pwc-archive/papers-with-abstracts huggingface dataset:
Label Design-based ELM Network for Timing Synchronization in OFDM Systems with Nonlinear Distortion
Authors: Chaojin Qing, Shuhai Tang, Chuangui Rao, Qing Ye, Jiafan Wang, Chuan Huang
Date: 2021-07-28 00:00:00

Due to the nonlinear distortion in Orthogonal frequency division multiplexing (OFDM) systems, the timing synchronization (TS) performance is inevitably degraded at the receiver. To relieve this issue, an extreme learning machine (ELM)-based network with a novel learning label is proposed to the TS of OFDM system in our work and increases the possibility of symbol timing offset (STO) estimation residing in inter-symbol interference (ISI)-free region. Especially, by exploiting the prior information of the ISI-free region, two types of learning labels are developed to facilitate the ELM-based TS network. With designed learning labels, a timing-processing by classic TS scheme is first executed to capture the coarse timing metric (TM) and then followed by an ELM network to refine the TM. According to experiments and analysis, our scheme shows its effectiveness in the improvement of TS performance and reveals its generalization performance in different training and testing channel scenarios.
Learning Site-Specific Probing Beams for Fast mmWave Beam Alignment
Authors: Yuqiang Heng, Jianhua Mo, Jeffrey G. Andrews
Date: 2021-07-28 00:00:00

Beam alignment - the process of finding an optimal directional beam pair - is a challenging procedure crucial to millimeter wave (mmWave) communication systems. We propose a novel beam alignment method that learns a site-specific probing codebook and uses the probing codebook measurements to predict the optimal narrow beam. An end-to-end neural network (NN) architecture is designed to jointly learn the probing codebook and the beam predictor. The learned codebook consists of site-specific probing beams that can capture particular characteristics of the propagation environment. The proposed method relies on beam sweeping of the learned probing codebook, does not require additional context information, and is compatible with the beam sweeping-based beam alignment framework in 5G. Using realistic ray-tracing datasets, we demonstrate that the proposed method can achieve high beam alignment accuracy and signal-to-noise ratio (SNR) while significantly - by roughly a factor of 3 in our setting - reducing the beam sweeping complexity and latency.
Analysis of Activity Dependent Development of Topographic Maps in Neural Field Theory with Short Time Scale Dependent Plasticity
Authors: Nicholas Gale, Jennifer Rodger, Michael Small, Stephen Eglen
Date: 2021-07-28 00:00:00

Topographic maps are a brain structure connecting pre-synpatic and post-synaptic brain regions. Topographic development is dependent on Hebbian-based plasticity mechanisms working in conjunction with spontaneous patterns of neural activity generated in the pre-synaptic regions. Studies performed in mouse have shown that these spontaneous patterns can exhibit complex spatial-temporal structures which existing models cannot incorporate. Neural field theories are appropriate modelling paradigms for topographic systems due to the dense nature of the connections between regions and can be augmented with a plasticity rule general enough to capture complex time-varying structures. We propose a theoretical framework for studying the development of topography in the context of complex spatial-temporal activity fed-forward from the pre-synaptic to post-synaptic regions. Analysis of the model leads to an analytic solution corroborating the conclusion that activity can drive the refinement of topographic projections. The analysis also suggests that biological noise is used in the development of topography to stabilise the dynamics. MCMC simulations are used to analyse and understand the differences in topographic refinement between wild-type and the $\beta2$ knock-out mutant in mice. The time scale of the synaptic plasticity window is estimated as $0.56$ seconds in this context with a model fit of $R^2 = 0.81$.
The loss landscape of deep linear neural networks: a second-order analysis
Authors: El Mehdi Achour, François Malgouyres, Sébastien Gerchinovitz
Date: 2021-07-28 00:00:00
Tasks: Diversity

We study the optimization landscape of deep linear neural networks with the square loss. It is known that, under weak assumptions, there are no spurious local minima and no local maxima. However, the existence and diversity of non-strict saddle points, which can play a role in first-order algorithms' dynamics, have only been lightly studied. We go a step further with a full analysis of the optimization landscape at order 2. We characterize, among all critical points, which are global minimizers, strict saddle points, and non-strict saddle points. We enumerate all the associated critical values. The characterization is simple, involves conditions on the ranks of partial matrix products, and sheds some light on global convergence or implicit regularization that have been proved or observed when optimizing linear neural networks. In passing, we provide an explicit parameterization of the set of all global minimizers and exhibit large sets of strict and non-strict saddle points.
Protein-protein interactions enhance the thermal resilience of SpyRing enzymes: a molecular dynamic simulation study
Authors: Qi Gao, Dengming Ming
Date: 2021-07-28 00:00:00
Tasks: Geometric Matching

