Hang Dong

Ren Yang, Radu Timofte, Meisong Zheng et al. · tencent-ai

This paper reviews the NTIRE 2022 Challenge on Super-Resolution and Quality Enhancement of Compressed Video. In this challenge, we proposed the LDV 2.0 dataset, which includes the LDV dataset (240 videos) and 95 additional videos. This challenge includes three tracks. Track 1 aims at enhancing the videos compressed by HEVC at a fixed QP. Track 2 and Track 3 target both the super-resolution and quality enhancement of HEVC compressed video. They require x2 and x4 super-resolution, respectively. The three tracks totally attract more than 600 registrations. In the test phase, 8 teams, 8 teams and 12 teams submitted the final results to Tracks 1, 2 and 3, respectively. The proposed methods and solutions gauge the state-of-the-art of super-resolution and quality enhancement of compressed video. The proposed LDV 2.0 dataset is available at https://github.com/RenYang-home/LDV_dataset. The homepage of this challenge (including open-sourced codes) is at https://github.com/RenYang-home/NTIRE22_VEnh_SR.

Yuan He, Jiaoyan Chen, Ernesto Jiménez-Ruiz et al. · oxford

Investigating whether pre-trained language models (LMs) can function as knowledge bases (KBs) has raised wide research interests recently. However, existing works focus on simple, triple-based, relational KBs, but omit more sophisticated, logic-based, conceptualised KBs such as OWL ontologies. To investigate an LM's knowledge of ontologies, we propose OntoLAMA, a set of inference-based probing tasks and datasets from ontology subsumption axioms involving both atomic and complex concepts. We conduct extensive experiments on ontologies of different domains and scales, and our results demonstrate that LMs encode relatively less background knowledge of Subsumption Inference (SI) than traditional Natural Language Inference (NLI) but can improve on SI significantly when a small number of samples are given. We will open-source our code and datasets.

Yong Liu, Hang Dong, Boyang Liang et al.

Recent years have witnessed a few attempts of vision transformers for single image super-resolution (SISR). Since the high resolution of intermediate features in SISR models increases memory and computational requirements, efficient SISR transformers are more favored. Based on some popular transformer backbone, many methods have explored reasonable schemes to reduce the computational complexity of the self-attention module while achieving impressive performance. However, these methods only focus on the performance on the training platform (e.g., Pytorch/Tensorflow) without further optimization for the deployment platform (e.g., TensorRT). Therefore, they inevitably contain some redundant operators, posing challenges for subsequent deployment in real-world applications. In this paper, we propose a deployment-friendly transformer unit, namely UFONE (i.e., UnFolding ONce is Enough), to alleviate these problems. In each UFONE, we introduce an Inner-patch Transformer Layer (ITL) to efficiently reconstruct the local structural information from patches and a Spatial-Aware Layer (SAL) to exploit the long-range dependencies between patches. Based on UFONE, we propose a Deployment-friendly Inner-patch Transformer Network (DITN) for the SISR task, which can achieve favorable performance with low latency and memory usage on both training and deployment platforms. Furthermore, to further boost the deployment efficiency of the proposed DITN on TensorRT, we also provide an efficient substitution for layer normalization and propose a fusion optimization strategy for specific operators. Extensive experiments show that our models can achieve competitive results in terms of qualitative and quantitative performance with high deployment efficiency. Code is available at \url{https://github.com/yongliuy/DITN}.

Wenhui Ren, Weikang Li, Shibo Xu et al. · tsinghua

Quantum computing promises to enhance machine learning and artificial intelligence. Different quantum algorithms have been proposed to improve a wide spectrum of machine learning tasks. Yet, recent theoretical works show that, similar to traditional classifiers based on deep classical neural networks, quantum classifiers would suffer from the vulnerability problem: adding tiny carefully-crafted perturbations to the legitimate original data samples would facilitate incorrect predictions at a notably high confidence level. This will pose serious problems for future quantum machine learning applications in safety and security-critical scenarios. Here, we report the first experimental demonstration of quantum adversarial learning with programmable superconducting qubits. We train quantum classifiers, which are built upon variational quantum circuits consisting of ten transmon qubits featuring average lifetimes of 150 $μ$s, and average fidelities of simultaneous single- and two-qubit gates above 99.94% and 99.4% respectively, with both real-life images (e.g., medical magnetic resonance imaging scans) and quantum data. We demonstrate that these well-trained classifiers (with testing accuracy up to 99%) can be practically deceived by small adversarial perturbations, whereas an adversarial training process would significantly enhance their robustness to such perturbations. Our results reveal experimentally a crucial vulnerability aspect of quantum learning systems under adversarial scenarios and demonstrate an effective defense strategy against adversarial attacks, which provide a valuable guide for quantum artificial intelligence applications with both near-term and future quantum devices.

Yuan He, Jiaoyan Chen, Hang Dong et al. · oxford

This work investigates the applicability of recent generative Large Language Models (LLMs), such as the GPT series and Flan-T5, to ontology alignment for identifying concept equivalence mappings across ontologies. To test the zero-shot performance of Flan-T5-XXL and GPT-3.5-turbo, we leverage challenging subsets from two equivalence matching datasets of the OAEI Bio-ML track, taking into account concept labels and structural contexts. Preliminary findings suggest that LLMs have the potential to outperform existing ontology alignment systems like BERTMap, given careful framework and prompt design.

