Miracle-dz/UniFAR-FTUs huggingface dataset:
Conserved Disease Modules Extracted From Multilayer Heterogeneous Disease and Gene Networks for Understanding Disease Mechanisms and Predicting Disease Treatments

Disease relationship studies for understanding the pathogenesis of complex diseases, diagnosis, prognosis, and drug development are important. Traditional approaches consider one type of disease data or aggregating multiple types of disease data into a single network, which results in important temporal- or context-related information loss and may distort the actual organization. Therefore, it is necessary to apply multilayer network model to consider multiple types of relationships between diseases and the important interplays between different relationships. Further, modules extracted from multilayer networks are smaller and have more overlap that better capture the actual organization. Here, we constructed a weighted four-layer disease-disease similarity network to characterize the associations at different levels between diseases. Then, a tensor-based computational framework was used to extract Conserved Disease Modules (CDMs) from the four-layer disease network. After filtering, nine significant CDMs were reserved. The statistical significance test proved the significance of the nine CDMs. Comparing with modules got from four single layer networks, CMDs are smaller, better represent the actual relationships, and contain potential disease-disease relationships. KEGG pathways enrichment analysis and literature mining further contributed to confirm that these CDMs are highly reliable. Furthermore, the CDMs can be applied to predict potential drugs for diseases. The molecular docking techniques were used to provide the direct evidence for drugs to treat related disease. Taking Rheumatoid Arthritis (RA) as a case, we found its three potential drugs Carvedilol, Metoprolol, and Ramipril. And many studies have pointed out that Carvedilol and Ramipril have an effect on RA. Overall, the CMDs extracted from multilayer networks provide us with an impressive understanding disease mechanisms from the perspective of multi-layer network and also provide an effective way to predict potential drugs for diseases based on its neighbors in a same CDM.
Bacterial Communities in the Alpaca Gastrointestinal Tract Vary With Diet and Body Site

Gut -associated microbes (‘gut microbiota’) impact the nutrition of their hosts, especially in ruminants and pseudoruminants that consume high-cellulose diets. Examples include the pseudoruminant alpaca. To better understand how body site and diet influence the alpaca microbiota, we performed three 16S rRNA gene surveys. First, we surveyed the compartment 1 (C1), duodenum, jejunum, ileum, cecum, and large intestine (LI) of alpacas fed a grass hay (GH; tall fescue) or alfalfa hay (AH) diet for 30 days. Second, we performed a C1 survey of alpacas fed a series of 2-week mixed grass hay (MGH) diets supplemented with ∼25% dry weight barley, quinoa, amaranth, or soybean meal. Third, we examined the microbial differences of alpacas with normal versus poor body condition. Samples from GH- and AH-fed alpacas grouped by diet and body site but none of the four supplements significantly altered C1 microbiota composition, relative to each other, and none of the OTUs were differentially abundant between alpacas with normal versus poor body conditions. Taken together, the findings of a diet- and body-site specific alpaca microbiota are consistent with previous findings in ruminants and other mammals, but we provide no evidence to link changes in alpaca body condition with variation in microbiota relative abundance or identity.
The Origin of Unpleasant Aftertastes in Synthetic Sweeteners: A Hypothesis

Most sweeteners are plagued with unwanted unpleasant aftertastes. Here we examined the possibility that one of the main reasons for this is the similarity of sweet and umami receptors. We performed docking calculations on models of sweet and umami receptors using as template the recently determined solid state structure of the first taste receptor, the medaka fish T1R2-T1R3 receptor. Our results show convincingly that sweeteners can be recognized also by the T1R1-T1R3 umami receptor, owing to the similarity of its architecture to that of the sweet receptor. We hypothesize that the T1R1-T1R3 receptor plays a key role in modulating the quality of sweet tastants, hinting at a simple explanation of their aftertaste. The prevailing ideas on taste coding favor strict labeling of taste cells, which would exclude that umami receptors can recognize other taste sensations. If some cross-talk based on the combinatorial model of taste is accepted, some sweet ligands can exert a bitter sensation. However, even if cross-talk is not admitted, direct stimulation of the umami receptor is bound to cause an aftertaste incompatible with good sweet quality.
Cloth Manipulation Using Random-Forest-Based Imitation Learning