Recently a technique based on the interaction between adhesion proteins extracted from Streptococcus pyogenes, known as SpyRing, has been widely used to improve the thermal resilience of enzymes, the assembly of biostructures, cancer cell recognition and other fields. In SpyRing, the two termini of the target enzyme are respectively linked to the peptide SpyTag and its protein partner SpyCatcher. SpyTag spontaneously reacts with SpyCatcher to form an isopeptide bond, with which the target enzyme forms a close ring structure. It was believed that the covalent cyclization of protein skeleton caused by SpyRing reduces the conformational entropy of biological structure and improves its rigidity, thus improving the thermal resilience of the target enzyme. However, the effects of SpyTag/ SpyCatcher interaction with this enzyme are poorly understood, and their regulation of enzyme properties remains unclear. Here, for simplicity, we took the single domain enzyme lichenase from Bacillus subtilis 168 as an example, studied the interface interactions in the SpyRing system by molecular dynamics simulations, and examined the effects of the changes of electrostatic interaction and van der Waals interaction on the thermal resilience of target enzyme. The simulations showed that the interface between SpyTag/SpyCatcher and lichenase is different from that found by geometric matching method and highlighted key mutations that affect the intensity of interactions at the interface and might have effect on the thermal resilience of the enzyme. Our calculations provided new insights into the rational designs in the SpyRing.
OncoEnrichR: cancer-dedicated gene set interpretation
Authors: Sigve Nakken, Sveinung Gundersen, Fabian L. M. Bernal, Dimitris Polychronopoulos, Eivind Hovig, Jørgen Wesche
Date: 2021-07-28 00:00:00

Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typically combine results from a variety of bioinformatics resources in an attempt to portray and understand cancer relevance. As a means to simplify and strengthen the support for this endeavor, we have developed oncoEnrichR, a flexible bioinformatics tool that allows cancer researchers to comprehensively interrogate a given gene list along multiple facets of cancer relevance. oncoEnrichR differs from general gene set analysis frameworks through the integration of an extensive set of prior knowledge specifically relevant for cancer, including ranked gene-tumor type associations, literature-supported proto-oncogene and tumor suppressor gene annotations, target druggability data, regulatory interactions, synthetic lethality predictions, as well as prognostic associations, gene aberrations, and co-expression patterns across tumor types. The software produces a structured and user-friendly analysis report as its main output, where versions of all underlying data resources are explicitly logged, the latter being a critical component for reproducible science. We demonstrate the usefulness of oncoEnrichR through interrogation of two candidate lists from proteomic and CRISPR screens. oncoEnrichR is freely available as a web-based workflow hosted by the Galaxy platform (https://oncotools.elixir.no), and can also be accessed as a stand-alone R package (https://github.com/sigven/oncoEnrichR).
Complex physical properties of an adaptive, self-organizing biological system
Authors: Jozsef Prechl
Date: 2021-07-28 00:00:00

The physical interpretation of the functioning of the adaptive immune system, which has been thoroughly characterized on genetic and molecular levels, provides a unique opportunity to define an adaptive self-organizing biological system in its entirety. This paper describes a configuration space model of immune function, where directed chemical potentials of the system constitute a space of interactions. In the physical sense, the humoral adaptive immune system adjusts the chemical potential of all available antigenic molecules by tuning the chemical potential and organizing the network hierarchy of its sensor-effector molecules, antibodies. The coupling of sensors and effectors allows the system to adjust the thermodynamic activity of antigens and antibodies, while network organization helps minimize chemical potentials and maximize diversity. Mathematically the system couples the variance of Gaussian distributed interaction energies in its interaction space to the exponentially distributed chemical potentials of its effector molecules to maintain its stationary state. This process creates a scale-free network in interaction space, where absolute thermodynamic activity corresponds to node degree. In the thermodynamic interpretation, the system is an ensemble carrying out {mu}N work, adjusting chemical potentials according to the changes in the chemical potentials of the surroundings. The validity of the model is supported by identifying an interaction flexibility index, the corresponding variables in thermodynamics and network science, and by confirming its applicability to the humoral immune system. Overall, this statistical thermodynamics model of adaptive immunity describes how adaptive biological self-organization arises from the maintenance of a scale-free, directed interaction network with fractal topology.
Inference on the structure of gene regulatory networks
Authors: Yue Wang, Zikun Wang
Date: 2021-07-27 00:00:00

