OpenRaiser/Intern-Atlas huggingface dataset:
PubMed and Beyond: Biomedical Literature Search in the Age of Artificial Intelligence
Venue: arXiv cs.IR 2023
Year: 2023

Biomedical research yields a wealth of information, much of which is only accessible through the literature. Consequently, literature search is an essential tool for building on prior knowledge in clinical and biomedical research. Although recent improvements in artificial intelligence have expanded functionality beyond keyword-based search, these advances may be unfamiliar to clinicians and researchers. In response, we present a survey of literature search tools tailored to both general and specific information needs in biomedicine, with the objective of helping readers efficiently fulfill their information needs. We first examine the widely used PubMed search engine, discussing recent improvements and continued challenges. We then describe literature search tools catering to five specific information needs: 1. Identifying high-quality clinical research for evidence-based medicine. 2. Retrieving gene-related information for precision medicine and genomics. 3. Searching by meaning, including natural language questions. 4. Locating related articles with literature recommendation. 5. Mining literature to discover associations between concepts such as diseases and genetic variants. Additionally, we cover practical considerations and best practices for choosing and using these tools. Finally, we provide a perspective on the future of literature search engines, considering recent breakthroughs in large language models such as ChatGPT. In summary, our survey provides a comprehensive view of biomedical literature search functionalities with 36 publicly available tools.
Efficient Guided Generation for Large Language Models
Venue: arXiv cs.CL 2023
Year: 2023

In this article we show how the problem of neural text generation can be constructively reformulated in terms of transitions between the states of a finite-state machine. This framework leads to an efficient approach to guiding text generation with regular expressions and context-free grammars by allowing the construction of an index over a language model's vocabulary. The approach is model agnostic, allows one to enforce domain-specific knowledge and constraints, and enables the construction of reliable interfaces by guaranteeing the structure of the generated text. It adds little overhead to the token sequence generation process and significantly outperforms existing solutions. An implementation is provided in the open source Python library Outlines
RaTE: a Reproducible automatic Taxonomy Evaluation by Filling the Gap
Venue: arXiv cs.CL 2023
Year: 2023

Taxonomies are an essential knowledge representation, yet most studies on automatic taxonomy construction (ATC) resort to manual evaluation to score proposed algorithms. We argue that automatic taxonomy evaluation (ATE) is just as important as taxonomy construction. We propose RaTE, an automatic label-free taxonomy scoring procedure, which relies on a large pre-trained language model. We apply our evaluation procedure to three state-of-the-art ATC algorithms with which we built seven taxonomies from the Yelp domain, and show that 1) RaTE correlates well with human judgments and 2) artificially degrading a taxonomy leads to decreasing RaTE score.
Reduction of the secret key length in the perfect cipher by data compression and randomisation
Venue: arXiv cs.CR 2023
Year: 2023

Perfect ciphers have been a very attractive cryptographic tool ever since C. Shannon described them. Note that, by definition, if a perfect cipher is used, no one can get any information about the encrypted message without knowing the secret key. We consider the problem of reducing the key length of perfect ciphers, because in many applications the length of the secret key is a crucial parameter. This paper describes a simple method of key length reduction. This method gives a perfect cipher and is based on the use of data compression and randomisation, and the average key length can be made close to Shannon entropy (which is the key length limit). It should be noted that the method can effectively use readily available data compressors (archivers).
Enhancing conversational quality in language learning chatbots: An evaluation of GPT4 for ASR error correction
Venue: arXiv cs.CL 2023
Year: 2023

The integration of natural language processing (NLP) technologies into educational applications has shown promising results, particularly in the language learning domain. Recently, many spoken open-domain chatbots have been used as speaking partners, helping language learners improve their language skills. However, one of the significant challenges is the high word-error-rate (WER) when recognizing non-native/non-fluent speech, which interrupts conversation flow and leads to disappointment for learners. This paper explores the use of GPT4 for ASR error correction in conversational settings. In addition to WER, we propose to use semantic textual similarity (STS) and next response sensibility (NRS) metrics to evaluate the impact of error correction models on the quality of the conversation. We find that transcriptions corrected by GPT4 lead to higher conversation quality, despite an increase in WER. GPT4 also outperforms standard error correction methods without the need for in-domain training data.
Are We Ready to Embrace Generative AI for Software Q&A?
Venue: arXiv cs.SE 2023
Year: 2023