Yuan He, Jiaoyan Chen, Hang Dong et al. · oxford

Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation of OM systems, it still suffers from several limitations including limited evaluation of subsumption mappings, suboptimal reference mappings, and limited support for the evaluation of ML-based systems. To tackle these limitations, we introduce five new biomedical OM tasks involving ontologies extracted from Mondo and UMLS. Each task includes both equivalence and subsumption matching; the quality of reference mappings is ensured by human curation, ontology pruning, etc.; and a comprehensive evaluation framework is proposed to measure OM performance from various perspectives for both ML-based and non-ML-based OM systems. We report evaluation results for OM systems of different types to demonstrate the usage of these resources, all of which are publicly available as part of the new BioML track at OAEI 2022.

Yuan He, Jiaoyan Chen, Hang Dong et al. · oxford

Integrating deep learning techniques, particularly language models (LMs), with knowledge representation techniques like ontologies has raised widespread attention, urging the need of a platform that supports both paradigms. Although packages such as OWL API and Jena offer robust support for basic ontology processing features, they lack the capability to transform various types of information within ontologies into formats suitable for downstream deep learning-based applications. Moreover, widely-used ontology APIs are primarily Java-based while deep learning frameworks like PyTorch and Tensorflow are mainly for Python programming. To address the needs, we present DeepOnto, a Python package designed for ontology engineering with deep learning. The package encompasses a core ontology processing module founded on the widely-recognised and reliable OWL API, encapsulating its fundamental features in a more "Pythonic" manner and extending its capabilities to incorporate other essential components including reasoning, verbalisation, normalisation, taxonomy, projection, and more. Building on this module, DeepOnto offers a suite of tools, resources, and algorithms that support various ontology engineering tasks, such as ontology alignment and completion, by harnessing deep learning methods, primarily pre-trained LMs. In this paper, we also demonstrate the practical utility of DeepOnto through two use-cases: the Digital Health Coaching in Samsung Research UK and the Bio-ML track of the Ontology Alignment Evaluation Initiative (OAEI).

Bo Qiao, Liqun Li, Xu Zhang et al.

Large Language Models (LLMs) have shown impressive abilities in natural language understanding and generation, leading to their widespread use in applications such as chatbots and virtual assistants. However, existing LLM frameworks face limitations in handling domain-specific data analytics tasks with rich data structures. Moreover, they struggle with flexibility to meet diverse user requirements. To address these issues, TaskWeaver is proposed as a code-first framework for building LLM-powered autonomous agents. It converts user requests into executable code and treats user-defined plugins as callable functions. TaskWeaver provides support for rich data structures, flexible plugin usage, and dynamic plugin selection, and leverages LLM coding capabilities for complex logic. It also incorporates domain-specific knowledge through examples and ensures the secure execution of generated code. TaskWeaver offers a powerful and flexible framework for creating intelligent conversational agents that can handle complex tasks and adapt to domain-specific scenarios. The code is open sourced at https://github.com/microsoft/TaskWeaver/.

David Oniani, Jordan Hilsman, Hang Dong et al. · oxford

The emergence of generative Large Language Models (LLMs) emphasizes the need for accurate and efficient prompting approaches. LLMs are often applied in Few-Shot Learning (FSL) contexts, where tasks are executed with minimal training data. FSL has become popular in many Artificial Intelligence (AI) subdomains, including AI for health. Rare diseases affect a small fraction of the population. Rare disease identification from clinical notes inherently requires FSL techniques due to limited data availability. Manual data collection and annotation is both expensive and time-consuming. In this paper, we propose Models-Vote Prompting (MVP), a flexible prompting approach for improving the performance of LLM queries in FSL settings. MVP works by prompting numerous LLMs to perform the same tasks and then conducting a majority vote on the resulting outputs. This method achieves improved results to any one model in the ensemble on one-shot rare disease identification and classification tasks. We also release a novel rare disease dataset for FSL, available to those who signed the MIMIC-IV Data Use Agreement (DUA). Furthermore, in using MVP, each model is prompted multiple times, substantially increasing the time needed for manual annotation, and to address this, we assess the feasibility of using JSON for automating generative LLM evaluation.

Zhangchi Zhu, Lu Wang, Pu Zhao et al.

Learning from positive and unlabeled data is known as positive-unlabeled (PU) learning in literature and has attracted much attention in recent years. One common approach in PU learning is to sample a set of pseudo-negatives from the unlabeled data using ad-hoc thresholds so that conventional supervised methods can be applied with both positive and negative samples. Owing to the label uncertainty among the unlabeled data, errors of misclassifying unlabeled positive samples as negative samples inevitably appear and may even accumulate during the training processes. Those errors often lead to performance degradation and model instability. To mitigate the impact of label uncertainty and improve the robustness of learning with positive and unlabeled data, we propose a new robust PU learning method with a training strategy motivated by the nature of human learning: easy cases should be learned first. Similar intuition has been utilized in curriculum learning to only use easier cases in the early stage of training before introducing more complex cases. Specifically, we utilize a novel ``hardness'' measure to distinguish unlabeled samples with a high chance of being negative from unlabeled samples with large label noise. An iterative training strategy is then implemented to fine-tune the selection of negative samples during the training process in an iterative manner to include more ``easy'' samples in the early stage of training. Extensive experimental validations over a wide range of learning tasks show that this approach can effectively improve the accuracy and stability of learning with positive and unlabeled data. Our code is available at https://github.com/woriazzc/Robust-PU

Hang Dong, Jiaoyan Chen, Yuan He et al. · oxford

Discovering entity mentions that are out of a Knowledge Base (KB) from texts plays a critical role in KB maintenance, but has not yet been fully explored. The current methods are mostly limited to the simple threshold-based approach and feature-based classification, and the datasets for evaluation are relatively rare. We propose BLINKout, a new BERT-based Entity Linking (EL) method which can identify mentions that do not have corresponding KB entities by matching them to a special NIL entity. To better utilize BERT, we propose new techniques including NIL entity representation and classification, with synonym enhancement. We also apply KB Pruning and Versioning strategies to automatically construct out-of-KB datasets from common in-KB EL datasets. Results on five datasets of clinical notes, biomedical publications, and Wikipedia articles in various domains show the advantages of BLINKout over existing methods to identify out-of-KB mentions for the medical ontologies, UMLS, SNOMED CT, and the general KB, WikiData.