In this paper, we conduct theoretical analyses on inferring the structure of gene regulatory networks. Depending on the experimental method and data type, the inference problem is classified into 20 different scenarios. For each scenario, we discuss the problem that with enough data, under what assumptions, what can be inferred about the structure. For scenarios that have been covered in the literature, we provide a brief review. For scenarios that have not been covered in literature, if the structure can be inferred, we propose new mathematical inference methods and evaluate them on simulated data. Otherwise, we prove that the structure cannot be inferred.
Moving outside the lab: The viability of conducting sensorimotor learning studies online
Authors: Jonathan S. Tsay, Alan Lee, Richard B. Ivry, Guy Avraham
Date: 2021-07-28 00:00:00

Collecting data online via crowdsourcing platforms has proven to be a very efficient way to recruit a large and diverse sample. Studies of motor learning, however, have been largely confined to the lab due to the need for special equipment to record movement kinematics and, as such, are typically only accessible to specific participants (e.g., college students). As a first foray to make motor learning studies accessible to a larger and more diverse audience, we developed an online, web-based platform (OnPoint) to collect kinematic data, serving as a template for researchers to create their own online sensorimotor control and learning experiments. As a proof-of-concept, we asked if fundamental motor learning phenomena discovered in the lab could be replicated online. In a series of three experiments, we observed a close correspondence between the results obtained online with those previously reported from research conducted in the laboratory. This web-based platform paired with online crowdsourcing can serve as a powerful new method for the study of motor control and learning.
Curved Micro-Electrode Arrays
Authors: Markus Meister
Date: 2021-07-26 00:00:00

Multi-electrode arrays serve to record electrical signals of many neurons in the brain simultaneously. For most of the past century, electrodes that penetrate brain tissue have had exactly one shape: a straight needle. Certainly this was a good starting choice at the time, but there is no reason to think that a straight line would be the optimal shape in all Neuroscience applications. Here I argue that, in fact, a wide variety of curved shapes is equally practical: all possible helices. I discuss the manufacture and manipulation of such devices, and illustrate a few use cases where they will likely outperform conventional needles. With some collective action from the research community, curved arrays could be manufactured and distributed at low cost.
Meaning Versus Information, Prediction Versus Memory, and Question Versus Answer
Authors: Yoonsuck Choe
Date: 2021-06-29 00:00:00
Tasks: Deep Learning

Brain science and artificial intelligence have made great progress toward the understanding and engineering of the human mind. The progress has accelerated significantly since the turn of the century thanks to new methods for probing the brain (both structure and function), and rapid development in deep learning research. However, despite these new developments, there are still many open questions, such as how to understand the brain at the system level, and various robustness issues and limitations of deep learning. In this informal essay, I will talk about some of the concepts that are central to brain science and artificial intelligence, such as information and memory, and discuss how a different view on these concepts can help us move forward, beyond current limits of our understanding in these fields.
Nonlinear State Space Modeling and Control of the Impact of Patients' Modifiable Lifestyle Behaviors on the Emergence of Multiple Chronic Conditions
Authors: Syed Hasib Akhter Faruqui, Adel Alaeddini, Jing Wang, Susan P Fisher-Hoch, Joseph B Mccormic
Date: 2021-07-14 00:00:00

The emergence and progression of multiple chronic conditions (MCC) over time often form a dynamic network that depends on patient's modifiable risk factors and their interaction with non-modifiable risk factors and existing conditions. Continuous time Bayesian networks (CTBNs) are effective methods for modeling the complex network of MCC relationships over time. However, CTBNs are not able to effectively formulate the dynamic impact of patient's modifiable risk factors on the emergence and progression of MCC. Considering a functional CTBN (FCTBN) to represent the underlying structure of the MCC relationships with respect to individuals' risk factors and existing conditions, we propose a nonlinear state-space model based on Extended Kalman filter (EKF) to capture the dynamics of the patients' modifiable risk factors and existing conditions on the MCC evolution over time. We also develop a tensor control chart to dynamically monitor the effect of changes in the modifiable risk factors of individual patients on the risk of new chronic conditions emergence. We validate the proposed approach based on a combination of simulation and real data from a dataset of 385 patients from Cameron County Hispanic Cohort (CCHC) over multiple years. The dataset examines the emergence of 5 chronic conditions (Diabetes, Obesity, Cognitive Impairment, Hyperlipidemia, and Hypertension) based on 4 modifiable risk factors representing lifestyle behaviors (Diet, Exercise, Smoking Habit, and Drinking Habit) and 3 non-modifiable risk factors, including demographic information (Age, Gender, Education). The results demonstrate the effectiveness of the proposed methodology for dynamic prediction and monitoring of the risk of MCC emergence in individual patients.
A Sustainable Ecosystem through Emergent Cooperation in Multi-Agent Reinforcement Learning
Authors: Fabian Ritz, Daniel Ratke, Thomy Phan, Lenz Belzner, Claudia Linnhoff-Popien
Date: 2021-07-19 00:00:00
Proceeding: ALIFE 2021 7
Tasks: Multi-agent Reinforcement Learning, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