We present a novel approach for manipulating high-DOF deformable objects such as cloth. Our approach uses a random-forest-based controller that maps the observed visual features of the cloth to an optimal control action of the manipulator. The topological structure of this random-forest is determined automatically based on the training data, which consists of visual features and control signals. The training data is constructed online using an imitation learning algorithm. We have evaluated our approach on different cloth manipulation benchmarks such as flattening, folding, and twisting. In all these tasks, we have observed convergent behavior for the random-forest. On convergence, the random-forest-based controller exhibits superior robustness to observation noise compared with other techniques such as convolutional neural networks and nearest neighbor searches. Videos and supplemental material are available at http://gamma.cs. unc.edu/ClothM/.
Bipartite Quantum Interactions: Entangling and Information Processing Abilities

The aim of this thesis is to advance the theory behind quantum information processing tasks, by deriving fundamental limits on bipartite quantum interactions and dynamics, which corresponds to an underlying Hamiltonian that governs the physical transformation of a two-body open quantum system. The goal is to determine entangling abilities of such arbitrary bipartite quantum interactions. Doing so provides fundamental limitations on information processing tasks, including entanglement distillation and secret key generation, over a bipartite quantum network. We also discuss limitations on the entropy change and its rate for dynamics of an open quantum system weakly interacting with the bath. We introduce a measure of non-unitarity to characterize the deviation of a doubly stochastic quantum process from a noiseless evolution. Next, we introduce information processing tasks for secure read-out of digital information encoded in read-only memory devices against adversaries of varying capabilities. The task of reading a memory device involves the identification of an interaction process between probe system, which is in known state, and the memory device. Essentially, the information is stored in the choice of channels, which are noisy quantum processes in general and are chosen from a publicly known set. Hence, it becomes pertinent to securely read memory devices against scrutiny of an adversary. In particular, for a secure read-out task called private reading when a reader is under surveillance of a passive eavesdropper, we have determined upper bounds on its performance. We do so by leveraging the fact that private reading of digital information stored in a memory device can be understood as secret key agreement via a specific kind of bipartite quantum interaction.
The Security of Smart Buildings: a Systematic Literature Review

Smart Buildings are networks of connected devices and software in charge of automatically managing and controlling several building functions such as HVAC, fire alarms, lighting, shading and more. These systems evolved from mostly electronic and mechanical elements to complex systems relying on IT and wireless technologies and networks. This exposes smart buildings to new risks and threats that need to be enumerated and addressed. Research efforts have been done in several areas related to security in smart buildings but a clear overview of the research field is missing. In this paper, we present the results of a systematic literature review that provides a thorough understanding of the state of the art in research on the security of smart buildings. We found that the field of smart buildings security is growing significantly in complexity due to the many protocols introduced recently and that the research community is already studying. We also found an important lack of empirical evaluations, though evaluations on testbeds and real systems seems to be growing. Finally, we found an almost complete lack of consideration of non-technical aspects, such as social, organisational, and human factors, which are crucial in this type of systems, where ownership and liability is not always clear.
Hybrid Modelling in Oncology: Sucesses, Challenges and Hopes

In this review we make the statement that hybrid models in oncology are required as a mean for enhanced data integration. In the context of systems oncology, experimental and clinical data need to be at the heart of the models developments from conception to validation to ensure a relevant use of the models in the clinical context. The main applications pursued are to improve diagnosis and to optimize therapies.We first present the Successes achieved thanks to hybrid modelling approaches to advance knowledge, treatments or drug discovery. Then we present the Challenges than need to be addressed to allow for a better integration of the model parts and of the data into the models. And Finally, the Hopes with a focus towards making personalised medicine a reality. Mathematics Subject Classification. 35Q92, 68U20, 68T05, 92-08, 92B05.
Transmitter and Receiver Architectures for Molecular Communications: A Survey on Physical Design With Modulation, Coding, and Detection Techniques

Inspired by nature, molecular communications (MC), i.e., the use of molecules to encode, transmit, and receive information, stands as the most promising communication paradigm to realize the nanonetworks. Even though there has been extensive theoretical research toward nanoscale MC, there are no examples of implemented nanoscale MC networks. The main reason for this lies in the peculiarities of nanoscale physics, challenges in nanoscale fabrication, and highly stochastic nature of the biochemical domain of envisioned nanonetwork applications. This mandates developing novel device architectures and communication methods compatible with MC constraints. To that end, various transmitter and receiver designs for MC have been proposed in the literature together with numerable modulation, coding, and detection techniques. However, these works fall into domains of a very wide spectrum of disciplines, including, but not limited to, information and communication theory, quantum physics, materials science, nanofabrication, physiology, and synthetic biology. Therefore, we believe it is imperative for the progress of the field that an organized exposition of cumulative knowledge on the subject matter can be compiled. Thus, to fill this gap, in this comprehensive survey, we review the existing literature on transmitter and receiver architectures toward realizing MC among nanomaterial-based nanomachines and/or biological entities and provide a complete overview of modulation, coding, and detection techniques employed for MC. Moreover, we identify the most significant shortcomings and challenges in all these research areas and propose potential solutions to overcome some of them.
Enhance the Motion Cues for Face Anti-Spoofing using CNN-LSTM Architecture

