Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph

Abstract Motivation Up-to-date pathway knowledge is usually presented in scientific publications for human reading, making it difficult to utilize these resources for semantic integration and computational analysis of biological pathways. We here present an approach to mining knowledge graphs by combining manual curation with automated named entity recognition and automated relation extraction. This approach allows us to study pathway-related questions in detail, which we here show using the ketamine pathway, aiming to help improve understanding of the role of gut microbiota in the antidepressant effects of ketamine. Results The thus devised ketamine pathway ‘KetPath’ knowledge graph comprises five parts: (i) manually curated pathway facts from images; (ii) recognized named entities in biomedical texts; (iii) identified relations between named entities; (iv) our previously constructed microbiota and pre-/probiotics knowledge bases; and (v) multiple community-accepted public databases. We first assessed the performance of automated extraction of relations between named entities using the specially designed state-of-the-art tool BioKetBERT. The query results show that we can retrieve drug actions, pathway relations, co-occurring entities, and their relations. These results uncover several biological findings, such as various gut microbes leading to increased expression of BDNF, which may contribute to the sustained antidepressant effects of ketamine. We envision that the methods and findings from this research will aid researchers who wish to integrate and query data and knowledge from multiple biomedical databases and literature simultaneously. Availability and implementation Data and query protocols are available in the KetPath repository at https://dx.doi. org/10.5281/zenodo.8398941 and https://github.com/tingcosmos/KetPath.
Precipitation variability and response to changing climatic condition in the Yarlung Tsangpo River basin, China

Hydroclimatic process in the Yarlung Tsangpo River (YTR) basin, a sensitive area to climate change, is obviously changing during recent years, but there has limited understanding about it. In this study, we investigated the spatiotemporal variation of precipitation over last four decades in the basin and the impact thereon of the changing Indian summer monsoon at interannual and decadal time scales. All the precipitation series have similar scaling behavior, reflecting similar climatic regime throughout the basin. However, the effect of the Indian monsoon strengthens from the downstream to upstream, causing spatial variability in the seasonal distribution of precipitation, and on this basis, the YTR basin is roughly divided into three regions: east, middle, and west. Both the occurrence times and magnitude of precipitation extremes, ranging 25–50 mm/d, are exhibiting downward trends over the last four decades, which bodes well for water disaster controls in the basin. The Indian summer monsoon index, as an intensity indicator for the Indian summer monsoon, shows a positive relationship with the summer precipitation in the YTR basin. Periodic variability of the Indian monsoon determines the interannual nonstationary fluctuations of precipitation. Especially, the weakening effect of the Indian summer monsoon has caused an obvious decrease in precipitation over the rainy season after 1998. If the Indian summer monsoon keeps weakening, the precipitation would decrease and potentially water shortage would become more severe in the basin. Effective adaptation strategy should therefore be developed proactively to handle the unfavorable water situation, which is likely to occur in the future.
On the mixed monotonicity of polynomial functions

In this paper, it is shown that every univariate polynomial function is mixed monotone globally with a polynomial decomposition function. The decomposition functions can be constructed from the Gram matrix representation of polynomial functions. The tightness of polynomial decomposition functions is discussed. An example is provided to show that polynomial decomposition functions, in addition to being global decomposition functions, can be much tighter than local decomposition functions constructed using local Jacobian bounds. Furthermore, an example is provided to demonstrate the application to reachable set over-approximation.
Efficient Conformal Prediction under Data Heterogeneity

Conformal Prediction (CP) stands out as a robust framework for uncertainty quantification, which is crucial for ensuring the reliability of predictions. However, common CP methods heavily rely on data exchangeability, a condition often violated in practice. Existing approaches for tackling non-exchangeability lead to methods that are not computable beyond the simplest examples. This work introduces a new efficient approach to CP that produces provably valid confidence sets for fairly general non-exchangeable data distributions. We illustrate the general theory with applications to the challenging setting of federated learning under data heterogeneity between agents. Our method allows constructing provably valid personalized prediction sets for agents in a fully federated way. The effectiveness of the proposed method is demonstrated in a series of experiments on real-world datasets.
Narrowing the semantic gaps in U-Net with learnable skip connections: The case of medical image segmentation

