pwc-archive/papers-with-abstracts huggingface dataset:
A Generalized Framework for Pulse-Shaping on Delay-Doppler Plane
Authors: Mohsen Bayat, Arman Farhang
Date: 2023-11-12 00:00:00

The primary objective of this paper is to establish a generalized framework for pulse-shaping on the delay-Doppler plane. To this end, we classify delay-Doppler pulse-shaping techniques into two types, namely, circular and linear pulse-shaping. This paves the way towards the development of a generalized pulse-shaping framework. Our generalized framework provides the opportunity to compare different pulse-shaping techniques under the same umbrella while bringing new insights into their properties. In particular, our derivations based on this framework reveal that the recently emerged waveform orthogonal delay-Doppler multiplexing modulation (ODDM) is a linear pulse-shaping technique. By presenting ODDM under our generalized framework, we clearly explain the observed staircase behavior of its spectrum which has not been previously reported in the literature. Another contribution of this paper is proposal of a simple out-of-band (OOB) emission reduction technique by inserting a small number of zero-guard (ZG) symbols along the delay dimension of the circularly pulse-shaped signals. Additionally, inserting the zero-guards improves the bit-error-rate (BER) performance of both circular and linear pulse-shaping techniques. Finally, our simulation results confirm the validity of our mathematical derivations, claims and the effectiveness of the ZGs in OOB reduction and BER performance improvement.
Multiuser Resource Allocation for Semantic-Relay-Aided Text Transmissions
Authors: Zeyang Hu, Tianyu Liu, Changsheng You, Zhaohui Yang, Mingzhe Chen
Date: 2023-11-12 00:00:00
Tasks: Decoder, Semantic Communication

Semantic communication (SemCom) is an emerging technology that extracts useful meaning from data and sends only relevant semantic information. Thus, it has the great potential to improve the spectrum efficiency of conventional wireless systems with bit transmissions, especially in low signal-to-noise ratio (SNR) and small bandwidth regions. However, the existing works have mostly overlooked the constraints of mobile devices, which may not have sufficient capabilities to implement resource-demanding semantic encoder/decoder based on deep learning. To address this issue, we propose in this paper a new semantic relay (SemRelay), which is equipped with a semantic receiver to assist multiuser text transmissions. Specifically, the SemRelay decodes semantic information from a base station and forwards it to the users using conventional bit transmission, hence effectively improving text transmission efficiency. To study the multiuser resource allocation, we formulate an optimization problem to maximize the multiuser weighted sum-rate by jointly designing the SemRelay transmit power allocation and system bandwidth allocation. Although this problem is non-convex and hence challenging to solve, we propose an efficient algorithm to obtain its high-quality suboptimal solution by using the block coordinate descent method. Last, numerical results show the effectiveness of the proposed algorithm as well as superior performance of the proposed SemRelay over the conventional decode-and-forward (DF) relay, especially in small bandwidth region.
Coexistence of OTFS Modulation With OFDM-based Communication Systems
Authors: Akram Shafie, Jinhong Yuan, Yuting Fang, Paul Fitzpatrick, Taka Sakurai
Date: 2023-11-12 00:00:00

This study examines the coexistence of orthogonal time-frequency space (OTFS) modulation with current fourth- and fifth-generation (4G/5G) wireless communication systems that primarily use orthogonal frequency-division multiplexing (OFDM) waveforms. We first derive the input-output-relation (IOR) of OTFS when it coexists with an OFDM system while considering the impact of unequal lengths of the cyclic prefixes (CPs) in the OTFS signal. We show analytically that the inclusion of multiple CPs to the OTFS signal results in the effective sampled delay-Doppler (DD) domain channel response to be less sparse. We also show that the effective DD domain channel coefficients for OTFS in coexisting systems are influenced by the unequal lengths of the CPs. Subsequently, we propose an embedded pilot-aided channel estimation (CE) technique for OTFS in coexisting systems that leverages the derived IOR for accurate channel characterization. Using numerical results, we show that ignoring the impact of unequal lengths of the CPs during signal detection can degrade the bit error rate performance of OTFS in coexisting systems. We also show that the proposed CE technique for OTFS in coexisting systems outperforms the state-of-the-art threshold-based CE technique.
Joint Design of Coding and Modulation for Digital Over-the-Air Computation
Authors: Xin Xie, Cunqinq Hua, Jianan Hong, Yuejun Wei
Date: 2023-11-12 00:00:00