Hang Dong, Jiaoyan Chen, Yuan He et al. · oxford

Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a new concept is pre-discovered and cannot support out-of-KB mention discovery; (ii) only using the concept label as the input along with the KB and thus lacking the contexts of a concept label; and (iii) mostly focusing on concept placement w.r.t a taxonomy of atomic concepts, instead of complex concepts, i.e., with logical operators. To address these issues, we propose a new benchmark, adapting MedMentions dataset (PubMed abstracts) with SNOMED CT versions in 2014 and 2017 under the Diseases sub-category and the broader categories of Clinical finding, Procedure, and Pharmaceutical / biologic product. We provide usage on the evaluation with the dataset for out-of-KB mention discovery and concept placement, adapting recent Large Language Model based methods.

Yuhao Huang, Hang Dong, Jinshan Pan et al.

The success of existing video super-resolution (VSR) algorithms stems mainly exploiting the temporal information from the neighboring frames. However, none of these methods have discussed the influence of the temporal redundancy in the patches with stationary objects and background and usually use all the information in the adjacent frames without any discrimination. In this paper, we observe that the temporal redundancy will bring adverse effect to the information propagation,which limits the performance of the most existing VSR methods. Motivated by this observation, we aim to improve existing VSR algorithms by handling the temporal redundancy patches in an optimized manner. We develop two simple yet effective plug and play methods to improve the performance of existing local and non-local propagation-based VSR algorithms on widely-used public videos. For more comprehensive evaluating the robustness and performance of existing VSR algorithms, we also collect a new dataset which contains a variety of public videos as testing set. Extensive evaluations show that the proposed methods can significantly improve the performance of existing VSR methods on the collected videos from wild scenarios while maintain their performance on existing commonly used datasets. The code is available at https://github.com/HYHsimon/Boosted-VSR.

Hang Dong, Víctor Suárez-Paniagua, Huayu Zhang et al. · oxford

Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts. We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-based framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations. The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes). We discuss the usefulness of the weak supervision approach and propose directions for future studies.

Hang Dong, Matúš Falis, William Whiteley et al.

Clinical coding is the task of transforming medical information in a patient's health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on the literature, our project experience over the past two and half years (late 2019 - early 2022), and discussions with clinical coding experts in Scotland and the UK. Our research reveals the gaps between the current deep learning-based approach applied to clinical coding and the need for explainability and consistency in real-world practice. Knowledge-based methods that represent and reason the standard, explainable process of a task may need to be incorporated into deep learning-based methods for clinical coding. Automated clinical coding is a promising task for AI, despite the technical and organisational challenges. Coders are needed to be involved in the development process. There is much to achieve to develop and deploy an AI-based automated system to support coding in the next five years and beyond.

Junjie Sheng, Lu Wang, Fangkai Yang et al.

Oversubscription is a common practice for improving cloud resource utilization. It allows the cloud service provider to sell more resources than the physical limit, assuming not all users would fully utilize the resources simultaneously. However, how to design an oversubscription policy that improves utilization while satisfying the some safety constraints remains an open problem. Existing methods and industrial practices are over-conservative, ignoring the coordination of diverse resource usage patterns and probabilistic constraints. To address these two limitations, this paper formulates the oversubscription for cloud as a chance-constrained optimization problem and propose an effective Chance Constrained Multi-Agent Reinforcement Learning (C2MARL) method to solve this problem. Specifically, C2MARL reduces the number of constraints by considering their upper bounds and leverages a multi-agent reinforcement learning paradigm to learn a safe and optimal coordination policy. We evaluate our C2MARL on an internal cloud platform and public cloud datasets. Experiments show that our C2MARL outperforms existing methods in improving utilization ($20\%\sim 86\%$) under different levels of safety constraints.

Qingyu Chen, Alexis Allot, Robert Leaman et al.

The COVID-19 pandemic has been severely impacting global society since December 2019. Massive research has been undertaken to understand the characteristics of the virus and design vaccines and drugs. The related findings have been reported in biomedical literature at a rate of about 10,000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200,000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g., Diagnosis and Treatment) to the articles in LitCovid. Despite the continuing advances in biomedical text mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset, consisting of over 30,000 articles with manually reviewed topics, was created for training and testing. It is one of the largest multilabel classification datasets in biomedical scientific literature. 19 teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181, and 0.9394 for macro F1-score, micro F1-score, and instance-based F1-score, respectively. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development.

Jiaoyan Chen, Hang Dong, Janna Hastings et al.

The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.

Lihao Sun, Hang Dong, Bo Qiao et al.

