pwc-archive/papers-with-abstracts huggingface dataset:
Existence of two distinct time scales in the Fairen-Velarde model of bacterial respiration
Authors: Soumyadeep Kundu, Muktish Acharyya
Date: 2023-10-09 00:00:00

We study the bacterial respiration through the numerical solution of the Fairen-Velarde coupled nonlinear differential equations. The instantaneous concentrations of the oxygen and the nutrients are computed. The fixed point solution and the stable limit cycle are found in different parameter ranges as predicted by the linearized differential equations. In a specified range of parameters, it is observed that the system spends some time near the stable limit cycle and eventually reaches the stable fixed point. This metastability has been investigated systematically. Interestingly, it is observed that the system exhibits two distinctly different time scales in reaching the stable fixed points. The slow time scale of the metastable lifetime near the stable limit cycle and a fast time scale (after leaving the zone of limit cycle) in rushing towards the stable fixed point. The gross residence time, near the limit cycle (described by a slow time scale), can be reduced by varying the concentrations of nutrients. This idea can be used to control the harmful metastable lifespan of active bacteria.
Dominance and multi-locus interaction
Authors: Juan Li, Claudia Bank
Date: 2023-10-07 00:00:00
Tasks: Position

Dominance is usually considered a constant value that describes the relative difference in fitness or phenotype between heterozygotes and the average of homozygotes at a focal polymorphic locus. However, the observed dominance can vary with the genetic background of the focal locus. Here, alleles at other loci modify the observed phenotype through position effects or dominance modifiers that are sometimes associated with pathogen resistance, lineage, sex, or mating type. Theoretical models have illustrated how variable dominance appears in the context of multi-locus interaction (epistasis). Here, we review empirical evidence for variable dominance and how the observed patterns may be captured by proposed epistatic models. We highlight how integrating epistasis and dominance is crucial for comprehensively understanding adaptation and speciation.
Fast protein backbone generation with SE(3) flow matching
Authors: Jason Yim, Andrew Campbell, Andrew Y. K. Foong, Michael Gastegger, José Jiménez-Luna, Sarah Lewis, Victor Garcia Satorras, Bastiaan S. Veeling, Regina Barzilay, Tommi Jaakkola, Frank Noé
Date: 2023-10-08 00:00:00
Tasks: Protein Design

We present FrameFlow, a method for fast protein backbone generation using SE(3) flow matching. Specifically, we adapt FrameDiff, a state-of-the-art diffusion model, to the flow-matching generative modeling paradigm. We show how flow matching can be applied on SE(3) and propose modifications during training to effectively learn the vector field. Compared to FrameDiff, FrameFlow requires five times fewer sampling timesteps while achieving two fold better designability. The ability to generate high quality protein samples at a fraction of the cost of previous methods paves the way towards more efficient generative models in de novo protein design.
PointGAT: A quantum chemical property prediction model integrating graph attention and 3D geometry
Authors: Rong Zhang, Rongqing Yuan, Boxue Tian
Date: 2023-10-08 00:00:00
Tasks: 3D geometry, Computational chemistry, Drug Design, Graph Attention, Molecular Property Prediction, molecular representation, Prediction, Property Prediction, Representation Learning