Due to its high communication efficiency, over-the-air computation (AirComp) has been expected to carry out various computing tasks in the next-generation wireless networks. However, up to now, most applications of AirComp are explored in the analog domain, which limits the capability of AirComp in resisting the complex wireless environment, not to mention to integrate the AirComp technique to the existing universal communication standards, most of which are based on the digital system. In this paper, we propose a joint design of channel coding and digital modulation for digital AirComp transmission to attempt to reinforce the foundation for the application of AirComp in the digital system. Specifically, we first propose a non-binary LDPC-based channel coding scheme to enhance the error-correction capability of AirComp. Then, a digital modulation scheme is proposed to achieve the number summation from multiple transmitters via the lattice coding technique. We also provide simulation results to demonstrate the feasibility and the performance of the proposed design.
One Signal-Noise Separation based Wiener Filter for Magnetogastrogram
Authors: Hua Li
Date: 2023-11-12 00:00:00
Tasks: Denoising

Magnetogastrogram (MGG) signal frequency is about 0.05 Hz, the low-frequency environmental noise interference is serious and can be several times stronger in magnitude than the signals of interest and may severely impede the extraction of relevant information. Wiener filter is one classic denoising solution for biomagnetic applications. Since the reference channels are usually placed not far enough from the biomagnetic sources under test, they will inevitably detect the signals and the Wiener filters may produce ill-conditioned solutions. Considering the solutions to improve the signal-to-noise ratio (SNR) of Wiener filter output, there are few methods to separate the signals from the noises of the reference signal at the filter input. In this paper, a new signal processing framework called signal-noise separation based Wiener filter (SNSWF) is proposed that it separates the main noise as the input signal of the filter to improve the output SNR of Wiener filter. The filter was successfully applied to the noise suppression for MGG signal detection. Using the SNSWF, the filter SNR is 16.7 dB better than the classic Wiener filter.
Semantic-aware Sampling and Transmission in Energy Harvesting Systems: A POMDP Approach
Authors: Abolfazl Zakeri, Mohammad Moltafet, Marian Codreanu
Date: 2023-11-11 00:00:00
Tasks: Deep Reinforcement Learning

We address the problem of real-time remote tracking of a partially observable Markov source in an energy harvesting system with an unreliable communication channel. We consider both sampling and transmission costs. Different from most prior studies that assume the source is fully observable, the sampling cost renders the source partially observable. The goal is to jointly optimize sampling and transmission policies for two semantic-aware metrics: i) a general distortion measure and ii) the age of incorrect information (AoII). We formulate a stochastic control problem. To solve the problem for each metric, we cast a partially observable Markov decision process (POMDP), which is transformed into a belief MDP. Then, for both AoII under the perfect channel setup and distortion, we express the belief as a function of the age of information (AoI). This expression enables us to effectively truncate the corresponding belief space and formulate a finite-state MDP problem, which is solved using the relative value iteration algorithm. For the AoII metric in the general setup, a deep reinforcement learning policy is proposed to solve the belief MDP problem. Simulation results show the effectiveness of the derived policies and, in particular, reveal a non-monotonic switching-type structure of the real-time optimal policy with respect to AoI.
Sum-Rate Optimization for RIS-Aided Multiuser Communications with Movable Antenna
Authors: Yunan Sun, Hao Xu, Chongjun Ouyang, Hongwen Yang
Date: 2023-11-11 00:00:00
Tasks: Position

