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The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field, current methods suffer from poor generalization and high complexity. In this work, we reformulate the RNA secondary structure prediction as a K-Rook problem, thereby simplifying the prediction process into probabilistic matching within a finite solution space. Building on this innovative perspective, we introduce RFold, a simple yet effective method that learns to predict the most matching K-Rook solution from the given sequence. RFold employs a bi-dimensional optimization strategy that decomposes the probabilistic matching problem into row-wise and column-wise components to reduce the matching complexity, simplifying the solving process while guaranteeing the validity of the output. Extensive experiments demonstrate that RFold achieves competitive performance and about eight times faster inference efficiency than the state-of-the-art approaches. The code and Colab demo are available in \href{//github.com/A4Bio/RFold}{//github.com/A4Bio/RFold}.

With the increasing availability of diverse data types, particularly images and time series data from medical experiments, there is a growing demand for techniques designed to combine various modalities of data effectively. Our motivation comes from the important areas of predicting mortality and phenotyping where using different modalities of data could significantly improve our ability to predict. To tackle this challenge, we introduce a new method that uses two separate encoders, one for each type of data, allowing the model to understand complex patterns in both visual and time-based information. Apart from the technical challenges, our goal is to make the predictive model more robust in noisy conditions and perform better than current methods. We also deal with imbalanced datasets and use an uncertainty loss function, yielding improved results while simultaneously providing a principled means of modeling uncertainty. Additionally, we include attention mechanisms to fuse different modalities, allowing the model to focus on what's important for each task. We tested our approach using the comprehensive multimodal MIMIC dataset, combining MIMIC-IV and MIMIC-CXR datasets. Our experiments show that our method is effective in improving multimodal deep learning for clinical applications. The code will be made available online.

We propose the Data Contamination Quiz (DCQ), a simple and effective approach to detect data contamination in large language models (LLMs) and estimate the amount of it. Specifically, we frame data contamination detection as a series of multiple-choice questions and devise a quiz format wherein three perturbed versions of each subsampled instance from a specific dataset partition (e.g., GSM8k test set) are created. These changes only include word-level perturbations. The generated perturbations, along with the original dataset instance, form the options in the DCQ, with an extra option accommodating the possibility of selecting none of the provided options. Given that the only distinguishing signal among the options is the exact wording with respect to the original dataset instance, an LLM, when tasked with identifying the original dataset instance, gravitates towards selecting the original one if it has been exposed to it in its pre-training phase -- a trait intrinsic to LLMs. While accounting for positional biases in LLMs, the quiz performance reveals the contamination level for the model being examined with the dataset partition to which the quiz pertains. Applied to various datasets with GPT-4 and GPT-3.5, our findings -- while fully lacking access to pre-training data and model parameters -- suggest that DCQ achieves state-of-the-art results and uncovers greater contamination/memorization levels compared to existing methods and proficiently bypasses more safety filters, especially those set to avoid generating copyrighted contents.

Context: In agile transformations, there are many challenges such as alignment between agile practices and the organizational goals and strategies or issues with shifts in how work is organized and executed. One very important challenge but less considered and treated in research are cultural challenges associated with an agile mindset. Although research shows that cultural clashes and general organizational resistance to change are part of the most significant agile adoption barriers. Objective: We identify challenges that arise from the interplay between agile culture and organizational culture. In doing so, we tackle this field and come up with important contributions for further research regarding a problem that practitioners face today. Method: This is done with a mixed-method research approach. First, we gathered qualitative data among our network of agile practitioners and derived in sum 15 challenges with agile culture. Then, we conducted quantitative data by means of a questionnaire study with 92 participants. Results: We identified 7 key challenges out of the 15 challenges with agile culture. These key challenges refer to the technical agility (doing agile) and the cultural agility (being agile). The results are presented in type of a conceptual model named the Agile Cultural Challenges (ACuCa). Conclusion: Based on our results, we started deriving future work aspects to do more detailed research on the topic of cultural challenges while transitioning or using agile methods in software development and beyond.

The spatiotemporal data generated by massive sensors in the Internet of Things (IoT) is extremely dynamic, heterogeneous, large scale and time-dependent. It poses great challenges (e.g. accuracy, reliability, and stability) in real-time analysis and decision making for different IoT applications. The complexity of IoT data prevents the common people from gaining a deeper understanding of it. Agentized systems help address the lack of data insight for the common people. We propose a generic framework, namely CityGPT, to facilitate the learning and analysis of IoT time series with an end-to-end paradigm. CityGPT employs three agents to accomplish the spatiotemporal analysis of IoT data. The requirement agent facilitates user inputs based on natural language. Then, the analysis tasks are decomposed into temporal and spatial analysis processes, completed by corresponding data analysis agents (temporal and spatial agents). Finally, the spatiotemporal fusion agent visualizes the system's analysis results by receiving analysis results from data analysis agents and invoking sub-visualization agents, and can provide corresponding textual descriptions based on user demands. To increase the insight for common people using our framework, we have agnentized the framework, facilitated by a large language model (LLM), to increase the data comprehensibility. Our evaluation results on real-world data with different time dependencies show that the CityGPT framework can guarantee robust performance in IoT computing.

