arXiv subjects

Xi Jiang

Publications and source records attributed to Xi Jiang.

At least 55 records · Page 3Linked to original sources

arXiv2023

ChatRadio-Valuer: A Chat Large Language Model for Generalizable Radiology Report Generation Based on Multi-institution and Multi-system Data

Radiology report generation, as a key step in medical image analysis, is critical to the quantitative analysis of clinically informed decision-making levels. However, complex and diverse radiology reports with cross-source heterogeneity pose a huge generalizability challenge to the current methods under massive data volume, mainly because the style and normativity of radiology reports are obviously distinctive among institutions, body regions inspected and radiologists. Recently, the advent of large language models (LLM) offers great potential for recognizing signs of health conditions. To resolve the above problem, we collaborate with the Second Xiangya Hospital in China and propose ChatRadio-Valuer based on the LLM, a tailored model for automatic radiology report generation that learns generalizable representations and provides a basis pattern for model adaptation in sophisticated analysts' cases. Specifically, ChatRadio-Valuer is trained based on the radiology reports from a single institution by means of supervised fine-tuning, and then adapted to disease diagnosis tasks for human multi-system evaluation (i.e., chest, abdomen, muscle-skeleton, head, and maxillofacial $\&$ neck) from six different institutions in clinical-level events. The clinical dataset utilized in this study encompasses a remarkable total of \textbf{332,673} observations. From the comprehensive results on engineering indicators, clinical efficacy and deployment cost metrics, it can be shown that ChatRadio-Valuer consistently outperforms state-of-the-art models, especially ChatGPT (GPT-3.5-Turbo) and GPT-4 et al., in terms of the diseases diagnosis from radiology reports. ChatRadio-Valuer provides an effective avenue to boost model generalization performance and alleviate the annotation workload of experts to enable the promotion of clinical AI applications in radiology reports.

cs.CL↗

arXiv2023

Review of Large Vision Models and Visual Prompt Engineering

Visual prompt engineering is a fundamental technology in the field of visual and image Artificial General Intelligence, serving as a key component for achieving zero-shot capabilities. As the development of large vision models progresses, the importance of prompt engineering becomes increasingly evident. Designing suitable prompts for specific visual tasks has emerged as a meaningful research direction. This review aims to summarize the methods employed in the computer vision domain for large vision models and visual prompt engineering, exploring the latest advancements in visual prompt engineering. We present influential large models in the visual domain and a range of prompt engineering methods employed on these models. It is our hope that this review provides a comprehensive and systematic description of prompt engineering methods based on large visual models, offering valuable insights for future researchers in their exploration of this field.

cs.CV↗

arXiv2023

Augmenting Rule-based DNS Censorship Detection at Scale with Machine Learning

The proliferation of global censorship has led to the development of a plethora of measurement platforms to monitor and expose it. Censorship of the domain name system (DNS) is a key mechanism used across different countries. It is currently detected by applying heuristics to samples of DNS queries and responses (probes) for specific destinations. These heuristics, however, are both platform-specific and have been found to be brittle when censors change their blocking behavior, necessitating a more reliable automated process for detecting censorship. In this paper, we explore how machine learning (ML) models can (1) help streamline the detection process, (2) improve the potential of using large-scale datasets for censorship detection, and (3) discover new censorship instances and blocking signatures missed by existing heuristic methods. Our study shows that supervised models, trained using expert-derived labels on instances of known anomalies and possible censorship, can learn the detection heuristics employed by different measurement platforms. More crucially, we find that unsupervised models, trained solely on uncensored instances, can identify new instances and variations of censorship missed by existing heuristics. Moreover, both methods demonstrate the capability to uncover a substantial number of new DNS blocking signatures, i.e., injected fake IP addresses overlooked by existing heuristics. These results are underpinned by an important methodological finding: comparing the outputs of models trained using the same probes but with labels arising from independent processes allows us to more reliably detect cases of censorship in the absence of ground-truth labels of censorship.