Most state-of-the-art methods for medical image segmentation adopt the encoder-decoder architecture. However, this U-shaped framework still has limitations in capturing the non-local multi-scale information with a simple skip connection. To solve the problem, we firstly explore the potential weakness of skip connections in U-Net on multiple segmentation tasks, and find that i) not all skip connections are useful, each skip connection has different contribution; ii) the optimal combinations of skip connections are different, relying on the specific datasets. Based on our findings, we propose a new segmentation framework, named UDTransNet, to solve three semantic gaps in U-Net. Specifically, we propose a Dual Attention Transformer (DAT) module for capturing the channel- and spatial-wise relationships to better fuse the encoder features, and a Decoder-guided Recalibration Attention (DRA) module for effectively connecting the DAT tokens and the decoder features to eliminate the inconsistency. Hence, both modules establish a learnable connection to solve the semantic gaps between the encoder and the decoder, which leads to a high-performance segmentation model for medical images. Comprehensive experimental results indicate that our UDTransNet produces higher evaluation scores and finer segmentation results with relatively fewer parameters over the state-of-the-art segmentation methods on different public datasets. Code: https://github.com/McGregorWwww/UDTransNet.
How children and young people negotiate a sense of identity and belonging in a tourist destination: a critical perspective.

A review of both the tourism literature and the childhood literature reveals that there is a lack of research on young people’s perceptions and experiences of tourism, particularly when the tourist destination is also the place where they live. This paper focuses on a study of the lived experiences of young people growing up in the Australian tourist destination of Byron Bay, New South Wales. Taking a critical approach, an important aspect of this research is to hear directly from young people about how they negotiate a sense of identity and belonging in their communities. The study adopts an ethnographic and participatory approach to gain a deeper understanding of the lived experiences of childhood in a tourist destination context. Preliminary findings suggest that children and young people have a strong sense of connection and belonging to their community, including the natural and built environment, which is challenged by the flow of visiting tourists. This paper contributes to the field of Critical Tourism Studies by addressing the lack of research focused on children and young people. In addition, the study brings to the fore the ‘voices’ of this silent population in tourism research with the ultimate purpose of contributing to policy and planning for social sustainability.
Solving Label Variation in Scientific Information Extraction via Multi-Task Learning

Scientific Information Extraction (ScientificIE) is a critical task that involves the identification of scientific entities and their relationships. The complexity of this task is compounded by the necessity for domain-specific knowledge and the limited availability of annotated data. Two of the most popular datasets for ScientificIE are SemEval-2018 Task-7 and SciERC. They have overlapping samples and differ in their annotation schemes, which leads to conflicts. In this study, we first introduced a novel approach based on multi-task learning to address label variations. We then proposed a soft labeling technique that converts inconsistent labels into probabilistic distributions. The experimental results demonstrated that the proposed method can enhance the model robustness to label noise and improve the end-to-end performance in both ScientificIE tasks. The analysis revealed that label variations can be particularly effective in handling ambiguous instances. Furthermore, the richness of the information captured by label variations can potentially reduce data size requirements. The findings highlight the importance of releasing variation labels and promote future research on other tasks in other domains. Overall, this study demonstrates the effectiveness of multi-task learning and the potential of label variations to enhance the performance of ScientificIE.
TypeFly: Flying Drones with Large Language Model

Commanding a drone with a natural language is not only user-friendly but also opens the door for emerging language agents to control the drone. Emerging large language models (LLMs) provide a previously impossible opportunity to automatically translate a task description in a natural language to a program that can be executed by the drone. However, powerful LLMs and their vision counterparts are limited in three important ways. First, they are only available as cloud-based services. Sending images to the cloud raises privacy concerns. Second, they are expensive, costing proportionally to the request size. Finally, without expensive fine-tuning, existing LLMs are quite limited in their capability of writing a program for specialized systems like drones. In this paper, we present a system called TypeFly that tackles the above three problems using a combination of edge-based vision intelligence, novel programming language design, and prompt engineering. Instead of the familiar Python, TypeFly gets a cloud-based LLM service to write a program in a small, custom language called MiniSpec, based on task and scene descriptions in English. Such MiniSpec programs are not only succinct (and therefore efficient) but also able to consult the LLM during their execution using a special skill called query. Using a set of increasingly challenging drone tasks, we show that design choices made by TypeFly can reduce both the cost of LLM service and the task execution time by more than 2x. More importantly, query and prompt engineering techniques contributed by TypeFly significantly improve the chance of success of complex tasks.
Targeted materials discovery using Bayesian algorithm execution