Spatio-temporal information is very important to capture the discriminative cues between genuine and fake faces from video sequences. To explore such a temporal feature, the fine-grained motions (e.g., eye blinking, mouth movements and head swing) across video frames are very critical. In this paper, we propose a joint CNN-LSTM network for face anti-spoofing, focusing on the motion cues across video frames. We first extract the high discriminative features of video frames using the conventional Convolutional Neural Network (CNN). Then we leverage Long Short-Term Memory (LSTM) with the extracted features as inputs to capture the temporal dynamics in videos. To ensure the fine-grained motions more easily to be perceived in the training process, the eulerian motion magnification is used as the preprocessing to enhance the facial expressions exhibited by individuals, and the attention mechanism is embedded in LSTM to ensure the model learn to focus selectively on the dynamic frames across the video clips. Experiments on Replay Attack and MSU-MFSD databases show that the proposed method yields state-of-the-art performance with better generalization ability compared with several other popular algorithms.
Exploring Communities in Large Profiled Graphs

Given a graph $G$G and a vertex $q\in G$q∈G, the community search (CS) problem aims to efficiently find a subgraph of $G$G whose vertices are closely related to $q$q. Communities are prevalent in social and biological networks, and can be used in product advertisement and social event recommendation. In this paper, we study profiled community search (PCS), where CS is performed on a profiled graph. This is a graph in which each vertex has labels arranged in a hierarchical manner. Extensive experiments show that PCS can identify communities with themes that are common to their vertices, and is more effective than existing CS approaches. As a naive solution for PCS is highly expensive, we have also developed a tree index, which facilitates efficient and online solutions for PCS.
Age of Information With Prioritized Streams: When to Buffer Preempted Packets?

In this paper, we consider N information streams sharing a common service facility. The streams are supposed to have different priorities based on their sensitivity. A higher priority stream will always preempt the service of a lower priority packet. By leveraging the notion of Stochastic Hybrid Systems (SHS), we investigate the Age of Information (AoI) in the case where each stream has its own waiting room; when preempted by a higher priority stream, the packet is stored in the waiting room for future resume. Interestingly, it will be shown that a "no waiting room" scenario, and consequently discarding preempted packets, is better in terms of average AoI in some cases. The exact cases where this happen are discussed and numerical results that corroborate the theoretical findings and highlight this trade-off are provided.
Easy to Fool? Testing the Anti-evasion Capabilities of PDF Malware Scanners

Malware scanners try to protect users from opening malicious documents by statically or dynamically analyzing documents. However, malware developers may apply evasions that conceal the maliciousness of a document. Given the variety of existing evasions, systematically assessing the impact of evasions on malware scanners remains an open challenge. This paper presents a novel methodology for testing the capability of malware scanners to cope with evasions. We apply the methodology to malicious Portable Document Format (PDF) documents and present an in-depth study of how current PDF evasions affect 41 state-of-the-art malware scanners. The study is based on a framework for creating malicious PDF documents that use one or more evasions. Based on such documents, we measure how effective different evasions are at concealing the maliciousness of a document. We find that many static and dynamic scanners can be easily fooled by relatively simple evasions and that the effectiveness of different evasions varies drastically. Our work not only is a call to arms for improving current malware scanners, but by providing a large-scale corpus of malicious PDF documents with evasions, we directly support the development of improved tools to detect document-based malware. Moreover, our methodology paves the way for a quantitative evaluation of evasions in other kinds of malware.
How to place your apps in the fog: State of the art and open challenges

Fog computing aims at extending the cloud towards the Internet of things so to achieve improved quality of service and to empower latency‐sensitive and bandwidth‐hungry applications. The fog calls for novel models and algorithms to distribute multiservice applications in such a way that data processing occurs wherever it is best placed, based on both functional and nonfunctional requirements.
A Random Walk Approach to First-Order Stochastic Convex Optimization