In recent years, with the realistic generation results and a wide range of personalized applications, diffusion-based generative models gain huge attention in both visual and audio generation areas. Compared to the considerable advancements of text2image or text2audio generation, research in audio2visual or visual2audio generation has been relatively slow. The recent audio-visual generation methods usually resort to huge large language model or composable diffusion models. Instead of designing another giant model for audio-visual generation, in this paper we take a step back showing a simple and lightweight generative transformer, which is not fully investigated in multi-modal generation, can achieve excellent results on image2audio generation. The transformer operates in the discrete audio and visual Vector-Quantized GAN space, and is trained in the mask denoising manner. After training, the classifier-free guidance could be deployed off-the-shelf achieving better performance, without any extra training or modification. Since the transformer model is modality symmetrical, it could also be directly deployed for audio2image generation and co-generation. In the experiments, we show that our simple method surpasses recent image2audio generation methods. Generated audio samples can be found at //docs.google.com/presentation/d/1ZtC0SeblKkut4XJcRaDsSTuCRIXB3ypxmSi7HTY3IyQ

Multimodality Representation Learning, as a technique of learning to embed information from different modalities and their correlations, has achieved remarkable success on a variety of applications, such as Visual Question Answering (VQA), Natural Language for Visual Reasoning (NLVR), and Vision Language Retrieval (VLR). Among these applications, cross-modal interaction and complementary information from different modalities are crucial for advanced models to perform any multimodal task, e.g., understand, recognize, retrieve, or generate optimally. Researchers have proposed diverse methods to address these tasks. The different variants of transformer-based architectures performed extraordinarily on multiple modalities. This survey presents the comprehensive literature on the evolution and enhancement of deep learning multimodal architectures to deal with textual, visual and audio features for diverse cross-modal and modern multimodal tasks. This study summarizes the (i) recent task-specific deep learning methodologies, (ii) the pretraining types and multimodal pretraining objectives, (iii) from state-of-the-art pretrained multimodal approaches to unifying architectures, and (iv) multimodal task categories and possible future improvements that can be devised for better multimodal learning. Moreover, we prepare a dataset section for new researchers that covers most of the benchmarks for pretraining and finetuning. Finally, major challenges, gaps, and potential research topics are explored. A constantly-updated paperlist related to our survey is maintained at //github.com/marslanm/multimodality-representation-learning.

Graph neural networks (GNNs) have emerged as a series of competent graph learning methods for diverse real-world scenarios, ranging from daily applications like recommendation systems and question answering to cutting-edge technologies such as drug discovery in life sciences and n-body simulation in astrophysics. However, task performance is not the only requirement for GNNs. Performance-oriented GNNs have exhibited potential adverse effects like vulnerability to adversarial attacks, unexplainable discrimination against disadvantaged groups, or excessive resource consumption in edge computing environments. To avoid these unintentional harms, it is necessary to build competent GNNs characterised by trustworthiness. To this end, we propose a comprehensive roadmap to build trustworthy GNNs from the view of the various computing technologies involved. In this survey, we introduce basic concepts and comprehensively summarise existing efforts for trustworthy GNNs from six aspects, including robustness, explainability, privacy, fairness, accountability, and environmental well-being. Additionally, we highlight the intricate cross-aspect relations between the above six aspects of trustworthy GNNs. Finally, we present a thorough overview of trending directions for facilitating the research and industrialisation of trustworthy GNNs.

A fundamental goal of scientific research is to learn about causal relationships. However, despite its critical role in the life and social sciences, causality has not had the same importance in Natural Language Processing (NLP), which has traditionally placed more emphasis on predictive tasks. This distinction is beginning to fade, with an emerging area of interdisciplinary research at the convergence of causal inference and language processing. Still, research on causality in NLP remains scattered across domains without unified definitions, benchmark datasets and clear articulations of the remaining challenges. In this survey, we consolidate research across academic areas and situate it in the broader NLP landscape. We introduce the statistical challenge of estimating causal effects, encompassing settings where text is used as an outcome, treatment, or as a means to address confounding. In addition, we explore potential uses of causal inference to improve the performance, robustness, fairness, and interpretability of NLP models. We thus provide a unified overview of causal inference for the computational linguistics community.

We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.