cs.LG↗

arXiv2023

PASSerRank: Prediction of Allosteric Sites with Learning to Rank

Allostery plays a crucial role in regulating protein activity, making it a highly sought-after target in drug development. One of the major challenges in allosteric drug research is the identification of allosteric sites. In recent years, many computational models have been developed for accurate allosteric site prediction. Most of these models focus on designing a general rule that can be applied to pockets of proteins from various families. In this study, we present a new approach using the concept of Learning to Rank (LTR). The LTR model ranks pockets based on their relevance to allosteric sites, i.e., how well a pocket meets the characteristics of known allosteric sites. The model outperforms other common machine learning models with higher F1 score and Matthews correlation coefficient. After the training and validation on two datasets, the Allosteric Database (ASD) and CASBench, the LTR model was able to rank an allosteric pocket in the top 3 positions for 83.6% and 80.5% of test proteins, respectively. The trained model is available on the PASSer platform (https://passer.smu.edu) to aid in drug discovery research.

q-bio.QM↗

arXiv2023

Instruction-ViT: Multi-Modal Prompts for Instruction Learning in ViT

Prompts have been proven to play a crucial role in large language models, and in recent years, vision models have also been using prompts to improve scalability for multiple downstream tasks. In this paper, we focus on adapting prompt design based on instruction tuning into a visual transformer model for image classification which we called Instruction-ViT. The key idea is to implement multi-modal prompts (text or image prompt) related to category information to guide the fine-tuning of the model. Based on the experiments of several image captionining tasks, the performance and domain adaptability were improved. Our work provided an innovative strategy to fuse multi-modal prompts with better performance and faster adaptability for visual classification models.

cs.CV↗

arXiv2023

ChatABL: Abductive Learning via Natural Language Interaction with ChatGPT

Large language models (LLMs) such as ChatGPT have recently demonstrated significant potential in mathematical abilities, providing valuable reasoning paradigm consistent with human natural language. However, LLMs currently have difficulty in bridging perception, language understanding and reasoning capabilities due to incompatibility of the underlying information flow among them, making it challenging to accomplish tasks autonomously. On the other hand, abductive learning (ABL) frameworks for integrating the two abilities of perception and reasoning has seen significant success in inverse decipherment of incomplete facts, but it is limited by the lack of semantic understanding of logical reasoning rules and the dependence on complicated domain knowledge representation. This paper presents a novel method (ChatABL) for integrating LLMs into the ABL framework, aiming at unifying the three abilities in a more user-friendly and understandable manner. The proposed method uses the strengths of LLMs' understanding and logical reasoning to correct the incomplete logical facts for optimizing the performance of perceptual module, by summarizing and reorganizing reasoning rules represented in natural language format. Similarly, perceptual module provides necessary reasoning examples for LLMs in natural language format. The variable-length handwritten equation deciphering task, an abstract expression of the Mayan calendar decoding, is used as a testbed to demonstrate that ChatABL has reasoning ability beyond most existing state-of-the-art methods, which has been well supported by comparative studies. To our best knowledge, the proposed ChatABL is the first attempt to explore a new pattern for further approaching human-level cognitive ability via natural language interaction with ChatGPT.

cs.CL↗

arXiv2023

Measuring and Evading Turkmenistan's Internet Censorship: A Case Study in Large-Scale Measurements of a Low-Penetration Country

Since 2006, Turkmenistan has been listed as one of the few Internet enemies by Reporters without Borders due to its extensively censored Internet and strictly regulated information control policies. Existing reports of filtering in Turkmenistan rely on a small number of vantage points or test a small number of websites. Yet, the country's poor Internet adoption rates and small population can make more comprehensive measurement challenging. With a population of only six million people and an Internet penetration rate of only 38%, it is challenging to either recruit in-country volunteers or obtain vantage points to conduct remote network measurements at scale. We present the largest measurement study to date of Turkmenistan's Web censorship. To do so, we developed TMC, which tests the blocking status of millions of domains across the three foundational protocols of the Web (DNS, HTTP, and HTTPS). Importantly, TMC does not require access to vantage points in the country. We apply TMC to 15.5M domains, our results reveal that Turkmenistan censors more than 122K domains, using different blocklists for each protocol. We also reverse-engineer these censored domains, identifying 6K over-blocking rules causing incidental filtering of more than 5.4M domains. Finally, we use Geneva, an open-source censorship evasion tool, to discover five new censorship evasion strategies that can defeat Turkmenistan's censorship at both transport and application layers. We will publicly release both the data collected by TMC and the code for censorship evasion.

