OpenRaiser/Intern-Atlas huggingface dataset:
Neural Network Predicts Ion Concentration Profiles under Nanoconfinement
Venue: arXiv cs.LG 2023
Year: 2023

Modeling the ion concentration profile in nanochannel plays an important role in understanding the electrical double layer and electroosmotic flow. Due to the non-negligible surface interaction and the effect of discrete solvent molecules, molecular dynamics (MD) simulation is often used as an essential tool to study the behavior of ions under nanoconfinement. Despite the accuracy of MD simulation in modeling nanoconfinement systems, it is computationally expensive. In this work, we propose neural network to predict ion concentration profiles in nanochannels with different configurations, including channel widths, ion molarity, and ion types. By modeling the ion concentration profile as a probability distribution, our neural network can serve as a much faster surrogate model for MD simulation with high accuracy. We further demonstrate the superior prediction accuracy of neural network over XGBoost. Lastly, we demonstrated that neural network is flexible in predicting ion concentration profiles with different bin sizes. Overall, our deep learning model is a fast, flexible, and accurate surrogate model to predict ion concentration profiles in nanoconfinement.
Federated Learning with Classifier Shift for Class Imbalance
Venue: arXiv cs.LG 2023
Year: 2023

Federated learning aims to learn a global model collaboratively while the training data belongs to different clients and is not allowed to be exchanged. However, the statistical heterogeneity challenge on non-IID data, such as class imbalance in classification, will cause client drift and significantly reduce the performance of the global model. This paper proposes a simple and effective approach named FedShift which adds the shift on the classifier output during the local training phase to alleviate the negative impact of class imbalance. We theoretically prove that the classifier shift in FedShift can make the local optimum consistent with the global optimum and ensure the convergence of the algorithm. Moreover, our experiments indicate that FedShift significantly outperforms the other state-of-the-art federated learning approaches on various datasets regarding accuracy and communication efficiency.
Biological Factor Regulatory Neural Network
Venue: arXiv cs.LG 2023
Year: 2023

Genes are fundamental for analyzing biological systems and many recent works proposed to utilize gene expression for various biological tasks by deep learning models. Despite their promising performance, it is hard for deep neural networks to provide biological insights for humans due to their black-box nature. Recently, some works integrated biological knowledge with neural networks to improve the transparency and performance of their models. However, these methods can only incorporate partial biological knowledge, leading to suboptimal performance. In this paper, we propose the Biological Factor Regulatory Neural Network (BFReg-NN), a generic framework to model relations among biological factors in cell systems. BFReg-NN starts from gene expression data and is capable of merging most existing biological knowledge into the model, including the regulatory relations among genes or proteins (e.g., gene regulatory networks (GRN), protein-protein interaction networks (PPI)) and the hierarchical relations among genes, proteins and pathways (e.g., several genes/proteins are contained in a pathway). Moreover, BFReg-NN also has the ability to provide new biologically meaningful insights because of its white-box characteristics. Experimental results on different gene expression-based tasks verify the superiority of BFReg-NN compared with baselines. Our case studies also show that the key insights found by BFReg-NN are consistent with the biological literature.
Learning Optimal Fair Scoring Systems for Multi-Class Classification
Venue: arXiv cs.LG 2023
Year: 2023

Machine Learning models are increasingly used for decision making, in particular in high-stakes applications such as credit scoring, medicine or recidivism prediction. However, there are growing concerns about these models with respect to their lack of interpretability and the undesirable biases they can generate or reproduce. While the concepts of interpretability and fairness have been extensively studied by the scientific community in recent years, few works have tackled the general multi-class classification problem under fairness constraints, and none of them proposes to generate fair and interpretable models for multi-class classification. In this paper, we use Mixed-Integer Linear Programming (MILP) techniques to produce inherently interpretable scoring systems under sparsity and fairness constraints, for the general multi-class classification setup. Our work generalizes the SLIM (Supersparse Linear Integer Models) framework that was proposed by Rudin and Ustun to learn optimal scoring systems for binary classification. The use of MILP techniques allows for an easy integration of diverse operational constraints (such as, but not restricted to, fairness or sparsity), but also for the building of certifiably optimal models (or sub-optimal models with bounded optimality gap).
An Empirical Evaluation of Columnar Storage Formats
Venue: arXiv cs.DB 2023
Year: 2023

Columnar storage is a core component of a modern data analytics system. Although many database management systems (DBMSs) have proprietary storage formats, most provide extensive support to open-source storage formats such as Parquet and ORC to facilitate cross-platform data sharing. But these formats were developed over a decade ago, in the early 2010s, for the Hadoop ecosystem. Since then, both the hardware and workload landscapes have changed. In this paper, we revisit the most widely adopted open-source columnar storage formats (Parquet and ORC) with a deep dive into their internals. We designed a benchmark to stress-test the formats' performance and space efficiency under different workload configurations. From our comprehensive evaluation of Parquet and ORC, we identify design decisions advantageous with modern hardware and real-world data distributions. These include using dictionary encoding by default, favoring decoding speed over compression ratio for integer encoding algorithms, making block compression optional, and embedding finer-grained auxiliary data structures. We also point out the inefficiencies in the format designs when handling common machine learning workloads and using GPUs for decoding. Our analysis identified important considerations that may guide future formats to better fit modern technology trends.
Simultaneous Adversarial Attacks On Multiple Face Recognition System Components
Venue: arXiv cs.CV 2023
Year: 2023