Predicting quantum chemical properties is a fundamental challenge for computational chemistry. While the development of graph neural networks has advanced molecular representation learning and property prediction, their performance could be further enhanced by incorporating 3D structural geometry into 2D molecular graph representation. In this study, we introduce the PointGAT model for quantum molecular property prediction, which integrates 3D molecular coordinates with graph-attention modeling. Comparison with other current models in molecular prediction tasks showed that PointGAT could provide higher predictive accuracy in various benchmark datasets from MoleculeNet, including ESOL, FreeSolv, Lipop, HIV, and 10 out of 12 tasks of the QM9 dataset. To further examine PointGAT prediction of quantum mechanical (QM) energies, we constructed a C10 dataset comprising 11,841 charged and chiral carbocation intermediates with QM energies calculated at the DM21/6-31G*//B3LYP/6-31G* levels. Notably, PointGAT achieved an R2 value of 0.950 and an MAE of 1.616 kcal/mol, outperforming other models. Additional ablation studies indicated that incorporating molecular geometry into the model resulted in markedly higher predictive accuracy, reducing the MAE value from 1.802 kcal/mol to 1.616 kcal/mol. Moreover, visualization of PointGAT atomic attention weights suggested its predictions were interpretable. Findings in this study support the application of PointGAT as a powerful and versatile tool for quantum chemical property prediction that can facilitate high-accuracy modeling for fundamental exploration of chemical space as well as drug design and molecular engineering.
Integration of Fractional Order Black-Scholes Merton with Neural Network
Authors: Sarit Maitra, Vivek Mishra, Goutam Kr. Kundu, Kapil Arora
Date: 2023-10-05 00:00:00

This study enhances option pricing by presenting unique pricing model fractional order Black-Scholes-Merton (FOBSM) which is based on the Black-Scholes-Merton (BSM) model. The main goal is to improve the precision and authenticity of option pricing, matching them more closely with the financial landscape. The approach integrates the strengths of both the BSM and neural network (NN) with complex diffusion dynamics. This study emphasizes the need to take fractional derivatives into account when analyzing financial market dynamics. Since FOBSM captures memory characteristics in sequential data, it is better at simulating real-world systems than integer-order models. Findings reveals that in complex diffusion dynamics, this hybridization approach in option pricing improves the accuracy of price predictions. the key contribution of this work lies in the development of a novel option pricing model (FOBSM) that leverages fractional calculus and neural networks to enhance accuracy in capturing complex diffusion dynamics and memory effects in financial data.
Market Crowds' Trading Behaviors, Agreement Prices, and the Implications of Trading Volume
Authors: Leilei Shi, Bing Han, Yingzi Zhu, Liyan Han, Yiwen Wang, Yan Piao
Date: 2023-10-09 00:00:00

It has been long that literature in financial academics focuses mainly on price and return but much less on trading volume. In the past twenty years, it has already linked both price and trading volume to economic fundamentals, and explored the behavioral implications of trading volume such as investor's attitude toward risks, overconfidence, disagreement, and attention etc. However, what is surprising is how little we really know about trading volume. Here we show that trading volume probability represents the frequency of market crowd's trading action in terms of behavior analysis, and test two adaptive hypotheses relevant to the volume uncertainty associated with price in China stock market. The empirical work reveals that market crowd trade a stock in efficient adaptation except for simple heuristics, gradually tend to achieve agreement on an outcome or an asset price widely on a trading day, and generate such a stationary equilibrium price very often in interaction and competition among themselves no matter whether it is highly overestimated or underestimated. This suggests that asset prices include not only a fundamental value but also private information, speculative, sentiment, attention, gamble, and entertainment values etc. Moreover, market crowd adapt to gain and loss by trading volume increase or decrease significantly in interaction with environment in any two consecutive trading days. Our results demonstrate how interaction between information and news, the trading action, and return outcomes in the three-term feedback loop produces excessive trading volume which includes various internal and external causes.
CFDBench: A Large-Scale Benchmark for Machine Learning Methods in Fluid Dynamics
Authors: Yining Luo, Yingfa Chen, Zhen Zhang
Date: 2023-09-13 00:00:00