Stack Overflow, the world's largest software Q&A (SQA) website, is facing a significant traffic drop due to the emergence of generative AI techniques. ChatGPT is banned by Stack Overflow after only 6 days from its release. The main reason provided by the official Stack Overflow is that the answers generated by ChatGPT are of low quality. To verify this, we conduct a comparative evaluation of human-written and ChatGPT-generated answers. Our methodology employs both automatic comparison and a manual study. Our results suggest that human-written and ChatGPT-generated answers are semantically similar, however, human-written answers outperform ChatGPT-generated ones consistently across multiple aspects, specifically by 10% on the overall score. We release the data, analysis scripts, and detailed results at https://anonymous.4open.science/r/GAI4SQA-FD5C.
How Curvature Enhance the Adaptation Power of Framelet GCNs
Venue: arXiv cs.LG 2023
Year: 2023

Graph neural network (GNN) has been demonstrated powerful in modeling graph-structured data. However, despite many successful cases of applying GNNs to various graph classification and prediction tasks, whether the graph geometrical information has been fully exploited to enhance the learning performance of GNNs is not yet well understood. This paper introduces a new approach to enhance GNN by discrete graph Ricci curvature. Specifically, the graph Ricci curvature defined on the edges of a graph measures how difficult the information transits on one edge from one node to another based on their neighborhoods. Motivated by the geometric analogy of Ricci curvature in the graph setting, we prove that by inserting the curvature information with different carefully designed transformation function $ζ$, several known computational issues in GNN such as over-smoothing can be alleviated in our proposed model. Furthermore, we verified that edges with very positive Ricci curvature (i.e., $κ_{i,j} \approx 1$) are preferred to be dropped to enhance model's adaption to heterophily graph and one curvature based graph edge drop algorithm is proposed. Comprehensive experiments show that our curvature-based GNN model outperforms the state-of-the-art baselines in both homophily and heterophily graph datasets, indicating the effectiveness of involving graph geometric information in GNNs.
DAPrompt: Deterministic Assumption Prompt Learning for Event Causality Identification
Venue: arXiv cs.CL 2023
Year: 2023

Event Causality Identification (ECI) aims at determining whether there is a causal relation between two event mentions. Conventional prompt learning designs a prompt template to first predict an answer word and then maps it to the final decision. Unlike conventional prompts, we argue that predicting an answer word may not be a necessary prerequisite for the ECI task. Instead, we can first make a deterministic assumption on the existence of causal relation between two events and then evaluate its rationality to either accept or reject the assumption. The design motivation is to try the most utilization of the encyclopedia-like knowledge embedded in a pre-trained language model. In light of such considerations, we propose a deterministic assumption prompt learning model, called DAPrompt, for the ECI task. In particular, we design a simple deterministic assumption template concatenating with the input event pair, which includes two masks as predicted events' tokens. We use the probabilities of predicted events to evaluate the assumption rationality for the final event causality decision. Experiments on the EventStoryLine corpus and Causal-TimeBank corpus validate our design objective in terms of significant performance improvements over the state-of-the-art algorithms.
Nonlinear Model Predictive Control with Obstacle Avoidance Constraints for Autonomous Navigation in a Canal Environment
Venue: arXiv cs.RO 2023
Year: 2023

In this paper, we describe the development process of autonomous navigation capabilities of a small cruise boat operating in a canal environment and present the results of a field experiment conducted in the Pohang Canal, South Korea. Nonlinear model predictive control (NMPC) was used for the online trajectory planning and tracking control of the cruise boat in a narrow passage in the canal. To consider the nonlinear characteristics of boat dynamics, system identification was performed using experimental data from various test maneuvers, such as acceleration-deceleration and zigzag trials. To efficiently represent the obstacle structures in the canal environment, we parameterized the canal walls as line segments with point cloud data, captured by an onboard LiDAR sensor, and considered them as constraints for obstacle avoidance. The proposed method was implemented in a single NMPC layer, and its real-world performance was verified through experimental runs in the Pohang Canal.
Towards a population-informed approach to the definition of data-driven models for structural dynamics
Venue: arXiv cs.LG 2023
Year: 2023

Machine learning has affected the way in which many phenomena for various domains are modelled, one of these domains being that of structural dynamics. However, because machine-learning algorithms are problem-specific, they often fail to perform efficiently in cases of data scarcity. To deal with such issues, combination of physics-based approaches and machine learning algorithms have been developed. Although such methods are effective, they also require the analyser's understanding of the underlying physics of the problem. The current work is aimed at motivating the use of models which learn such relationships from a population of phenomena, whose underlying physics are similar. The development of such models is motivated by the way that physics-based models, and more specifically finite element models, work. Such models are considered transferrable, explainable and trustworthy, attributes which are not trivially imposed or achieved for machine-learning models. For this reason, machine-learning approaches are less trusted by industry and often considered more difficult to form validated models. To achieve such data-driven models, a population-based scheme is followed here and two different machine-learning algorithms from the meta-learning domain are used. The two algorithms are the model-agnostic meta-learning (MAML) algorithm and the conditional neural processes (CNP) model. The algorithms seem to perform as intended and outperform a traditional machine-learning algorithm at approximating the quantities of interest. Moreover, they exhibit behaviour similar to traditional machine learning algorithms (e.g. neural networks or Gaussian processes), concerning their performance as a function of the available structures in the training population.
A3D: Adaptive, Accurate, and Autonomous Navigation for Edge-Assisted Drones
Venue: arXiv cs.NI 2023
Year: 2023