cs.CR↗

arXiv2023

When Brain-inspired AI Meets AGI

Artificial General Intelligence (AGI) has been a long-standing goal of humanity, with the aim of creating machines capable of performing any intellectual task that humans can do. To achieve this, AGI researchers draw inspiration from the human brain and seek to replicate its principles in intelligent machines. Brain-inspired artificial intelligence is a field that has emerged from this endeavor, combining insights from neuroscience, psychology, and computer science to develop more efficient and powerful AI systems. In this article, we provide a comprehensive overview of brain-inspired AI from the perspective of AGI. We begin with the current progress in brain-inspired AI and its extensive connection with AGI. We then cover the important characteristics for both human intelligence and AGI (e.g., scaling, multimodality, and reasoning). We discuss important technologies toward achieving AGI in current AI systems, such as in-context learning and prompt tuning. We also investigate the evolution of AGI systems from both algorithmic and infrastructural perspectives. Finally, we explore the limitations and future of AGI.

cs.AI↗

arXiv2023

Mask-guided BERT for Few Shot Text Classification

Transformer-based language models have achieved significant success in various domains. However, the data-intensive nature of the transformer architecture requires much labeled data, which is challenging in low-resource scenarios (i.e., few-shot learning (FSL)). The main challenge of FSL is the difficulty of training robust models on small amounts of samples, which frequently leads to overfitting. Here we present Mask-BERT, a simple and modular framework to help BERT-based architectures tackle FSL. The proposed approach fundamentally differs from existing FSL strategies such as prompt tuning and meta-learning. The core idea is to selectively apply masks on text inputs and filter out irrelevant information, which guides the model to focus on discriminative tokens that influence prediction results. In addition, to make the text representations from different categories more separable and the text representations from the same category more compact, we introduce a contrastive learning loss function. Experimental results on public-domain benchmark datasets demonstrate the effectiveness of Mask-BERT.

cs.CL↗

arXiv2023

AC-DC: Adaptive Ensemble Classification for Network Traffic Identification

Accurate and efficient network traffic classification is important for many network management tasks, from traffic prioritization to anomaly detection. Although classifiers using pre-computed flow statistics (e.g., packet sizes, inter-arrival times) can be efficient, they may experience lower accuracy than techniques based on raw traffic, including packet captures. Past work on representation learning-based classifiers applied to network traffic captures has shown to be more accurate, but slower and requiring considerable additional memory resources, due to the substantial costs in feature preprocessing. In this paper, we explore this trade-off and develop the Adaptive Constraint-Driven Classification (AC-DC) framework to efficiently curate a pool of classifiers with different target requirements, aiming to provide comparable classification performance to complex packet-capture classifiers while adapting to varying network traffic load. AC-DC uses an adaptive scheduler that tracks current system memory availability and incoming traffic rates to determine the optimal classifier and batch size to maximize classification performance given memory and processing constraints. Our evaluation shows that AC-DC improves classification performance by more than 100% compared to classifiers that rely on flow statistics alone; compared to the state-of-the-art packet-capture classifiers, AC-DC achieves comparable performance (less than 12.3% lower in F1-Score), but processes traffic over 150x faster.

cs.NI↗

arXiv2022

Automating Internet of Things Network Traffic Collection with Robotic Arm Interactions

Consumer Internet of things research often involves collecting network traffic sent or received by IoT devices. These data are typically collected via crowdsourcing or while researchers manually interact with IoT devices in a laboratory setting. However, manual interactions and crowdsourcing are often tedious, expensive, inaccurate, or do not provide comprehensive coverage of possible IoT device behaviors. We present a new method for generating IoT network traffic using a robotic arm to automate user interactions with devices. This eliminates manual button pressing and enables permutation-based interaction sequences that rigorously explore the range of possible device behaviors. We test this approach with an Arduino-controlled robotic arm, a smart speaker, and a smart thermostat, using machine learning to demonstrate that collected network traffic contains information about device interactions that could be useful for network, security, or privacy analyses. We also provide source code and documentation allowing researchers to easily automate IoT device interactions and network traffic collection in future studies.

cs.NI↗

arXiv2022

Identification of the anomalous fast bulk events in a p-type point contact germanium detector

The ultralow detection threshold, ultralow intrinsic background, and excellent energy resolution of p-type point-contact germanium detector are important for rare-event searches, in particular for the detection of direct dark matter interactions, coherent elastic neutrino-nucleus scattering, and neutrinoless double beta decay. Anomalous bulk events with an extremely fast rise time are observed in the CDEX-1B detector. We report a method of extracting fast bulk events from bulk events using a pulse shape simulation and reconstructed source experiment signature. Calibration data and the distribution of X-rays generated by intrinsic radioactivity verified that the fast bulk experienced a single hit near the passivation layer. The performance of this germanium detector indicates that it is capable of single-hit bulk spatial resolution and thus provides a background removal technique.