In recent years, applying deep learning to solve physics problems has attracted much attention. Data-driven deep learning methods produce fast numerical operators that can learn approximate solutions to the whole system of partial differential equations (i.e., surrogate modeling). Although these neural networks may have lower accuracy than traditional numerical methods, they, once trained, are orders of magnitude faster at inference. Hence, one crucial feature is that these operators can generalize to unseen PDE parameters without expensive re-training.In this paper, we construct CFDBench, a benchmark tailored for evaluating the generalization ability of neural operators after training in computational fluid dynamics (CFD) problems. It features four classic CFD problems: lid-driven cavity flow, laminar boundary layer flow in circular tubes, dam flows through the steps, and periodic Karman vortex street. The data contains a total of 302K frames of velocity and pressure fields, involving 739 cases with different operating condition parameters, generated with numerical methods. We evaluate the effectiveness of popular neural operators including feed-forward networks, DeepONet, FNO, U-Net, etc. on CFDBnech by predicting flows with non-periodic boundary conditions, fluid properties, and flow domain shapes that are not seen during training. Appropriate modifications were made to apply popular deep neural networks to CFDBench and enable the accommodation of more changing inputs. Empirical results on CFDBench show many baseline models have errors as high as 300% in some problems, and severe error accumulation when performing autoregressive inference. CFDBench facilitates a more comprehensive comparison between different neural operators for CFD compared to existing benchmarks.
Dual Latent State Learning: Exploiting Regional Network Similarities for QoS Prediction
Authors: Ziliang Wang, Xiaohong Zhang, Kechi Zhang, Ze Shi Li, Meng Yan
Date: 2023-10-07 00:00:00
Tasks: Prediction

Individual objects, whether users or services, within a specific region often exhibit similar network states due to their shared origin from the same city or autonomous system (AS). Despite this regional network similarity, many existing techniques overlook its potential, resulting in subpar performance arising from challenges such as data sparsity and label imbalance. In this paper, we introduce the regional-based dual latent state learning network(R2SL), a novel deep learning framework designed to overcome the pitfalls of traditional individual object-based prediction techniques in Quality of Service (QoS) prediction. Unlike its predecessors, R2SL captures the nuances of regional network behavior by deriving two distinct regional network latent states: the city-network latent state and the AS-network latent state. These states are constructed utilizing aggregated data from common regions rather than individual object data. Furthermore, R2SL adopts an enhanced Huber loss function that adjusts its linear loss component, providing a remedy for prevalent label imbalance issues. To cap off the prediction process, a multi-scale perception network is leveraged to interpret the integrated feature map, a fusion of regional network latent features and other pertinent information, ultimately accomplishing the QoS prediction. Through rigorous testing on real-world QoS datasets, R2SL demonstrates superior performance compared to prevailing state-of-the-art methods. Our R2SL approach ushers in an innovative avenue for precise QoS predictions by fully harnessing the regional network similarities inherent in objects.
Vulnerability Clustering and other Machine Learning Applications of Semantic Vulnerability Embeddings
Authors: Mark-Oliver Stehr, Minyoung Kim
Date: 2023-08-23 00:00:00
Tasks: Clustering, Form

Cyber-security vulnerabilities are usually published in form of short natural language descriptions (e.g., in form of MITRE's CVE list) that over time are further manually enriched with labels such as those defined by the Common Vulnerability Scoring System (CVSS). In the Vulnerability AI (Analytics and Intelligence) project, we investigated different types of semantic vulnerability embeddings based on natural language processing (NLP) techniques to obtain a concise representation of the vulnerability space. We also evaluated their use as a foundation for machine learning applications that can support cyber-security researchers and analysts in risk assessment and other related activities. The particular applications we explored and briefly summarize in this report are clustering, classification, and visualization, as well as a new logic-based approach to evaluate theories about the vulnerability space.
Learning Cyber Defence Tactics from Scratch with Multi-Agent Reinforcement Learning
Authors: Jacob Wiebe, Ranwa Al Mallah, Li Li
Date: 2023-08-25 00:00:00
Tasks: Multi-agent Reinforcement Learning, reinforcement-learning