This work characterizes large language models' chain-of-thought generation as a structured trajectory through representation space. We show that mathematical reasoning traverses functionally ordered, step-specific subspaces that become increasingly separable with layer depth. This structure already exists in base models, while reasoning training primarily accelerates convergence toward termination-related subspaces rather than introducing new representational organization. While early reasoning steps follow similar trajectories, correct and incorrect solutions diverge systematically at late stages. This late-stage divergence enables mid-reasoning prediction of final-answer correctness with ROC-AUC up to 0.87. Furthermore, we introduce trajectory-based steering, an inference-time intervention framework that enables reasoning correction and length control based on derived ideal trajectories. Together, these results establish reasoning trajectories as a geometric lens for interpreting, predicting, and controlling LLM reasoning behavior.

Xiangguo Sun, Hong Cheng, Hang Dong et al.

Scoring systems are commonly seen for platforms in the era of big data. From credit scoring systems in financial services to membership scores in E-commerce shopping platforms, platform managers use such systems to guide users towards the encouraged activity pattern, and manage resources more effectively and more efficiently thereby. To establish such scoring systems, several "empirical criteria" are firstly determined, followed by dedicated top-down design for each factor of the score, which usually requires enormous effort to adjust and tune the scoring function in the new application scenario. What's worse, many fresh projects usually have no ground-truth or any experience to evaluate a reasonable scoring system, making the designing even harder. To reduce the effort of manual adjustment of the scoring function in every new scoring system, we innovatively study the scoring system from the preset empirical criteria without any ground truth, and propose a novel framework to improve the system from scratch. In this paper, we propose a "counter-empirical attacking" mechanism that can generate "attacking" behavior traces and try to break the empirical rules of the scoring system. Then an adversarial "enhancer" is applied to evaluate the scoring system and find the improvement strategy. By training the adversarial learning problem, a proper scoring function can be learned to be robust to the attacking activity traces that are trying to violate the empirical criteria. Extensive experiments have been conducted on two scoring systems including a shared computing resource platform and a financial credit system. The experimental results have validated the effectiveness of our proposed framework.

Qingji Dong, Hang Dong, Mingqin Chen et al.

Large-scale pre-trained diffusion models have been extensively adopted for real-world image Super-Resolution because of their powerful generative priors through textual guidance. However, when super-resolving high-resolution images with patch-wise inference strategy, most existing diffusion-based SR methods tend to suffer from over-generation, due to the misalignment between the global prompt from LR image and the incomplete semantic information of local patches during each inference step. On the other hand, most existing methods also failed to generate detailed texture in local patches due to the overemphasis on global generation capabilities in network designs and training strategies. To address this issue, we present DreamSR, a novel SR model that suppresses local over-generation and improves fine-detail synthesis, thereby achieving visually faithful results with ultra-high-quality details. Specifically, we propose a dual-branch MM-ControlNet, where the ControlNet generates local textual feature with patch-level prompts while the pre-trained DiT provides global textual feature with global prompts, thereby mitigating over-generation and ensuring semantic consistency across patches. We also design a comprehensive training strategy with stage-specific data processing pipelines and a Receptive-Field Enhancement strategy, enhancing the model's capability to capture patch information and effectively restore local textures. Extensive experiments demonstrate that DreamSR outperforms state-of-the-art methods, providing high-quality SR results. Code and model are available at https://github.com/jerrydong0219/DreamSR.

Chao Zhu, Hang Dong, Jinshan Pan et al.

The success of the state-of-the-art video deblurring methods stems mainly from implicit or explicit estimation of alignment among the adjacent frames for latent video restoration. However, due to the influence of the blur effect, estimating the alignment information from the blurry adjacent frames is not a trivial task. Inaccurate estimations will interfere the following frame restoration. Instead of estimating alignment information, we propose a simple and effective deep Recurrent Neural Network with Multi-scale Bi-directional Propagation (RNN-MBP) to effectively propagate and gather the information from unaligned neighboring frames for better video deblurring. Specifically, we build a Multi-scale Bi-directional Propagation~(MBP) module with two U-Net RNN cells which can directly exploit the inter-frame information from unaligned neighboring hidden states by integrating them in different scales. Moreover, to better evaluate the proposed algorithm and existing state-of-the-art methods on real-world blurry scenes, we also create a Real-World Blurry Video Dataset (RBVD) by a well-designed Digital Video Acquisition System (DVAS) and use it as the training and evaluation dataset. Extensive experimental results demonstrate that the proposed RBVD dataset effectively improves the performance of existing algorithms on real-world blurry videos, and the proposed algorithm performs favorably against the state-of-the-art methods on three typical benchmarks. The code is available at https://github.com/XJTU-CVLAB-LOWLEVEL/RNN-MBP.

Arlene Casey, Emma Davidson, Michael Poon et al.

NLP has a significant role in advancing healthcare and has been found to be key in extracting structured information from radiology reports. Understanding recent developments in NLP application to radiology is of significance but recent reviews on this are limited. This study systematically assesses recent literature in NLP applied to radiology reports. Our automated literature search yields 4,799 results using automated filtering, metadata enriching steps and citation search combined with manual review. Our analysis is based on 21 variables including radiology characteristics, NLP methodology, performance, study, and clinical application characteristics. We present a comprehensive analysis of the 164 publications retrieved with each categorised into one of 6 clinical application categories. Deep learning use increases but conventional machine learning approaches are still prevalent. Deep learning remains challenged when data is scarce and there is little evidence of adoption into clinical practice. Despite 17% of studies reporting greater than 0.85 F1 scores, it is hard to comparatively evaluate these approaches given that most of them use different datasets. Only 14 studies made their data and 15 their code available with 10 externally validating results. Automated understanding of clinical narratives of the radiology reports has the potential to enhance the healthcare process but reproducibility and explainability of models are important if the domain is to move applications into clinical use. More could be done to share code enabling validation of methods on different institutional data and to reduce heterogeneity in reporting of study properties allowing inter-study comparisons. Our results have significance for researchers providing a systematic synthesis of existing work to build on, identify gaps, opportunities for collaboration and avoid duplication.