Rapid discovery and synthesis of new materials requires intelligent data acquisition strategies to navigate large design spaces. A popular strategy is Bayesian optimization, which aims to find candidates that maximize material properties; however, materials design often requires finding specific subsets of the design space which meet more complex or specialized goals. We present a framework that captures experimental goals through straightforward user-defined filtering algorithms. These algorithms are automatically translated into one of three intelligent, parameter-free, sequential data acquisition strategies (SwitchBAX, InfoBAX, and MeanBAX). Our framework is tailored for typical discrete search spaces involving multiple measured physical properties and short time-horizon decision making. We evaluate this approach on datasets for TiO$_2$ nanoparticle synthesis and magnetic materials characterization, and show that our methods are significantly more efficient than state-of-the-art approaches.
Generalizable Task Representation Learning for Offline Meta-Reinforcement Learning with Data Limitations

Generalization and sample efficiency have been long-standing issues concerning reinforcement learning, and thus the field of Offline Meta-Reinforcement Learning (OMRL) has gained increasing attention due to its potential of solving a wide range of problems with static and limited offline data. Existing OMRL methods often assume sufficient training tasks and data coverage to apply contrastive learning to extract task representations. However, such assumptions are not applicable in several real-world applications and thus undermine the generalization ability of the representations. In this paper, we consider OMRL with two types of data limitations: limited training tasks and limited behavior diversity and propose a novel algorithm called GENTLE for learning generalizable task representations in the face of data limitations. GENTLE employs Task Auto-Encoder (TAE), which is an encoder-decoder architecture to extract the characteristics of the tasks. Unlike existing methods, TAE is optimized solely by reconstruction of the state transition and reward, which captures the generative structure of the task models and produces generalizable representations when training tasks are limited. To alleviate the effect of limited behavior diversity, we consistently construct pseudo-transitions to align the data distribution used to train TAE with the data distribution encountered during testing. Empirically, GENTLE significantly outperforms existing OMRL methods on both in-distribution tasks and out-of-distribution tasks across both the given-context protocol and the one-shot protocol.
Enhancing Redundancy-based Automated Program Repair by Fine-grained Pattern Mining

Redundancy-based automated program repair (APR), which generates patches by referencing existing source code, has gained much attention since they are effective in repairing real-world bugs with good interpretability. However, since existing approaches either demand the existence of multi-line similar code or randomly reference existing code, they can only repair a small number of bugs with many incorrect patches, hindering their wide application in practice. In this work, we aim to improve the effectiveness of redundancy-based APR by exploring more effective source code reuse methods for improving the number of correct patches and reducing incorrect patches. Specifically, we have proposed a new repair technique named Repatt, which incorporates a two-level pattern mining process for guiding effective patch generation (i.e., token and expression levels). We have conducted an extensive experiment on the widely-used Defects4J benchmark and compared Repatt with eight state-of-the-art APR approaches. The results show that our approach complements existing approaches by repairing {15} unique bugs compared with the latest deep learning-based methods and {19} unique bugs compared with traditional repair methods when providing the perfect fault localization. In addition, when the perfect fault localization is unknown in real practice, Repatt significantly outperforms the baseline approaches by achieving much higher patch precision, i.e., {83.8\%}. Moreover, we further proposed an effective patch ranking strategy for combining the strength of Repatt and the baseline methods. The result shows that it repairs 124 bugs when only considering the Top-1 patches and improves the best-performing repair method by repairing 39 more bugs. The results demonstrate the effectiveness of our approach for practical use.
A Variational Autoencoder for Neural Temporal Point Processes with Dynamic Latent Graphs

Continuously observed event occurrences, often exhibit self and mutually exciting effects, which can be well modeled using temporal point processes. Beyond that, these event dynamics may also change over time, with certain periodic trends. We propose a novel variational autoencoder to capture such a mixture of temporal dynamics. More specifically, the whole time interval of the input sequence is partitioned into a set of sub intervals. The event dynamics are assumed to be stationary within each subinterval, but could be changing across those subintervals. In particular, we use a sequential latent variable model to learn a dependency graph between the observed dimensions, for each subinterval. The model predicts the future event times, by using the learned dependency graph to remove the non contributing influences of past events. By doing so, the proposed model demonstrates its higher accuracy in predicting inter event times and event types for several real world event sequences, compared with existing state of the art neural point processes.
ChartBench: A Benchmark for Complex Visual Reasoning in Charts