Recent advancements in deep learning techniques have opened new possibilities for designing solutions for autonomous cyber defence. Teams of intelligent agents in computer network defence roles may reveal promising avenues to safeguard cyber and kinetic assets. In a simulated game environment, agents are evaluated on their ability to jointly mitigate attacker activity in host-based defence scenarios. Defender systems are evaluated against heuristic attackers with the goals of compromising network confidentiality, integrity, and availability. Value-based Independent Learning and Centralized Training Decentralized Execution (CTDE) cooperative Multi-Agent Reinforcement Learning (MARL) methods are compared revealing that both approaches outperform a simple multi-agent heuristic defender. This work demonstrates the ability of cooperative MARL to learn effective cyber defence tactics against varied threats.
Analysis of Learned Features and Framework for Potato Disease Detection
Authors: Shikha Gupta, Soma Chakraborty, Renu Rameshan
Date: 2023-08-29 00:00:00

For applications like plant disease detection, usually, a model is trained on publicly available data and tested on field data. This means that the test data distribution is not the same as the training data distribution, which affects the classifier performance adversely. We handle this dataset shift by ensuring that the features are learned from disease spots in the leaf or healthy regions, as applicable. This is achieved using a faster Region-based convolutional neural network (RCNN) as one of the solutions and an attention-based network as the other. The average classification accuracies of these classifiers are approximately 95% while evaluated on the test set corresponding to their training dataset. These classifiers also performed equivalently, with an average score of 84% on a dataset not seen during the training phase.
Robust and Efficient Interference Neural Networks for Defending Against Adversarial Attacks in ImageNet
Authors: Yunuo Xiong, Shujuan Liu, Hongwei Xiong
Date: 2023-09-03 00:00:00
Tasks: Deep Learning

The existence of adversarial images has seriously affected the task of image recognition and practical application of deep learning, it is also a key scientific problem that deep learning urgently needs to solve. By far the most effective approach is to train the neural network with a large number of adversarial examples. However, this adversarial training method requires a huge amount of computing resources when applied to ImageNet, and has not yet achieved satisfactory results for high-intensity adversarial attacks. In this paper, we construct an interference neural network by applying additional background images and corresponding labels, and use pre-trained ResNet-152 to efficiently complete the training. Compared with the state-of-the-art results under the PGD attack, it has a better defense effect with much smaller computing resources. This work provides new ideas for academic research and practical applications of effective defense against adversarial attacks.
Mitigating Denial of Service Attacks in Fog-Based Wireless Sensor Networks Using Machine Learning Techniques
Authors: Ademola Abidoye, Ibidun Obagbuwa, Nureni Azeez
Date: 2023-09-10 00:00:00

Wireless sensor networks are considered to be among the most significant and innovative technologies in the 21st century due to their wide range of industrial applications. Sensor nodes in these networks are susceptible to a variety of assaults due to their special qualities and method of deployment. In WSNs, denial of service attacks are common attacks in sensor networks. It is difficult to design a detection and prevention system that would effectively reduce the impact of these attacks on WSNs. In order to identify assaults on WSNs, this study suggests using two machine learning models: decision trees and XGBoost. The WSNs dataset was the subject of extensive tests to identify denial of service attacks. The experimental findings demonstrate that the XGBoost model, when applied to the entire dataset, has a higher true positive rate (98.3%) than the Decision tree approach (97.3%) and a lower false positive rate (1.7%) than the Decision tree technique (2.7%). Like this, with selected dataset assaults, the XGBoost approach has a higher true positive rate (99.01%) than the Decision tree technique (97.50%) and a lower false positive rate (0.99%) than the Decision tree technique (2.50%).
Classification of Spam URLs Using Machine Learning Approaches
Authors: Omar Husni Odeh, Anas Arram, Murad Njoum
Date: 2023-09-10 00:00:00
Tasks: Classification

The Internet is used by billions of users every day because it offers fast and free communication tools and platforms. Nevertheless, with this significant increase in usage, huge amounts of spam are generated every second, which wastes internet resources and, more importantly, users' time. This study investigates the use of machine learning models to classify URLs as spam or nonspam. We first extract the features from the URL as it has only one feature, and then we compare the performance of several models, including k nearest neighbors, bagging, random forest, logistic regression, and others. Experimental results demonstrate that bagging outperformed other models and achieved the highest accuracy of 98.64%. In addition, bagging outperformed the current state-of-the-art approaches which emphasize its effectiveness in addressing spam-related challenges on the Internet. This suggests that bagging is a promising approach for URL spam classification.
Bayesian Quality-Diversity approaches for constrained optimization problems with mixed continuous, discrete and categorical variables
Authors: Loic Brevault, Mathieu Balesdent
Date: 2023-09-11 00:00:00
Tasks: Bayesian Optimization, Diversity, Gaussian Processes

