The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to the patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are continuously produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph encompassing biological knowledge about RNAs gathered from more than 50 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.
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A crucial challenge for solving problems in conflict research is in leveraging the semi-supervised nature of the data that arise. Observed response data such as counts of battle deaths over time indicate latent processes of interest such as intensity and duration of conflicts, but defining and labeling instances of these unobserved processes requires nuance and imprecision. The availability of such labels, however, would make it possible to study the effect of intervention-related predictors - such as ceasefires - directly on conflict dynamics (e.g., latent intensity) rather than through an intermediate proxy like observed counts of battle deaths. Motivated by this problem and the new availability of the ETH-PRIO Civil Conflict Ceasefires data set, we propose a Bayesian autoregressive (AR) hidden Markov model (HMM) framework as a sufficiently flexible machine learning approach for semi-supervised regime labeling with uncertainty quantification. We motivate our approach by illustrating the way it can be used to study the role that ceasefires play in shaping conflict dynamics. This ceasefires data set is the first systematic and globally comprehensive data on ceasefires, and our work is the first to analyze this new data and to explore the effect of ceasefires on conflict dynamics in a comprehensive and cross-country manner.
This paper introduces a novel multimodal and high-resolution human brain cerebellum lobule segmentation method. Unlike current tools that operate at standard resolution ($1 \text{ mm}^{3}$) or using mono-modal data, the proposed method improves cerebellum lobule segmentation through the use of a multimodal and ultra-high resolution ($0.125 \text{ mm}^{3}$) training dataset. To develop the method, first, a database of semi-automatically labelled cerebellum lobules was created to train the proposed method with ultra-high resolution T1 and T2 MR images. Then, an ensemble of deep networks has been designed and developed, allowing the proposed method to excel in the complex cerebellum lobule segmentation task, improving precision while being memory efficient. Notably, our approach deviates from the traditional U-Net model by exploring alternative architectures. We have also integrated deep learning with classical machine learning methods incorporating a priori knowledge from multi-atlas segmentation, which improved precision and robustness. Finally, a new online pipeline, named DeepCERES, has been developed to make available the proposed method to the scientific community requiring as input only a single T1 MR image at standard resolution.
Study Objectives: Polysomnography (PSG) currently serves as the benchmark for evaluating sleep disorders. Its discomfort, impracticality for home-use, and introduction of bias in sleep quality assessment necessitate the exploration of less invasive, cost-effective, and portable alternatives. One promising contender is the in-ear-EEG sensor, which offers advantages in terms of comfort, fixed electrode positions, resistance to electromagnetic interference, and user-friendliness. This study aims to establish a methodology to assess the similarity between the in-ear-EEG signal and standard PSG. Methods: We assess the agreement between the PSG and in-ear-EEG derived hypnograms. We extract features in the time- and frequency- domain from PSG and in-ear-EEG 30-second epochs. We only consider the epochs where the PSG-scorers and the in-ear-EEG-scorers were in agreement. We introduce a methodology to quantify the similarity between PSG derivations and the single-channel in-ear-EEG. The approach relies on a comparison of distributions of selected features -- extracted for each sleep stage and subject on both PSG and the in-ear-EEG signals -- via a Jensen-Shannon Divergence Feature-based Similarity Index (JSD-FSI). Results: We found a high intra-scorer variability, mainly due to the uncertainty the scorers had in evaluating the in-ear-EEG signals. We show that the similarity between PSG and in-ear-EEG signals is high (JSD-FSI: 0.61 +/- 0.06 in awake, 0.60 +/- 0.07 in NREM and 0.51 +/- 0.08 in REM), and in line with the similarity values computed independently on standard PSG-channel-combinations. Conclusions: In-ear-EEG is a valuable solution for home-based sleep monitoring, however further studies with a larger and more heterogeneous dataset are needed.