Jun Wang, Fengpeng Li, Hang Dong et al.

Remote sensing lithology interpretation is fundamental to geological surveys, mineral exploration, and regional geological mapping. Unlike general land-cover recognition, lithology interpretation is a knowledge-intensive task that requires experts to infer rock types from various features, e.g., subtle visual, spectral, textural, geomorphological, and contextual cues, making reliable automated interpretation highly challenging. Geological knowledge-guided large multimodal models offer new opportunities, yet their evaluation remains constrained by the lack of benchmarks that capture lithological annotations, multi-level geological semantics, and expert-informed assessment. Here, we propose LithoBench, a multi-level benchmark for evaluating geological semantic understanding in remote sensing lithology interpretation. LithoBench contains 10,000 expert-annotated interpretation instances across 12 representative lithological categories, including 4,000 multiple-choice and 6,000 open-ended tasks organized into five cognitive levels: Identification and Description, Comparative Analysis, Mechanism Explanation, Practical Application, and Comprehensive Reasoning. We further develop an expert-in-the-loop, knowledge-grounded semi-automated construction pipeline, coupling multi sub-processes, e.g., structured geological image descriptions, to enhance geological validity and evaluation reliability. Experiments with multiple large vision-language models eveal substantial limitations in geological semantic understanding, particularly on higher-order explanation, application, and reasoning tasks.

Jinge Wu, Hang Dong, Zexi Li et al.

Rare diseases pose significant challenges in diagnosis and treatment due to their low prevalence and heterogeneous clinical presentations. Unstructured clinical notes contain valuable information for identifying rare diseases, but manual curation is time-consuming and prone to subjectivity. This study aims to develop a hybrid approach combining dictionary-based natural language processing (NLP) tools with large language models (LLMs) to improve rare disease identification from unstructured clinical reports. We propose a novel hybrid framework that integrates the Orphanet Rare Disease Ontology (ORDO) and the Unified Medical Language System (UMLS) to create a comprehensive rare disease vocabulary. The proposed hybrid approach demonstrates superior performance compared to traditional NLP systems and standalone LLMs. Notably, the approach uncovers a significant number of potential rare disease cases not documented in structured diagnostic records, highlighting its ability to identify previously unrecognized patients.

Hang Dong, Jiaoyan Chen, Yuan He et al. · oxford

We investigate the task of inserting new concepts extracted from texts into an ontology using language models. We explore an approach with three steps: edge search which is to find a set of candidate locations to insert (i.e., subsumptions between concepts), edge formation and enrichment which leverages the ontological structure to produce and enhance the edge candidates, and edge selection which eventually locates the edge to be placed into. In all steps, we propose to leverage neural methods, where we apply embedding-based methods and contrastive learning with Pre-trained Language Models (PLMs) such as BERT for edge search, and adapt a BERT fine-tuning-based multi-label Edge-Cross-encoder, and Large Language Models (LLMs) such as GPT series, FLAN-T5, and Llama 2, for edge selection. We evaluate the methods on recent datasets created using the SNOMED CT ontology and the MedMentions entity linking benchmark. The best settings in our framework use fine-tuned PLM for search and a multi-label Cross-encoder for selection. Zero-shot prompting of LLMs is still not adequate for the task, and we propose explainable instruction tuning of LLMs for improved performance. Our study shows the advantages of PLMs and highlights the encouraging performance of LLMs that motivates future studies.

Dapeng Li, Hang Dong, Lu Wang et al.

In recent years, multi-agent reinforcement learning algorithms have made significant advancements in diverse gaming environments, leading to increased interest in the broader application of such techniques. To address the prevalent challenge of partial observability, communication-based algorithms have improved cooperative performance through the sharing of numerical embedding between agents. However, the understanding of the formation of collaborative mechanisms is still very limited, making designing a human-understandable communication mechanism a valuable problem to address. In this paper, we propose a novel multi-agent reinforcement learning algorithm that embeds large language models into agents, endowing them with the ability to generate human-understandable verbal communication. The entire framework has a message module and an action module. The message module is responsible for generating and sending verbal messages to other agents, effectively enhancing information sharing among agents. To further enhance the message module, we employ a teacher model to generate message labels from the global view and update the student model through Supervised Fine-Tuning (SFT). The action module receives messages from other agents and selects actions based on current local observations and received messages. Experiments conducted on the Overcooked game demonstrate our method significantly enhances the learning efficiency and performance of existing methods, while also providing an interpretable tool for humans to understand the process of multi-agent cooperation.

Lu Wang, Mayukh Das, Fangkai Yang et al.

We address the challenge of learning safe and robust decision policies in presence of uncertainty in context of the real scientific problem of adaptive resource oversubscription to enhance resource efficiency while ensuring safety against resource congestion risk. Traditional supervised prediction or forecasting models are ineffective in learning adaptive policies whereas standard online optimization or reinforcement learning is difficult to deploy on real systems. Offline methods such as imitation learning (IL) are ideal since we can directly leverage historical resource usage telemetry. But, the underlying aleatoric uncertainty in such telemetry is a critical bottleneck. We solve this with our proposed novel chance-constrained imitation learning framework, which ensures implicit safety against uncertainty in a principled manner via a combination of stochastic (chance) constraints on resource congestion risk and ensemble value functions. This leads to substantial ($\approx 3-4\times$) improvement in resource efficiency and safety in many oversubscription scenarios, including resource management in cloud services.