Complex system design problems, such as those involved in aerospace engineering, require the use of numerically costly simulation codes in order to predict the performance of the system to be designed. In this context, these codes are often embedded into an optimization process to provide the best design while satisfying the design constraints. Recently, new approaches, called Quality-Diversity, have been proposed in order to enhance the exploration of the design space and to provide a set of optimal diversified solutions with respect to some feature functions. These functions are interesting to assess trade-offs. Furthermore, complex design problems often involve mixed continuous, discrete, and categorical design variables allowing to take into account technological choices in the optimization problem. Existing Bayesian Quality-Diversity approaches suited for intensive high-fidelity simulations are not adapted to mixed variables constrained optimization problems. In order to overcome these limitations, a new Quality-Diversity methodology based on mixed variables Bayesian optimization strategy is proposed in the context of limited simulation budget. Using adapted covariance models and dedicated enrichment strategy for the Gaussian processes in Bayesian optimization, this approach allows to reduce the computational cost up to two orders of magnitude, with respect to classical Quality-Diversity approaches while dealing with discrete choices and the presence of constraints. The performance of the proposed method is assessed on a benchmark of analytical problems as well as on two aerospace system design problems highlighting its efficiency in terms of speed of convergence. The proposed approach provides valuable trade-offs for decision-markers for complex system design.
Automating global landslide detection with heterogeneous ensemble deep-learning classification
Authors: Alexandra Jarna Ganerød, Gabriele Franch, Erin Lindsay, Martina Calovi
Date: 2023-09-12 00:00:00
Tasks: Deep Learning

With changing climatic conditions, we are already seeing an increase in extreme weather events and their secondary consequences, including landslides. Landslides threaten infrastructure, including roads, railways, buildings, and human life. Hazard-based spatial planning and early warning systems are cost-effective strategies to reduce the risk to society from landslides. However, these both rely on data from previous landslide events, which is often scarce. Many deep learning (DL) models have recently been applied for landside mapping using medium- to high-resolution satellite images as input. However, they often suffer from sensitivity problems, overfitting, and low mapping accuracy. This study addresses some of these limitations by using a diverse global landslide dataset, using different segmentation models, such as Unet, Linknet, PSP-Net, PAN, and DeepLab and based on their performances, building an ensemble model. The ensemble model achieved the highest F1-score (0.69) when combining both Sentinel-1 and Sentinel-2 bands, with the highest average improvement of 6.87 % when the ensemble size was 20. On the other hand, Sentinel-2 bands only performed very well, with an F1 score of 0.61 when the ensemble size is 20 with an improvement of 14.59 % when the ensemble size is 20. This result shows considerable potential in building a robust and reliable monitoring system based on changes in vegetation index dNDVI only.
Fingerprint Attack: Client De-Anonymization in Federated Learning
Authors: Qiongkai Xu, Trevor Cohn, Olga Ohrimenko
Date: 2023-09-12 00:00:00
Tasks: Clustering, Federated Learning

Federated Learning allows collaborative training without data sharing in settings where participants do not trust the central server and one another. Privacy can be further improved by ensuring that communication between the participants and the server is anonymized through a shuffle; decoupling the participant identity from their data. This paper seeks to examine whether such a defense is adequate to guarantee anonymity, by proposing a novel fingerprinting attack over gradients sent by the participants to the server. We show that clustering of gradients can easily break the anonymization in an empirical study of learning federated language models on two language corpora. We then show that training with differential privacy can provide a practical defense against our fingerprint attack.