Accurate navigation is of paramount importance to ensure flight safety and efficiency for autonomous drones. Recent research starts to use Deep Neural Networks to enhance drone navigation given their remarkable predictive capability for visual perception. However, existing solutions either run DNN inference tasks on drones in situ, impeded by the limited onboard resource, or offload the computation to external servers which may incur large network latency. Few works consider jointly optimizing the offloading decisions along with image transmission configurations and adapting them on the fly. In this paper, we propose A3D, an edge server assisted drone navigation framework that can dynamically adjust task execution location, input resolution, and image compression ratio in order to achieve low inference latency, high prediction accuracy, and long flight distances. Specifically, we first augment state-of-the-art convolutional neural networks for drone navigation and define a novel metric called Quality of Navigation as our optimization objective which can effectively capture the above goals. We then design a deep reinforcement learning based neural scheduler at the drone side for which an information encoder is devised to reshape the state features and thus improve its learning ability. To further support simultaneous multi-drone serving, we extend the edge server design by developing a network-aware resource allocation algorithm, which allows provisioning containerized resources aligned with drones' demand. We finally implement a proof-of-concept prototype with realistic devices and validate its performance in a real-world campus scene, as well as a simulation environment for thorough evaluation upon AirSim. Extensive experimental results show that A3D can reduce end-to-end latency by 28.06% and extend the flight distance by up to 27.28% compared with non-adaptive solutions.
Test-takers have a say: understanding the implications of the use of AI in language tests
Venue: arXiv cs.CY 2023
Year: 2023

Language tests measure a person's ability to use a language in terms of listening, speaking, reading, or writing. Such tests play an integral role in academic, professional, and immigration domains, with entities such as educational institutions, professional accreditation bodies, and governments using them to assess candidate language proficiency. Recent advances in Artificial Intelligence (AI) and the discipline of Natural Language Processing have prompted language test providers to explore AI's potential applicability within language testing, leading to transformative activity patterns surrounding language instruction and learning. However, with concerns over AI's trustworthiness, it is imperative to understand the implications of integrating AI into language testing. This knowledge will enable stakeholders to make well-informed decisions, thus safeguarding community well-being and testing integrity. To understand the concerns and effects of AI usage in language tests, we conducted interviews and surveys with English test-takers. To the best of our knowledge, this is the first empirical study aimed at identifying the implications of AI adoption in language tests from a test-taker perspective. Our study reveals test-taker perceptions and behavioral patterns. Specifically, we identify that AI integration may enhance perceptions of fairness, consistency, and availability. Conversely, it might incite mistrust regarding reliability and interactivity aspects, subsequently influencing the behaviors and well-being of test-takers. These insights provide a better understanding of potential societal implications and assist stakeholders in making informed decisions concerning AI usage in language testing.
A Shared Control Approach Based on First-Order Dynamical Systems and Closed-Loop Variable Stiffness Control
Venue: arXiv cs.RO 2023
Year: 2023

In this paper, we present a novel learning-based shared control framework. This framework deploys first-order Dynamical Systems (DS) as motion generators providing the desired reference motion, and a Variable Stiffness Dynamical Systems (VSDS) \cite{chen2021closed} for haptic guidance. We show how to shape several features of our controller in order to achieve authority allocation, local motion refinement, in addition to the inherent ability of the controller to automatically synchronize with the human state during joint task execution. We validate our approach in a teleoperated task scenario, where we also showcase the ability of our framework to deal with situations that require updating task knowledge due to possible changes in the task scenario, or changes in the environment. Finally, we conduct a user study to compare the performance of our VSDS controller for guidance generation to two state-of-the-art controllers in a target reaching task. The result shows that our VSDS controller has the highest successful rate of task execution among all conditions. Besides, our VSDS controller helps reduce the execution time and task load significantly, and was selected as the most favorable controller by participants.
PyTAG: Challenges and Opportunities for Reinforcement Learning in Tabletop Games
Venue: arXiv cs.AI 2023
Year: 2023