Recent advancements in artificial intelligence, particularly with the emergence of large language models (LLMs), have sparked a rethinking of artificial general intelligence possibilities. The increasing human-like capabilities of AI are also attracting attention in social science research, leading to various studies exploring the combination of these two fields. In this survey, we systematically categorize previous explorations in the combination of AI and social science into two directions that share common technical approaches but differ in their research objectives. The first direction is focused on AI for social science, where AI is utilized as a powerful tool to enhance various stages of social science research. While the second direction is the social science of AI, which examines AI agents as social entities with their human-like cognitive and linguistic capabilities. By conducting a thorough review, particularly on the substantial progress facilitated by recent advancements in large language models, this paper introduces a fresh perspective to reassess the relationship between AI and social science, provides a cohesive framework that allows researchers to understand the distinctions and connections between AI for social science and social science of AI, and also summarized state-of-art experiment simulation platforms to facilitate research in these two directions. We believe that as AI technology continues to advance and intelligent agents find increasing applications in our daily lives, the significance of the combination of AI and social science will become even more prominent.
We show that the known list-decoding algorithms for univariate multiplicity and folded Reed-Solomon (FRS) codes can be made to run in nearly-linear time. This yields, to our knowledge, the first known family of codes that can be decoded in nearly linear time, even as they approach the list decoding capacity. Univariate multiplicity codes and FRS codes are natural variants of Reed-Solomon codes that were discovered and studied for their applications to list-decoding. It is known that for every $\epsilon >0$, and rate $R \in (0,1)$, there exist explicit families of these codes that have rate $R$ and can be list-decoded from a $(1-R-\epsilon)$ fraction of errors with constant list size in polynomial time (Guruswami & Wang (IEEE Trans. Inform. Theory, 2013) and Kopparty, Ron-Zewi, Saraf & Wootters (SIAM J. Comput. 2023)). In this work, we present randomized algorithms that perform the above tasks in nearly linear time. Our algorithms have two main components. The first builds upon the lattice-based approach of Alekhnovich (IEEE Trans. Inf. Theory 2005), who designed a nearly linear time list-decoding algorithm for Reed-Solomon codes approaching the Johnson radius. As part of the second component, we design nearly-linear time algorithms for two natural algebraic problems. The first algorithm solves linear differential equations of the form $Q\left(x, f(x), \frac{df}{dx}, \dots,\frac{d^m f}{dx^m}\right) \equiv 0$ where $Q$ has the form $Q(x,y_0,\dots,y_m) = \tilde{Q}(x) + \sum_{i = 0}^m Q_i(x)\cdot y_i$. The second solves functional equations of the form $Q\left(x, f(x), f(\gamma x), \dots,f(\gamma^m x)\right) \equiv 0$ where $\gamma$ is a high-order field element. These algorithms can be viewed as generalizations of classical algorithms of Sieveking (Computing 1972) and Kung (Numer. Math. 1974) for computing the modular inverse of a power series, and might be of independent interest.
The recent progress in artificial intelligence has led to an ever-increasing usage of images and videos by machine analysis algorithms, mainly neural networks. Nonetheless, compression, storage and transmission of media have traditionally been designed considering human beings as the viewers of the content. Recent research on image and video coding for machine analysis has progressed mainly in two almost orthogonal directions. The first is represented by end-to-end (E2E) learned codecs which, while offering high performance on image coding, are not yet on par with state-of-the-art conventional video codecs and lack interoperability. The second direction considers using the Versatile Video Coding (VVC) standard or any other conventional video codec (CVC) together with pre- and post-processing operations targeting machine analysis. While the CVC-based methods benefit from interoperability and broad hardware and software support, the machine task performance is often lower than the desired level, particularly in low bitrates. This paper proposes a hybrid codec for machines called NN-VVC, which combines the advantages of an E2E-learned image codec and a CVC to achieve high performance in both image and video coding for machines. Our experiments show that the proposed system achieved up to -43.20% and -26.8% Bj{\o}ntegaard Delta rate reduction over VVC for image and video data, respectively, when evaluated on multiple different datasets and machine vision tasks. To the best of our knowledge, this is the first research paper showing a hybrid video codec that outperforms VVC on multiple datasets and multiple machine vision tasks.
Dynamical systems across the sciences, from electrical circuits to ecological networks, undergo qualitative and often catastrophic changes in behavior, called bifurcations, when their underlying parameters cross a threshold. Existing methods predict oncoming catastrophes in individual systems but are primarily time-series-based and struggle both to categorize qualitative dynamical regimes across diverse systems and to generalize to real data. To address this challenge, we propose a data-driven, physically-informed deep-learning framework for classifying dynamical regimes and characterizing bifurcation boundaries based on the extraction of topologically invariant features. We focus on the paradigmatic case of the supercritical Hopf bifurcation, which is used to model periodic dynamics across a wide range of applications. Our convolutional attention method is trained with data augmentations that encourage the learning of topological invariants which can be used to detect bifurcation boundaries in unseen systems and to design models of biological systems like oscillatory gene regulatory networks. We further demonstrate our method's use in analyzing real data by recovering distinct proliferation and differentiation dynamics along pancreatic endocrinogenesis trajectory in gene expression space based on single-cell data. Our method provides valuable insights into the qualitative, long-term behavior of a wide range of dynamical systems, and can detect bifurcations or catastrophic transitions in large-scale physical and biological systems.