Austin Drake, Hang Dong

We present a novel architecture for safely integrating Large Language Models (LLMs) into interactive game engines, allowing players to "program" new behaviors using natural language. Our framework mitigates risks by using an LLM to translate commands into a constrained Domain-Specific Language (DSL), which configures a custom Entity-Component-System (ECS) at runtime. We evaluated this system in a 2D spell-crafting game prototype by experimentally assessing models from the Gemini, GPT, and Claude families with various prompting strategies. A validated LLM judge qualitatively rated the outputs, showing that while larger models better captured creative intent, the optimal prompting strategy is task-dependent: Chain-of-Thought improved creative alignment, while few-shot examples were necessary to generate more complex DSL scripts. This work offers a validated LLM-ECS pattern for emergent gameplay and a quantitative performance comparison for developers.

Boan Zhang, Hang Dong, Jiongge Zhang et al.

Traditional range-instantaneous Doppler (RID) methods for rigid-body target imaging often suffer from low resolution due to the limitations of time-frequency analysis (TFA). To address this challenge, our primary focus is on obtaining high resolution time-frequency representations (TFRs) from their low resolution counterparts. Recognizing that the curve features of TFRs are a specific type of texture feature, we argue that pre trained generative models such as Stable Diffusion (SD) are well suited for enhancing TFRs, thanks to their powerful capability in capturing texture representations. Building on this insight, we propose a novel inverse synthetic aperture radar (ISAR) imaging method for rigid-body targets, leveraging the low-rank adaptation (LoRA) of a pre-trained SD model. Our approach adopts the basic structure and pre-trained parameters of SD Turbo while incorporating additional linear operations for LoRA and adversarial training to achieve super-resolution and noise suppression. Then we integrate LoRA-SD into the RID-based ISAR imaging, enabling sharply focused and denoised imaging with super-resolution capabilities. We evaluate our method using both simulated and real radar data. The experimental results demonstrate the superiority of our approach in frequency es timation and ISAR imaging compared to traditional methods. Notably, the generalization capability is verified by training on simulated radar data and testing on measured radar data.

Ke Wang, Weikang Li, Shibo Xu et al.

Quantum nonlocality describes a stronger form of quantum correlation than that of entanglement. It refutes Einstein's belief of local realism and is among the most distinctive and enigmatic features of quantum mechanics. It is a crucial resource for achieving quantum advantages in a variety of practical applications, ranging from cryptography and certified random number generation via self-testing to machine learning. Nevertheless, the detection of nonlocality, especially in quantum many-body systems, is notoriously challenging. Here, we report an experimental certification of genuine multipartite Bell correlations, which signal nonlocality in quantum many-body systems, up to 24 qubits with a fully programmable superconducting quantum processor. In particular, we employ energy as a Bell correlation witness and variationally decrease the energy of a many-body system across a hierarchy of thresholds, below which an increasing Bell correlation depth can be certified from experimental data. As an illustrating example, we variationally prepare the low-energy state of a two-dimensional honeycomb model with 73 qubits and certify its Bell correlations by measuring an energy that surpasses the corresponding classical bound with up to 48 standard deviations. In addition, we variationally prepare a sequence of low-energy states and certify their genuine multipartite Bell correlations up to 24 qubits via energies measured efficiently by parity oscillation and multiple quantum coherence techniques. Our results establish a viable approach for preparing and certifying multipartite Bell correlations, which provide not only a finer benchmark beyond entanglement for quantum devices, but also a valuable guide towards exploiting multipartite Bell correlation in a wide spectrum of practical applications.

Hang Dong, Liwen Zhu, Zhao Shan et al.

Efficient resource utilization and perfect user experience usually conflict with each other in cloud computing platforms. Great efforts have been invested in increasing resource utilization but trying not to affect users' experience for cloud computing platforms. In order to better utilize the remaining pieces of computing resources spread over the whole platform, deferrable jobs are provided with a discounted price to users. For this type of deferrable jobs, users are allowed to submit jobs that will run for a specific uninterrupted duration in a flexible range of time in the future with a great discount. With these deferrable jobs to be scheduled under the remaining capacity after deploying those on-demand jobs, it remains a challenge to achieve high resource utilization and meanwhile shorten the waiting time for users as much as possible in an online manner. In this paper, we propose an online deferrable job scheduling method called \textit{Online Scheduling for DEferrable jobs in Cloud} (\OSDEC{}), where a deep reinforcement learning model is adopted to learn the scheduling policy, and several auxiliary tasks are utilized to provide better state representations and improve the performance of the model. With the integrated reinforcement learning framework, the proposed method can well plan the deployment schedule and achieve a short waiting time for users while maintaining a high resource utilization for the platform. The proposed method is validated on a public dataset and shows superior performance.

Matúš Falis, Aryo Pradipta Gema, Hang Dong et al.