Online minimization of an unknown convex function over a convex and compact set is considered under first-order stochastic bandit feedback, which returns a random realization of the gradient of the function at each query point. Without knowing the distribution of the random gradients, a learning algorithm sequentially chooses query points with the objective of minimizing regret defined as the expected cumulative loss of the function values at the query points in excess to the minimum value of the function. An active search strategy based on devising a biased random walk on an infinite-depth tree constructed through successive partitioning of the domain of the function is developed. It is shown that the biased random walk moves toward the optimal point in a geometric rate, leading to an order-optimal regret performance of $\tilde {\mathcal{O}}\left( {\sqrt T } \right)$. The structural properties of this random-walk based strategy admits detailed finite-time regret analysis. By localizing data processing to small subsets of the input domain based on the tree structure, it enjoys $\mathcal{O}\left( 1 \right)$ computation and memory complexity per query and allows dynamic allocation of limited data storage.
Using DNNs to Detect Materials in a Room based on Sound Absorption

The materials of surfaces in a room play an important room in shaping the auditory experience within them. Different materials absorb energy at different levels. The level of absorption also varies across frequencies. This paper investigates how cues from a measured impulse response in the room can be exploited by machines to detect the materials present. With this motivation, this paper proposes a method for estimating the probability of presence of 10 material categories, based on their frequency-dependent absorption characteristics. The method is based on a CNN-RNN, trained as a multi-task classifier. The network is trained using a priori knowledge about the absorption characteristics of materials from the literature. In the experiments shown, the network is tested on over 5,00 impulse responses and 167 materials. The F1 score of the detections was 98%, with an even precision and recall. The method finds direct applications in architectural acoustics and in creating more parsimonious models for acoustic reflections.
Navigating through the R packages for movement.

The advent of miniaturized biologging devices has provided ecologists with unprecedented opportunities to record animal movement across scales, and led to the collection of ever-increasing quantities of tracking data. In parallel, sophisticated tools have been developed to process, visualize and analyse tracking data, however many of these tools have proliferated in isolation, making it challenging for users to select the most appropriate method for the question in hand. Indeed, within the R software alone, we listed 58 packages created to deal with tracking data or 'tracking packages'. Here we reviewed and described each tracking package based on a workflow centered around tracking data (i.e. spatio-temporal locations (x,y,t)), broken down into three stages: pre-processing, post-processing and analysis, the latter consisting of data visualization, track description, path reconstruction behavioral pattern identification, space use characterization, trajectory simulation and others. Supporting documentation is key to render a package accessible for users. Based on a user survey, we reviewed the quality of packages' documentation, and identified 11 packages with good or excellent documentation. Links between packages were assessed through a network graph analysis. Although a large group of packages showed some degree of connectivity (either depending on functions or suggesting the use of another tracking package), one third of the packages worked in isolation, reflecting a fragmentation in the R movement-ecology programming community. Finally, we provide recommendations for users when choosing packages, and for developers to maximize the usefulness of their contribution and strengthen the links within the programming community.
An Underwater Image Enhancement Benchmark Dataset and Beyond

Underwater image enhancement has been attracting much attention due to its significance in marine engineering and aquatic robotics. Numerous underwater image enhancement algorithms have been proposed in the last few years. However, these algorithms are mainly evaluated using either synthetic datasets or few selected real-world images. It is thus unclear how these algorithms would perform on images acquired in the wild and how we could gauge the progress in the field. To bridge this gap, we present the first comprehensive perceptual study and analysis of underwater image enhancement using large-scale real-world images. In this paper, we construct an Underwater Image Enhancement Benchmark (UIEB) including 950 real-world underwater images, 890 of which have the corresponding reference images. We treat the rest 60 underwater images which cannot obtain satisfactory reference images as challenging data. Using this dataset, we conduct a comprehensive study of the state-of-the-art underwater image enhancement algorithms qualitatively and quantitatively. In addition, we propose an underwater image enhancement network (called Water-Net) trained on this benchmark as a baseline, which indicates the generalization of the proposed UIEB for training Convolutional Neural Networks (CNNs). The benchmark evaluations and the proposed Water-Net demonstrate the performance and limitations of state-of-the-art algorithms, which shed light on future research in underwater image enhancement. The dataset and code are available at https://li-chongyi.github. io/proj_benchmark. html.
Video Captioning with Visual and Semantic Features

Video captioning refers to the process of extracting features from a video and generating video captions using the extracted features. This paper introduces a deep neural network model and its learning method for effective video captioning. In this study, visual features as well as semantic features, which effectively express the video, are also used. The visual features of the video are extracted using convolutional neural networks, such as C3D and ResNet, while the semantic features are extracted using a semantic feature extraction network proposed in this paper. Further, an attention-based caption generation network is proposed for effective generation of video captions using the extracted features. The performance and effectiveness of the proposed model is verified through various experiments using two large-scale video benchmarks such as the Microsoft Video Description (MSVD) and the Microsoft Research Video-To-Text (MSR-VTT).