Reconfigurable intelligent surface (RIS) is known as a promising technology to improve the performance of wireless communication networks, which has been extensively studied. Movable antenna (MA) is a novel technology that fully exploits the antenna position for enhancing the channel capacity. In this paper, we propose a new RIS-aided multiuser communication system with MAs. The sum-rate is maximized by jointly optimizing the beamforming, the reflection coefficient (RC) values of RIS and the positions of MAs. A fractional programming-based iterative algorithm is proposed to solve the formulated non-convex problem, considering three assumptions for the RIS. Numerical results are presented to verify the effectiveness of the proposed algorithm and the superiority of the proposed MA-based system in terms of sum-rate.
Heuristic Optimal Transport in Branching Networks
Authors: M. Andrecut
Date: 2023-11-11 00:00:00

Optimal transport aims to learn a mapping of sources to targets by minimizing the cost, which is typically defined as a function of distance. The solution to this problem consists of straight line segments optimally connecting sources to targets, and it does not exhibit branching. These optimal solutions are in stark contrast with both natural, and man-made transportation networks, where branching structures are prevalent. Here we discuss a fast heuristic branching method for optimal transport in networks. We also provide several numerical applications to synthetic examples, a simplified cardiovascular network, and the "Santa Claus" distribution network which includes 141,182 cities around the world, with known location and population.
Higher-Order Newton Methods with Polynomial Work per Iteration
Authors: Amir Ali Ahmadi, Abraar Chaudhry, Jeffrey Zhang
Date: 2023-11-10 00:00:00

We present generalizations of Newton's method that incorporate derivatives of an arbitrary order $d$ but maintain a polynomial dependence on dimension in their cost per iteration. At each step, our $d^{\text{th}}$-order method uses semidefinite programming to construct and minimize a sum of squares-convex approximation to the $d^{\text{th}}$-order Taylor expansion of the function we wish to minimize. We prove that our $d^{\text{th}}$-order method has local convergence of order $d$. This results in lower oracle complexity compared to the classical Newton method. We show on numerical examples that basins of attraction around local minima can get larger as $d$ increases. Under additional assumptions, we present a modified algorithm, again with polynomial cost per iteration, which is globally convergent and has local convergence of order $d$.
Evolution of SLiM-mediated hijack functions in intrinsically disordered viral proteins
Authors: Juliana Glavina, Nicolas Palopoli, Lucía B Chemes
Date: 2023-11-13 00:00:00

Viruses and their hosts are involved in an 'arms race' where they continually evolve mechanisms to overcome each other. It has long been proposed that intrinsic disorder provides a substrate for the evolution of viral hijack functions and that short linear motifs (SLiMs) are important players in this process. Here, we review evidence in support of this tenet from two model systems: the papillomavirus E7 protein and the adenovirus E1A protein. Phylogenetic reconstructions reveal that SLiMs appear and disappear multiple times across evolution, providing evidence of convergent evolution within individual viral phylogenies. Multiple functionally related SLiMs show strong co-evolution signals that persist across long distances in the primary sequence and occur in unrelated viral proteins. Moreover, changes in SLiMs are associated with changes in phenotypic traits such as host range and tropism. Tracking viral evolutionary events reveals that host switch events are associated with the loss of several SLiMs, suggesting that SLiMs are under functional selection and that changes in SLiMs support viral adaptation. Fine-tuning of viral SLiM sequences can improve affinity, allowing them to outcompete host counterparts. However, viral SLiMs are not always competitive by themselves, and tethering of two suboptimal SLiMs by a disordered linker may instead enable viral hijack. Coevolution between the SLiMs and the linker indicates that the evolution of disordered regions may be more constrained than previously thought. In summary, experimental and computational studies support a role for SLiMs and intrinsic disorder in viral hijack functions and in viral adaptive evolution.
A comparative study of the lipid panel levels at different duration time and temperature storage
Authors: Mohammed Mahdi Sami, Mataz J. Jamai, Bushra A. Jassam
Date: 2023-11-13 00:00:00