Objective: To investigate GPT-3.5 in generating and coding medical documents with ICD-10 codes for data augmentation on low-resources labels. Materials and Methods: Employing GPT-3.5 we generated and coded 9,606 discharge summaries based on lists of ICD-10 code descriptions of patients with infrequent (generation) codes within the MIMIC-IV dataset. Combined with the baseline training set, this formed an augmented training set. Neural coding models were trained on baseline and augmented data and evaluated on a MIMIC-IV test set. We report micro- and macro-F1 scores on the full codeset, generation codes, and their families. Weak Hierarchical Confusion Matrices were employed to determine within-family and outside-of-family coding errors in the latter codesets. The coding performance of GPT-3.5 was evaluated both on prompt-guided self-generated data and real MIMIC-IV data. Clinical professionals evaluated the clinical acceptability of the generated documents. Results: Augmentation slightly hinders the overall performance of the models but improves performance for the generation candidate codes and their families, including one unseen in the baseline training data. Augmented models display lower out-of-family error rates. GPT-3.5 can identify ICD-10 codes by the prompted descriptions, but performs poorly on real data. Evaluators note the correctness of generated concepts while suffering in variety, supporting information, and narrative. Discussion and Conclusion: GPT-3.5 alone is unsuitable for ICD-10 coding. Augmentation positively affects generation code families but mainly benefits codes with existing examples. Augmentation reduces out-of-family errors. Discharge summaries generated by GPT-3.5 state prompted concepts correctly but lack variety, and authenticity in narratives. They are unsuitable for clinical practice.

Liting Chen, Lu Wang, Hang Dong et al.

The emergence of large language models (LLMs) has substantially influenced natural language processing, demonstrating exceptional results across various tasks. In this study, we employ ``Introspective Tips" to facilitate LLMs in self-optimizing their decision-making. By introspectively examining trajectories, LLM refines its policy by generating succinct and valuable tips. Our method enhances the agent's performance in both few-shot and zero-shot learning situations by considering three essential scenarios: learning from the agent's past experiences, integrating expert demonstrations, and generalizing across diverse games. Importantly, we accomplish these improvements without fine-tuning the LLM parameters; rather, we adjust the prompt to generalize insights from the three aforementioned situations. Our framework not only supports but also emphasizes the advantage of employing LLM in in-contxt decision-making. Experiments involving over 100 games in TextWorld illustrate the superior performance of our approach.

Jiaoyan Chen, Yuan He, Yuxia Geng et al.

Automating ontology construction and curation is an important but challenging task in knowledge engineering and artificial intelligence. Prediction by machine learning techniques such as contextual semantic embedding is a promising direction, but the relevant research is still preliminary especially for expressive ontologies in Web Ontology Language (OWL). In this paper, we present a new subsumption prediction method named BERTSubs for classes of OWL ontology. It exploits the pre-trained language model BERT to compute contextual embeddings of a class, where customized templates are proposed to incorporate the class context (e.g., neighbouring classes) and the logical existential restriction. BERTSubs is able to predict multiple kinds of subsumers including named classes from the same ontology or another ontology, and existential restrictions from the same ontology. Extensive evaluation on five real-world ontologies for three different subsumption tasks has shown the effectiveness of the templates and that BERTSubs can dramatically outperform the baselines that use (literal-aware) knowledge graph embeddings, non-contextual word embeddings and the state-of-the-art OWL ontology embeddings.

Shaoxiong Ji, Wei Sun, Xiaobo Li et al.

Automated medical coding, an essential task for healthcare operation and delivery, makes unstructured data manageable by predicting medical codes from clinical documents. Recent advances in deep learning and natural language processing have been widely applied to this task. However, deep learning-based medical coding lacks a unified view of the design of neural network architectures. This review proposes a unified framework to provide a general understanding of the building blocks of medical coding models and summarizes recent advanced models under the proposed framework. Our unified framework decomposes medical coding into four main components, i.e., encoder modules for text feature extraction, mechanisms for building deep encoder architectures, decoder modules for transforming hidden representations into medical codes, and the usage of auxiliary information. Finally, we introduce the benchmarks and real-world usage and discuss key research challenges and future directions.

Matúš Falis, Hang Dong, Alexandra Birch et al.

Large-Scale Multi-Label Text Classification (LMTC) includes tasks with hierarchical label spaces, such as automatic assignment of ICD-9 codes to discharge summaries. Performance of models in prior art is evaluated with standard precision, recall, and F1 measures without regard for the rich hierarchical structure. In this work we argue for hierarchical evaluation of the predictions of neural LMTC models. With the example of the ICD-9 ontology we describe a structural issue in the representation of the structured label space in prior art, and propose an alternative representation based on the depth of the ontology. We propose a set of metrics for hierarchical evaluation using the depth-based representation. We compare the evaluation scores from the proposed metrics with previously used metrics on prior art LMTC models for ICD-9 coding in MIMIC-III. We also propose further avenues of research involving the proposed ontological representation.

Hang Dong, Víctor Suárez-Paniagua, Huayu Zhang et al.

The identification of rare diseases from clinical notes with Natural Language Processing (NLP) is challenging due to the few cases available for machine learning and the need of data annotation from clinical experts. We propose a method using ontologies and weak supervision. The approach includes two steps: (i) Text-to-UMLS, linking text mentions to concepts in Unified Medical Language System (UMLS), with a named entity linking tool (e.g. SemEHR) and weak supervision based on customised rules and Bidirectional Encoder Representations from Transformers (BERT) based contextual representations, and (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). Using MIMIC-III US intensive care discharge summaries as a case study, we show that the Text-to-UMLS process can be greatly improved with weak supervision, without any annotated data from domain experts. Our analysis shows that the overall pipeline processing discharge summaries can surface rare disease cases, which are mostly uncaptured in manual ICD codes of the hospital admissions.

Hang Dong, Víctor Suárez-Paniagua, William Whiteley et al.