In recent years, Game AI research has made important breakthroughs using Reinforcement Learning (RL). Despite this, RL for modern tabletop games has gained little to no attention, even when they offer a range of unique challenges compared to video games. To bridge this gap, we introduce PyTAG, a Python API for interacting with the Tabletop Games framework (TAG). TAG contains a growing set of more than 20 modern tabletop games, with a common API for AI agents. We present techniques for training RL agents in these games and introduce baseline results after training Proximal Policy Optimisation algorithms on a subset of games. Finally, we discuss the unique challenges complex modern tabletop games provide, now open to RL research through PyTAG.
Chit-Chat or Deep Talk: Prompt Engineering for Process Mining
Venue: arXiv cs.AI 2023
Year: 2023

This research investigates the application of Large Language Models (LLMs) to augment conversational agents in process mining, aiming to tackle its inherent complexity and diverse skill requirements. While LLM advancements present novel opportunities for conversational process mining, generating efficient outputs is still a hurdle. We propose an innovative approach that amend many issues in existing solutions, informed by prior research on Natural Language Processing (NLP) for conversational agents. Leveraging LLMs, our framework improves both accessibility and agent performance, as demonstrated by experiments on public question and data sets. Our research sets the stage for future explorations into LLMs' role in process mining and concludes with propositions for enhancing LLM memory, implementing real-time user testing, and examining diverse data sets.
TREEMENT: Interpretable Patient-Trial Matching via Personalized Dynamic Tree-Based Memory Network
Venue: arXiv cs.LG 2023
Year: 2023

Clinical trials are critical for drug development but often suffer from expensive and inefficient patient recruitment. In recent years, machine learning models have been proposed for speeding up patient recruitment via automatically matching patients with clinical trials based on longitudinal patient electronic health records (EHR) data and eligibility criteria of clinical trials. However, they either depend on trial-specific expert rules that cannot expand to other trials or perform matching at a very general level with a black-box model where the lack of interpretability makes the model results difficult to be adopted. To provide accurate and interpretable patient trial matching, we introduce a personalized dynamic tree-based memory network model named TREEMENT. It utilizes hierarchical clinical ontologies to expand the personalized patient representation learned from sequential EHR data, and then uses an attentional beam-search query learned from eligibility criteria embedding to offer a granular level of alignment for improved performance and interpretability. We evaluated TREEMENT against existing models on real-world datasets and demonstrated that TREEMENT outperforms the best baseline by 7% in terms of error reduction in criteria-level matching and achieves state-of-the-art results in its trial-level matching ability. Furthermore, we also show TREEMENT can offer good interpretability to make the model results easier for adoption.
Bias in Internet Measurement Platforms
Venue: arXiv cs.NI 2023
Year: 2023

Network operators and researchers frequently use Internet measurement platforms (IMPs), such as RIPE Atlas, RIPE RIS, or RouteViews for, e.g., monitoring network performance, detecting routing events, topology discovery, or route optimization. To interpret the results of their measurements and avoid pitfalls or wrong generalizations, users must understand a platform's limitations. To this end, this paper studies an important limitation of IMPs, the \textit{bias}, which exists due to the non-uniform deployment of the vantage points. Specifically, we introduce a generic framework to systematically and comprehensively quantify the multi-dimensional (e.g., across location, topology, network types, etc.) biases of IMPs. Using the framework and open datasets, we perform a detailed analysis of biases in IMPs that confirms well-known (to the domain experts) biases and sheds light on less-known or unexplored biases. To facilitate IMP users to obtain awareness of and explore bias in their measurements, as well as further research and analyses (e.g., methods for mitigating bias), we publicly share our code and data, and provide online tools (API, Web app, etc.) that calculate and visualize the bias in measurement setups.
Learner Referral for Cost-Effective Federated Learning Over Hierarchical IoT Networks
Venue: arXiv cs.LG 2023
Year: 2023

The paradigm of federated learning (FL) to address data privacy concerns by locally training parameters on resource-constrained clients in a distributed manner has garnered significant attention. Nonetheless, FL is not applicable when not all clients within the coverage of the FL server are registered with the FL network. To bridge this gap, this paper proposes joint learner referral aided federated client selection (LRef-FedCS), along with communications and computing resource scheduling, and local model accuracy optimization (LMAO) methods. These methods are designed to minimize the cost incurred by the worst-case participant and ensure the long-term fairness of FL in hierarchical Internet of Things (HieIoT) networks. Utilizing the Lyapunov optimization technique, we reformulate the original problem into a stepwise joint optimization problem (JOP). Subsequently, to tackle the mixed-integer non-convex JOP, we separatively and iteratively address LRef-FedCS and LMAO through the centralized method and self-adaptive global best harmony search (SGHS) algorithm, respectively. To enhance scalability, we further propose a distributed LRef-FedCS approach based on a matching game to replace the centralized method described above. Numerical simulations and experimental results on the MNIST/CIFAR-10 datasets demonstrate that our proposed LRef-FedCS approach could achieve a good balance between pursuing high global accuracy and reducing cost.