physics.ins-det↗

arXiv2022

Coupling Visual Semantics of Artificial Neural Networks and Human Brain Function via Synchronized Activations

Artificial neural networks (ANNs), originally inspired by biological neural networks (BNNs), have achieved remarkable successes in many tasks such as visual representation learning. However, whether there exists semantic correlations/connections between the visual representations in ANNs and those in BNNs remains largely unexplored due to both the lack of an effective tool to link and couple two different domains, and the lack of a general and effective framework of representing the visual semantics in BNNs such as human functional brain networks (FBNs). To answer this question, we propose a novel computational framework, Synchronized Activations (Sync-ACT), to couple the visual representation spaces and semantics between ANNs and BNNs in human brain based on naturalistic functional magnetic resonance imaging (nfMRI) data. With this approach, we are able to semantically annotate the neurons in ANNs with biologically meaningful description derived from human brain imaging for the first time. We evaluated the Sync-ACT framework on two publicly available movie-watching nfMRI datasets. The experiments demonstrate a) the significant correlation and similarity of the semantics between the visual representations in FBNs and those in a variety of convolutional neural networks (CNNs) models; b) the close relationship between CNN's visual representation similarity to BNNs and its performance in image classification tasks. Overall, our study introduces a general and effective paradigm to couple the ANNs and BNNs and provides novel insights for future studies such as brain-inspired artificial intelligence.

cs.CV↗

arXiv2022

Rectify ViT Shortcut Learning by Visual Saliency

Shortcut learning is common but harmful to deep learning models, leading to degenerated feature representations and consequently jeopardizing the model's generalizability and interpretability. However, shortcut learning in the widely used Vision Transformer framework is largely unknown. Meanwhile, introducing domain-specific knowledge is a major approach to rectifying the shortcuts, which are predominated by background related factors. For example, in the medical imaging field, eye-gaze data from radiologists is an effective human visual prior knowledge that has the great potential to guide the deep learning models to focus on meaningful foreground regions of interest. However, obtaining eye-gaze data is time-consuming, labor-intensive and sometimes even not practical. In this work, we propose a novel and effective saliency-guided vision transformer (SGT) model to rectify shortcut learning in ViT with the absence of eye-gaze data. Specifically, a computational visual saliency model is adopted to predict saliency maps for input image samples. Then, the saliency maps are used to distil the most informative image patches. In the proposed SGT, the self-attention among image patches focus only on the distilled informative ones. Considering this distill operation may lead to global information lost, we further introduce, in the last encoder layer, a residual connection that captures the self-attention across all the image patches. The experiment results on four independent public datasets show that our SGT framework can effectively learn and leverage human prior knowledge without eye gaze data and achieves much better performance than baselines. Meanwhile, it successfully rectifies the harmful shortcut learning and significantly improves the interpretability of the ViT model, demonstrating the promise of transferring human prior knowledge derived visual saliency in rectifying shortcut learning

cs.CV↗

arXiv2022

Eye-gaze-guided Vision Transformer for Rectifying Shortcut Learning

Learning harmful shortcuts such as spurious correlations and biases prevents deep neural networks from learning the meaningful and useful representations, thus jeopardizing the generalizability and interpretability of the learned representation. The situation becomes even more serious in medical imaging, where the clinical data (e.g., MR images with pathology) are limited and scarce while the reliability, generalizability and transparency of the learned model are highly required. To address this problem, we propose to infuse human experts' intelligence and domain knowledge into the training of deep neural networks. The core idea is that we infuse the visual attention information from expert radiologists to proactively guide the deep model to focus on regions with potential pathology and avoid being trapped in learning harmful shortcuts. To do so, we propose a novel eye-gaze-guided vision transformer (EG-ViT) for diagnosis with limited medical image data. We mask the input image patches that are out of the radiologists' interest and add an additional residual connection in the last encoder layer of EG-ViT to maintain the correlations of all patches. The experiments on two public datasets of INbreast and SIIM-ACR demonstrate our EG-ViT model can effectively learn/transfer experts' domain knowledge and achieve much better performance than baselines. Meanwhile, it successfully rectifies the harmful shortcut learning and significantly improves the EG-ViT model's interpretability. In general, EG-ViT takes the advantages of both human expert's prior knowledge and the power of deep neural networks. This work opens new avenues for advancing current artificial intelligence paradigms by infusing human intelligence.