Diagnostic or procedural coding of clinical notes aims to derive a coded summary of disease-related information about patients. Such coding is usually done manually in hospitals but could potentially be automated to improve the efficiency and accuracy of medical coding. Recent studies on deep learning for automated medical coding achieved promising performances. However, the explainability of these models is usually poor, preventing them to be used confidently in supporting clinical practice. Another limitation is that these models mostly assume independence among labels, ignoring the complex correlation among medical codes which can potentially be exploited to improve the performance. We propose a Hierarchical Label-wise Attention Network (HLAN), which aimed to interpret the model by quantifying importance (as attention weights) of words and sentences related to each of the labels. Secondly, we propose to enhance the major deep learning models with a label embedding (LE) initialisation approach, which learns a dense, continuous vector representation and then injects the representation into the final layers and the label-wise attention layers in the models. We evaluated the methods using three settings on the MIMIC-III discharge summaries: full codes, top-50 codes, and the UK NHS COVID-19 shielding codes. Experiments were conducted to compare HLAN and LE initialisation to the state-of-the-art neural network based methods. HLAN achieved the best Micro-level AUC and $F_1$ on the top-50 code prediction and comparable results on the NHS COVID-19 shielding code prediction to other models. By highlighting the most salient words and sentences for each label, HLAN showed more meaningful and comprehensive model interpretation compared to its downgraded baselines and the CNN-based models. LE initialisation consistently boosted most deep learning models for automated medical coding.

Omar Delarosa, Hang Dong, Mindy Ruan et al.

This paper introduces RL Brush, a level-editing tool for tile-based games designed for mixed-initiative co-creation. The tool uses reinforcement-learning-based models to augment manual human level-design through the addition of AI-generated suggestions. Here, we apply RL Brush to designing levels for the classic puzzle game Sokoban. We put the tool online and tested it in 39 different sessions. The results show that users using the AI suggestions stay around longer and their created levels on average are more playable and more complex than without.

Hang Dong, Jinshan Pan, Lei Xiang et al.

In this paper, we propose a Multi-Scale Boosted Dehazing Network with Dense Feature Fusion based on the U-Net architecture. The proposed method is designed based on two principles, boosting and error feedback, and we show that they are suitable for the dehazing problem. By incorporating the Strengthen-Operate-Subtract boosting strategy in the decoder of the proposed model, we develop a simple yet effective boosted decoder to progressively restore the haze-free image. To address the issue of preserving spatial information in the U-Net architecture, we design a dense feature fusion module using the back-projection feedback scheme. We show that the dense feature fusion module can simultaneously remedy the missing spatial information from high-resolution features and exploit the non-adjacent features. Extensive evaluations demonstrate that the proposed model performs favorably against the state-of-the-art approaches on the benchmark datasets as well as real-world hazy images.

Xinyi Zhang, Hang Dong, Zhe Hu et al.

Single image super resolution aims to enhance image quality with respect to spatial content, which is a fundamental task in computer vision. In this work, we address the task of single frame super resolution with the presence of image degradation, e.g., blur, haze, or rain streaks. Due to the limitations of frame capturing and formation processes, image degradation is inevitable, and the artifacts would be exacerbated by super resolution methods. To address this problem, we propose a dual-branch convolutional neural network to extract base features and recovered features separately. The base features contain local and global information of the input image. On the other hand, the recovered features focus on the degraded regions and are used to remove the degradation. Those features are then fused through a recursive gate module to obtain sharp features for super resolution. By decomposing the feature extraction step into two task-independent streams, the dual-branch model can facilitate the training process by avoiding learning the mixed degradation all-in-one and thus enhance the final high-resolution prediction results. We evaluate the proposed method in three degradation scenarios. Experiments on these scenarios demonstrate that the proposed method performs more efficiently and favorably against the state-of-the-art approaches on benchmark datasets.

Shanxin Yuan, Radu Timofte, Gregory Slabaugh et al.

This paper reviews the first-ever image demoireing challenge that was part of the Advances in Image Manipulation (AIM) workshop, held in conjunction with ICCV 2019. This paper describes the challenge, and focuses on the proposed solutions and their results. Demoireing is a difficult task of removing moire patterns from an image to reveal an underlying clean image. A new dataset, called LCDMoire was created for this challenge, and consists of 10,200 synthetically generated image pairs (moire and clean ground truth). The challenge was divided into 2 tracks. Track 1 targeted fidelity, measuring the ability of demoire methods to obtain a moire-free image compared with the ground truth, while Track 2 examined the perceptual quality of demoire methods. The tracks had 60 and 39 registered participants, respectively. A total of eight teams competed in the final testing phase. The entries span the current the state-of-the-art in the image demoireing problem.

Xinyi Zhang, Hang Dong, Zhe Hu et al.

Single-image super-resolution is a fundamental task for vision applications to enhance the image quality with respect to spatial resolution. If the input image contains degraded pixels, the artifacts caused by the degradation could be amplified by super-resolution methods. Image blur is a common degradation source. Images captured by moving or still cameras are inevitably affected by motion blur due to relative movements between sensors and objects. In this work, we focus on the super-resolution task with the presence of motion blur. We propose a deep gated fusion convolution neural network to generate a clear high-resolution frame from a single natural image with severe blur. By decomposing the feature extraction step into two task-independent streams, the dual-branch design can facilitate the training process by avoiding learning the mixed degradation all-in-one and thus enhance the final high-resolution prediction results. Extensive experiments demonstrate that our method generates sharper super-resolved images from low-resolution inputs with high computational efficiency.