Background: the stability of serum specimen during time storage is importance in clinical and medical science researches in addition of diagnosis. Lipids are organic molecules that classified into 8 classes: fatty acids, phospholipids, glycerolipids, saccharolipids, polyketides, prenol lipids, sterol, and sphingolipids. Lipid analysis (cholesterol, triglyceride, high density lipoprotein, low density lipoprotein, very low-density lipoprotein) is a vital tool for diagnosis of numerous disease such as cardiovascular disease. follow-up the lipid profile progression is essential of numerous diseases. Methods: a 72 apparently healthy individual were participated in current study the serum sample was taken after 12-14 hours of fasting. The serum cholesterol, triglyceride, high density cholesterol, low density cholesterol, and very low-density cholesterol were determined. Results: there are no significant value found in all groups when compared to control except triglyceride that was significant after 24 hours of freezing.
Probing omics data via harmonic persistent homology
Authors: Davide Gurnari, Aldo Guzmán-Sáenz, Filippo Utro, Aritra Bose, Saugata Basu, Laxmi Parida
Date: 2023-11-10 00:00:00
Tasks: Topological Data Analysis

Identifying molecular signatures from complex disease patients with underlying symptomatic similarities is a significant challenge in the analysis of high dimensional multi-omics data. Topological data analysis (TDA) provides a way of extracting such information from the geometric structure of the data and identifying multiway higher-order relationships. Here, we propose an application of Harmonic persistent homology, which overcomes the limitations of ambiguous assignment of the topological information to the original elements in a representative topological cycle from the data. When applied to multi-omics data, this leads to the discovery of hidden patterns highlighting the relationships between different omic profiles, while allowing for common tasks in multi-omics analyses, such as disease subtyping, and most importantly biomarker identification for similar latent biological pathways that are associated with complex diseases. Our experiments on multiple cancer data show that harmonic persistent homology effectively dissects multi-omics data to identify biomarkers by detecting representative cycles predictive of disease subtypes.
Biodiversity analysis of metaproteomics samples with Unipept: a comprehensive tutorial
Authors: Tim Van Den Bossche, Pieter Verschaffelt, Tibo Vande Moortele, Peter Dawyndt, Lennart Martens, Bart Mesuere
Date: 2023-11-13 00:00:00

Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers in-depth insights into both taxonomic distributions and functional characteristics of complex ecosystems. This tutorial explains essential concepts like Lowest Common Ancestor (LCA) determination and the handling of peptides with missed cleavages. It also provides a detailed, step-by-step guide on using the Unipept Web application and Unipept Desktop for thorough metaproteomics analyses. By integrating theoretical principles with practical methodologies, this tutorial empowers researchers with the essential knowledge and tools needed to fully utilize metaproteomics in their microbiome studies.
Grounding Neuroscience in Behavioral Changes using Artificial Neural Networks
Authors: Grace W. Lindsay
Date: 2023-11-13 00:00:00

Connecting neural activity to function is a common aim in neuroscience. How to define and conceptualize function, however, can vary. Here I focus on grounding this goal in the specific question of how a given change in behavior is produced by a change in neural circuits or activity. Artificial neural network models offer a particularly fruitful format for tackling such questions because they use neural mechanisms to perform complex transformations and produce appropriate behavior. Therefore, they can be a means of causally testing the extent to which a neural change can be responsible for an experimentally observed behavioral change. Furthermore, because the field of interpretability in artificial intelligence has similar aims, neuroscientists can look to interpretability methods for new ways of identifying neural features that drive performance and behaviors.
Impossibility results on stability of phylogenetic consensus methods
Authors: Emanuele Delucchi, Linard Hoessly, Giovanni Paolini
Date: 2018-10-08 00:00:00