cs.CV↗

arXiv2022

Mask-guided Vision Transformer (MG-ViT) for Few-Shot Learning

Learning with little data is challenging but often inevitable in various application scenarios where the labeled data is limited and costly. Recently, few-shot learning (FSL) gained increasing attention because of its generalizability of prior knowledge to new tasks that contain only a few samples. However, for data-intensive models such as vision transformer (ViT), current fine-tuning based FSL approaches are inefficient in knowledge generalization and thus degenerate the downstream task performances. In this paper, we propose a novel mask-guided vision transformer (MG-ViT) to achieve an effective and efficient FSL on ViT model. The key idea is to apply a mask on image patches to screen out the task-irrelevant ones and to guide the ViT to focus on task-relevant and discriminative patches during FSL. Particularly, MG-ViT only introduces an additional mask operation and a residual connection, enabling the inheritance of parameters from pre-trained ViT without any other cost. To optimally select representative few-shot samples, we also include an active learning based sample selection method to further improve the generalizability of MG-ViT based FSL. We evaluate the proposed MG-ViT on both Agri-ImageNet classification task and ACFR apple detection task with gradient-weighted class activation mapping (Grad-CAM) as the mask. The experimental results show that the MG-ViT model significantly improves the performance when compared with general fine-tuning based ViT models, providing novel insights and a concrete approach towards generalizing data-intensive and large-scale deep learning models for FSL.

cs.CV↗

arXiv2022

A Unified and Biologically-Plausible Relational Graph Representation of Vision Transformers

Vision transformer (ViT) and its variants have achieved remarkable successes in various visual tasks. The key characteristic of these ViT models is to adopt different aggregation strategies of spatial patch information within the artificial neural networks (ANNs). However, there is still a key lack of unified representation of different ViT architectures for systematic understanding and assessment of model representation performance. Moreover, how those well-performing ViT ANNs are similar to real biological neural networks (BNNs) is largely unexplored. To answer these fundamental questions, we, for the first time, propose a unified and biologically-plausible relational graph representation of ViT models. Specifically, the proposed relational graph representation consists of two key sub-graphs: aggregation graph and affine graph. The former one considers ViT tokens as nodes and describes their spatial interaction, while the latter one regards network channels as nodes and reflects the information communication between channels. Using this unified relational graph representation, we found that: a) a sweet spot of the aggregation graph leads to ViTs with significantly improved predictive performance; b) the graph measures of clustering coefficient and average path length are two effective indicators of model prediction performance, especially when applying on the datasets with small samples; c) our findings are consistent across various ViT architectures and multiple datasets; d) the proposed relational graph representation of ViT has high similarity with real BNNs derived from brain science data. Overall, our work provides a novel unified and biologically-plausible paradigm for more interpretable and effective representation of ViT ANNs.

cs.NE↗

arXiv2022

LAST: Latent Space Assisted Adaptive Sampling for Protein Trajectories

Molecular dynamics (MD) simulation is widely used to study protein conformations and dynamics. However, conventional simulation suffers from being trapped in some local energy minima that are hard to escape. Thus, most computational time is spent sampling in the already visited regions. This leads to an inefficient sampling process and further hinders the exploration of protein movements in affordable simulation time. The advancement of deep learning provides new opportunities for protein sampling. Variational autoencoders are a class of deep learning models to learn a low-dimensional representation (referred to as the latent space) that can capture the key features of the input data. Based on this characteristic, we proposed a new adaptive sampling method, latent space assisted adaptive sampling for protein trajectories (LAST), to accelerate the exploration of protein conformational space. This method comprises cycles of (i) variational autoencoders training, (ii) seed structure selection on the latent space and (iii) conformational sampling through additional MD simulations. The proposed approach is validated through the sampling of four structures of two protein systems: two metastable states of E. Coli adenosine kinase (ADK) and two native states of Vivid (VVD). In all four conformations, seed structures were shown to lie on the boundary of conformation distributions. Moreover, large conformational changes were observed in a shorter simulation time when compared with conventional MD (cMD) simulations in both systems. In metastable ADK simulations, LAST explored two transition paths toward two stable states while cMD became trapped in an energy basin. In VVD light state simulations, LAST was three times faster than cMD simulation with a similar conformational space.

q-bio.QM↗