This study explores the nuanced capabilities and inherent biases of Recommender Systems using Large Language Models (RecLLMs), with a focus on ChatGPT-based systems. It studies into the contrasting behaviors of generative models and traditional collaborative filtering models in movie recommendations. The research primarily investigates prompt design strategies and their impact on various aspects of recommendation quality, including accuracy, provider fairness, diversity, stability, genre dominance, and temporal freshness (recency). Our experimental analysis reveals that the introduction of specific 'system roles' and 'prompt strategies' in RecLLMs significantly influences their performance. For instance, role-based prompts enhance fairness and diversity in recommendations, mitigating popularity bias. We find that while GPT-based models do not always match the performance of CF baselines, they exhibit a unique tendency to recommend newer and more diverse movie genres. Notably, GPT-based models tend to recommend more recent films, particularly those released post-2000, and show a preference for genres like \sq{Drama} and Comedy, and Romance (compared to CF Action, Adventure) presumably due to the RecLLMs' training on varied data sets, which allows them to capture recent trends and discussions more effectively than CF models. Interestingly, our results demonstrate that the 'Simple' and 'Chain of Thought (COT)' paradigms yield the highest accuracy. These findings imply the potential of combining these strategies with scenarios that favor more recent content, thereby offering a more balanced and up-to-date recommendation experience. This study contributes significantly to the understanding of emerging RecLLMs, particularly in the context of harms and biases within these systems.
Due to the subjective nature of image quality assessment (IQA), assessing which image has better quality among a sequence of images is more reliable than assigning an absolute mean opinion score for an image. Thus, IQA models are evaluated by global correlation consistency (GCC) metrics like PLCC and SROCC, rather than mean opinion consistency (MOC) metrics like MAE and MSE. However, most existing methods adopt MOC metrics to define their loss functions, due to the infeasible computation of GCC metrics during training. In this work, we construct a novel loss function and network to exploit Global-correlation and Mean-opinion Consistency, forming a GMC-IQA framework. Specifically, we propose a novel GCC loss by defining a pairwise preference-based rank estimation to solve the non-differentiable problem of SROCC and introducing a queue mechanism to reserve previous data to approximate the global results of the whole data. Moreover, we propose a mean-opinion network, which integrates diverse opinion features to alleviate the randomness of weight learning and enhance the model robustness. Experiments indicate that our method outperforms SOTA methods on multiple authentic datasets with higher accuracy and generalization. We also adapt the proposed loss to various networks, which brings better performance and more stable training.
Radiologist is "doctor's doctor", biomedical image segmentation plays a central role in quantitative analysis, clinical diagnosis, and medical intervention. In the light of the fully convolutional networks (FCN) and U-Net, deep convolutional networks (DNNs) have made significant contributions in biomedical image segmentation applications. In this paper, based on U-Net, we propose MDUnet, a multi-scale densely connected U-net for biomedical image segmentation. we propose three different multi-scale dense connections for U shaped architectures encoder, decoder and across them. The highlights of our architecture is directly fuses the neighboring different scale feature maps from both higher layers and lower layers to strengthen feature propagation in current layer. Which can largely improves the information flow encoder, decoder and across them. Multi-scale dense connections, which means containing shorter connections between layers close to the input and output, also makes much deeper U-net possible. We adopt the optimal model based on the experiment and propose a novel Multi-scale Dense U-Net (MDU-Net) architecture with quantization. Which reduce overfitting in MDU-Net for better accuracy. We evaluate our purpose model on the MICCAI 2015 Gland Segmentation dataset (GlaS). The three multi-scale dense connections improve U-net performance by up to 1.8% on test A and 3.5% on test B in the MICCAI Gland dataset. Meanwhile the MDU-net with quantization achieves the superiority over U-Net performance by up to 3% on test A and 4.1% on test B.
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