This paper considers sustainable and cooperative behavior in multi-agent systems. In the proposed predator-prey simulation, multiple selfish predators can learn to act sustainably by maintaining a herd of reproducing prey and further hunt cooperatively for long term benefit. Since the predators face starvation pressure, the scenario can also turn in a tragedy of the commons if selfish individuals decide to greedily hunt down the prey population before their conspecifics do, ultimately leading to extinction of prey and predators. This paper uses Multi-Agent Reinforcement Learning to overcome a collapse of the simulated ecosystem, analyzes the impact factors over multiple dimensions and proposes suitable metrics. We show that up to three predators are able to learn sustainable behavior in form of collective herding under starvation pressure. Complex cooperation in form of group hunting emerges between the predators as their speed is handicapped and the prey is given more degrees of freedom to escape. The implementation of environment and reinforcement learning pipeline is available online.
Amplitude Mean of Functional Data on $\mathbb{S}^2$
Authors: Zhengwu Zhang, Bayan Saparbayeva
Date: 2021-07-29 00:00:00

Manifold-valued functional data analysis (FDA) recently becomes an active area of research motivated by the raising availability of trajectories or longitudinal data observed on non-linear manifolds. The challenges of analyzing such data come from many aspects, including infinite dimensionality and nonlinearity, as well as time-domain or phase variability. In this paper, we study the amplitude part of manifold-valued functions on $\mathbb{S}^2$, which is invariant to random time warping or re-parameterization. Utilizing the nice geometry of $\mathbb{S}^2$, we develop a set of efficient and accurate tools for temporal alignment of functions, geodesic computing, and sample mean calculation. At the heart of these tools, they rely on gradient descent algorithms with carefully derived gradients. We show the advantages of these newly developed tools over its competitors with extensive simulations and real data and demonstrate the importance of considering the amplitude part of functions instead of mixing it with phase variability in manifold-valued FDA.
Physics-informed Guided Disentanglement in Generative Networks
Authors: Fabio Pizzati, Pietro Cerri, Raoul de Charette
Date: 2021-07-29 00:00:00
Tasks: Disentanglement, Image-to-Image Translation, Translation

Image-to-image translation (i2i) networks suffer from entanglement effects in presence of physics-related phenomena in target domain (such as occlusions, fog, etc), lowering altogether the translation quality, controllability and variability. In this paper, we propose a general framework to disentangle visual traits in target images. Primarily, we build upon collection of simple physics models, guiding the disentanglement with a physical model that renders some of the target traits, and learning the remaining ones. Because physics allows explicit and interpretable outputs, our physical models (optimally regressed on target) allows generating unseen scenarios in a controllable manner. Secondarily, we show the versatility of our framework to neural-guided disentanglement where a generative network is used in place of a physical model in case the latter is not directly accessible. Altogether, we introduce three strategies of disentanglement being guided from either a fully differentiable physics model, a (partially) non-differentiable physics model, or a neural network. The results show our disentanglement strategies dramatically increase performances qualitatively and quantitatively in several challenging scenarios for image translation.
Learning more skills through optimistic exploration
Authors: DJ Strouse, Kate Baumli, David Warde-Farley, Vlad Mnih, Steven Hansen
Date: 2021-07-29 00:00:00
Proceeding: ICLR 2022 4

Unsupervised skill learning objectives (Gregor et al., 2016, Eysenbach et al., 2018) allow agents to learn rich repertoires of behavior in the absence of extrinsic rewards. They work by simultaneously training a policy to produce distinguishable latent-conditioned trajectories, and a discriminator to evaluate distinguishability by trying to infer latents from trajectories. The hope is for the agent to explore and master the environment by encouraging each skill (latent) to reliably reach different states. However, an inherent exploration problem lingers: when a novel state is actually encountered, the discriminator will necessarily not have seen enough training data to produce accurate and confident skill classifications, leading to low intrinsic reward for the agent and effective penalization of the sort of exploration needed to actually maximize the objective. To combat this inherent pessimism towards exploration, we derive an information gain auxiliary objective that involves training an ensemble of discriminators and rewarding the policy for their disagreement. Our objective directly estimates the epistemic uncertainty that comes from the discriminator not having seen enough training examples, thus providing an intrinsic reward more tailored to the true objective compared to pseudocount-based methods (Burda et al., 2019). We call this exploration bonus discriminator disagreement intrinsic reward, or DISDAIN. We demonstrate empirically that DISDAIN improves skill learning both in a tabular grid world (Four Rooms) and the 57 games of the Atari Suite (from pixels). Thus, we encourage researchers to treat pessimism with DISDAIN.