We answer two questions raised by Bryant, Francis and Steel in their work on consensus methods in phylogenetics. Consensus methods apply to every practical instance where it is desired to aggregate a set of given phylogenetic trees (say, gene evolution trees) into a resulting, "consensus" tree (say, a species tree). Various stability criteria have been explored in this context, seeking to model desirable consistency properties of consensus methods as the experimental data are updated (e.g., more taxa, or more trees, are mapped). However, such stability conditions can be incompatible with some basic regularity properties that are widely accepted to be essential in any meaningful consensus method. Here, we prove that such an incompatibility does arise in the case of extension stability on binary trees and in the case of associative stability. Our methods combine general theoretical considerations with the use of computer programs tailored to the given stability requirements.
Misuse of Antibiotics in Poultry Threatens Pakistan Communitys Health
Authors: Muhammad Hamza, Hafeez Ur Rehman Ali Khera, Muhammad Umair Waqas, Ayesha Muazzam, Sania Tariq, Zain Kaleem, Waseem Akram, M Talha Mumtaz, Shehroz Ahmad, Abdul Samad
Date: 2023-11-13 00:00:00
Tasks: Survey

A survey was conducted from February 2022 to May 2022 on the usage of antibiotics at a poultry farm in different areas of Multan, Punjab Pakistan. A well-organized questionnaire was used for the collection of data. Sixty poultry farms were surveyed randomly in the Multan district. All of these Farms were using antibiotics. Antibiotics are commonly used for the treatment of diseases. Some are used as preventive medicine and a few are used as growth promotors. neomycin, erythromycin, oxytetracycline, streptomycin, and colistin are the broad-spectrum antibiotics that are being used commercially. Enrofloxacin and Furazolidone are the common antibiotics that are being used in Studies these days. The class of Fluoroquinolones is commonly used in poultry farms. Thirty-three patterns of antibiotic usage were observed at poultry farms. multi-drug practices were also observed on various farms. In this study, 25% of antibiotics are prescribed by the veterans while more than 90 % were acquired from the veterinary store. This study provides information about the antibiotics which are commonly being used in the study location district Multan. It is expected that the finding of this survey will be helpful in the development of new strategies against the misuse of antibiotics on farms.
Combined certainty and uncertainty across development frees phenotypic variation in evolution
Authors: Yue Zhang
Date: 2023-11-11 00:00:00

Developmental bias plays a major role in phenotypic evolution. Some researchers have argued that phenotypes, regulated by development, can only evolve along restricted trajectory under certain scenarios, such as the case for mammalian molar size ratios. However, this view has been challenged. Broadly speaking, sources for phenotypic variation remain largely unknown. The study here presents a generalized Inhibitory Cascade Model and explains that the original model described only means of phenotypes resulting from selection when viewed under a higher taxonomic scope. Consequently, I propose the combined property of development: certainty, when the prior intersegmental inhibition is strong, and uncertainty, when the opposite holds. This property potentially not only explains counterintuitively high levels of developmental instability, but also plays an essential role in generating phenotypic variation.
Extirpation of Atlantic Cod from a Northwest Atlantic ecosystem in the absence of predator control: inference from an ecosystem model of intermediate complexity
Authors: Steven P. Rossi, Sean P. Cox. Hugues P. Benoît
Date: 2023-11-11 00:00:00

Atlantic cod (Gadus morhua) in the southern Gulf of St. Lawrence (sGSL) declined to low abundance in the early 1990s and have since failed to recover due to high natural mortality, which has been linked to grey seal (Halichoerus grypus) predation. Increased grey seal harvests have been suggested to improve cod survival, however, predicting the response of cod to seal abundance changes in the sGSL is complicated by a hypothesized triangular food web involving seals, cod, and small pelagic fishes, wherein the pelagic fishes are prey for cod and grey seals, but may also prey on young cod. Grey seals may therefore have an indirect positive effect on prerecruit cod survival via predation on pelagic fish. Using a multispecies model of intermediate complexity fitted to various scientific and fisheries data, we found that seal predation accounted for the majority of recent cod mortality and that cod will likely be extirpated without a strong and rapid reduction in grey seal abundance. We did not find evidence that reducing grey seal abundance will result in large increases to herring biomass that could impair cod recovery.