Multimodal Large Language Models (MLLMs) demonstrate impressive image understanding and generating capabilities. However, existing benchmarks employ limited charts that deviate from real-world scenarios, posing challenges in accurately assessing the chart comprehension of MLLMs. To overcome this constraint, we propose ChartBench, an exhaustive chart benchmark specifically designed to evaluate MLLMs' chart comprehension and data reliability through complex visual reasoning. ChartBench encompasses a wide spectrum, including 42 categories, 2.1K charts, and 16.8K question-answer pairs. Diverging from previous benchmarks, ChartBench avoids employing data point annotation charts or metadata prompts directly. Instead, it compels MLLMs to derive values akin to human understanding by leveraging inherent chart elements such as color, legends, or coordinate systems. Additionally, we propose an enhanced evaluation metric, Acc+, which facilitates the evaluation of MLLMs without needing labor-intensive manual efforts or costly evaluations based on GPT. Our extensive experimental evaluation involves 12 widely-used open-sourced and 2 proprietary MLLMs, revealing the limitations of MLLMs in interpreting charts and providing valuable insights to encourage closer scrutiny of this aspect.
Enhancing Code Intelligence Tasks with ChatGPT

Pre-trained code models have emerged as crucial tools in various code intelligence tasks. However, their effectiveness depends on the quality of the pre-training dataset, particularly the human reference comments, which serve as a bridge between the programming language and natural language. One significant challenge is that such comments can become inconsistent with the corresponding code as the software evolves. This discrepancy can lead to suboptimal training of the models, decreasing their performances. LLMs have demonstrated superior capabilities in generating high-quality code comments. In light of that, we try to tackle the quality issue of the dataset by harnessing the power of LLMs. Specifically, we raise the question: Can we rebuild the pre-training dataset by substituting the original comments with LLM-generated ones for more effective pre-trained code models? To answer the question, we first conduct a comprehensive evaluation to compare ChatGPT-generated comments with human reference comments. As existing reference-based metrics treat the reference comments as gold standards, we introduce two auxiliary tasks as novel reference-free metrics to assess the quality of comments, i.e., code-comment inconsistency detection and code search. Experimental results show that ChatGPT-generated comments demonstrate superior semantic consistency with the code compared to human references, indicating the potential of utilizing ChatGPT to enhance the quality of the pre-training dataset. We rebuilt the widely used dataset, CodeSearchNet, with ChatGPT-generated comments. Subsequent experiments involve re-pre-training the CodeT5 with our refined dataset.Evaluation results on four generation tasks and one understanding code intelligence tasks show that the model pre-trained by ChatGPT-enhanced data outperforms its counterpart on code summarization, code generation, and code translation tasks.
Self-Supervised Depth Completion Guided by 3D Perception and Geometry Consistency

Depth completion, aiming to predict dense depth maps from sparse depth measurements, plays a crucial role in many computer vision related applications. Deep learning approaches have demonstrated overwhelming success in this task. However, high-precision depth completion without relying on the ground-truth data, which are usually costly, still remains challenging. The reason lies on the ignorance of 3D structural information in most previous unsupervised solutions, causing inaccurate spatial propagation and mixed-depth problems. To alleviate the above challenges, this paper explores the utilization of 3D perceptual features and multi-view geometry consistency to devise a high-precision self-supervised depth completion method. Firstly, a 3D perceptual spatial propagation algorithm is constructed with a point cloud representation and an attention weighting mechanism to capture more reasonable and favorable neighboring features during the iterative depth propagation process. Secondly, the multi-view geometric constraints between adjacent views are explicitly incorporated to guide the optimization of the whole depth completion model in a self-supervised manner. Extensive experiments on benchmark datasets of NYU-Depthv2 and VOID demonstrate that the proposed model achieves the state-of-the-art depth completion performance compared with other unsupervised methods, and competitive performance compared with previous supervised methods.
Multi-RIS Communication Systems: Asymptotic analysis of best RIS selection for i.n.i.d. Random Variables using Extreme Value Theory

This paper investigates the performance of multiple reconfigurable intelligent surfaces (multi-RIS) communication systems where the RIS link with the highest signal-to-noise-ratio (SNR) is selected at the destination. In practice, all the RISs will not have the same number of reflecting elements. Hence, selecting the RIS link with the highest SNR will involve characterizing the distribution of the maximum of independent, non-identically distributed (i.n.i.d.) SNR random variables (RVs). Using extreme value theory (EVT), we derive the asymptotic distribution of the normalized maximum of i.n. i.d. non-central chi-square (NCCS) distributed SNR RVs with one degree of freedom (d.o.f) and then extend the results for k-th order statistics. Using these asymptotic results, the outage capacity and average throughput expressions are derived for the multi-RIS system. The results for independent and identically distributed (i.i.d.) SNR RVs are then derived as a special case of i.n. i.d. RVs. All the derivations are validated through extensive Monte Carlo simulations, and their utility is discussed.