applying this novel method to the assembly of wild rice Oryza longistaminata genome, we achieved much improved contig N50, 18.8k, compared with other assemblers. The assembly was further validated by contigs constructed from an independent library of long 454 reads.

The phonon properties, electronic structures and optical properties of novel carbon allotropes, such as monolayer penta-graphene (PG), double-layer PG and T12-carbon, were explored by means of first-principles calculations. Results of phonon calculations demonstrate that these exotic carbon allotropes are dynamically stable. In addition, the bulk T12 phase is an indirect-gap semiconductor having a bandgap of ~4.89 eV. Whereas the bulk material transforms to a 2D phase, the monolayer and double-layer PG become quasi-direct gap semiconductors with smaller band gaps of ~2.64 eV and ~3.27eV, respectively. Furthermore, the partial charge density analysis indicates that the 2D phases retain part of the electronic characteristics of the T12 phase. The linear photon energy-dependent dielectric functions and related optical properties including refractive index, extinction coefficient, absorption spectrum, reflectivity, and energy loss spectrum were also computed and discussed. The structural estimation obtained as well as other findings are in agreement with existing theoretical data. The calculated results are beneficial to the practical applications of these exotic carbon allotropes in optoelectronics and electronics.