In this work, we investigate the potential threat of adversarial examples to the security of face recognition systems. Although previous research has explored the adversarial risk to individual components of FRSs, our study presents an initial exploration of an adversary simultaneously fooling multiple components: the face detector and feature extractor in an FRS pipeline. We propose three multi-objective attacks on FRSs and demonstrate their effectiveness through a preliminary experimental analysis on a target system. Our attacks achieved up to 100% Attack Success Rates against both the face detector and feature extractor and were able to manipulate the face detection probability by up to 50% depending on the adversarial objective. This research identifies and examines novel attack vectors against FRSs and suggests possible ways to augment the robustness by leveraging the attack vector's knowledge during training of an FRS's components.
Static Analysis of Graph Database Transformations
Venue: arXiv cs.DB 2023
Year: 2023

We investigate graph transformations, defined using Datalog-like rules based on acyclic conjunctive two-way regular path queries (acyclic C2RPQs), and we study two fundamental static analysis problems: type checking and equivalence of transformations in the presence of graph schemas. Additionally, we investigate the problem of target schema elicitation, which aims to construct a schema that closely captures all outputs of a transformation over graphs conforming to the input schema. We show all these problems are in EXPTIME by reducing them to C2RPQ containment modulo schema; we also provide matching lower bounds. We use cycle reversing to reduce query containment to the problem of unrestricted (finite or infinite) satisfiability of C2RPQs modulo a theory expressed in a description logic.
Enhancement in Reliability for Multi-core system consisting of One Instruction Cores
Venue: arXiv cs.AR 2023
Year: 2023

Rapid CMOS device size reduction resulted in billions of transistors on a chip have led to integration of many cores leading to many challenges such as increased power dissipation, thermal dissipation, occurrence of transient faults and permanent faults. The mitigation of transient faults and permanent faults at the core level has become an important design parameter in a multi-core scenario. Core level techniques is a redundancy-based fault mitigation technique that improves the lifetime reliability of multi-core systems. In an asymmetric multi-core system, the smaller cores provide fault tolerance to larger cores is a core level fault mitigation technique that has gained momentum and focus from many researchers. The paper presents an economical, asymmetric multi-core system with one instruction cores (MCSOIC). The term Hardware Cost Estimation signifies power and area estimation for MCS-OIC. In MCSOIC, OIC is a warm standby redundant core. OICs provide functional support to conventional cores for shorter periods of time. To evaluate the idea, different configurations of MCSOIC is synthesized using FPGA and ASIC. The maximum power overhead and maximum area overhead are 0.46% and 11.4% respectively. The behavior of OICs in MCS-OIC is modelled using a One-Shot System (OSS) model for reliability analysis. The model parameters namely, readiness, wakeup probability and start-up-strategy for OSS are mapped to the multi-core systems with OICs. Expressions for system reliability is derived. System reliability is estimated for special cases.
A Self-attention Knowledge Domain Adaptation Network for Commercial Lithium-ion Batteries State-of-health Estimation under Shallow Cycles
Venue: arXiv cs.LG 2023
Year: 2023

Accurate state-of-health (SOH) estimation is critical to guarantee the safety, efficiency and reliability of battery-powered applications. Most SOH estimation methods focus on the 0-100\% full state-of-charge (SOC) range that has similar distributions. However, the batteries in real-world applications usually work in the partial SOC range under shallow-cycle conditions and follow different degradation profiles with no labeled data available, thus making SOH estimation challenging. To estimate shallow-cycle battery SOH, a novel unsupervised deep transfer learning method is proposed to bridge different domains using self-attention distillation module and multi-kernel maximum mean discrepancy technique. The proposed method automatically extracts domain-variant features from charge curves to transfer knowledge from the large-scale labeled full cycles to the unlabeled shallow cycles. The CALCE and SNL battery datasets are employed to verify the effectiveness of the proposed method to estimate the battery SOH for different SOC ranges, temperatures, and discharge rates. The proposed method achieves a root-mean-square error within 2\% and outperforms other transfer learning methods for different SOC ranges. When applied to batteries with different operating conditions and from different manufacturers, the proposed method still exhibits superior SOH estimation performance. The proposed method is the first attempt at accurately estimating battery SOH under shallow-cycle conditions without needing a full-cycle characteristic test.
Lecture Notes: Neural Network Architectures
Venue: arXiv cs.LG 2023
Year: 2023

These lecture notes provide an overview of Neural Network architectures from a mathematical point of view. Especially, Machine Learning with Neural Networks is seen as an optimization problem. Covered are an introduction to Neural Networks and the following architectures: Feedforward Neural Network, Convolutional Neural Network, ResNet, and Recurrent Neural Network.
Modeling and design of heterogeneous hierarchical bioinspired spider web structures using generative deep learning and additive manufacturing
Venue: arXiv cs.LG 2023
Year: 2023

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.
Dexterous In-Hand Manipulation of Slender Cylindrical Objects through Deep Reinforcement Learning with Tactile Sensing
Venue: arXiv cs.RO 2023
Year: 2023

Continuous in-hand manipulation is an important physical interaction skill, where tactile sensing provides indispensable contact information to enable dexterous manipulation of small objects. This work proposed a framework for end-to-end policy learning with tactile feedback and sim-to-real transfer, which achieved fine in-hand manipulation that controls the pose of a thin cylindrical object, such as a long stick, to track various continuous trajectories through multiple contacts of three fingertips of a dexterous robot hand with tactile sensor arrays. We estimated the central contact position between the stick and each fingertip from the high-dimensional tactile information and showed that the learned policies achieved effective manipulation performance with the processed tactile feedback. The policies were trained with deep reinforcement learning in simulation and successfully transferred to real-world experiments, using coordinated model calibration and domain randomization. We evaluated the effectiveness of tactile information via comparative studies and validated the sim-to-real performance through real-world experiments.
Artificial Collective Intelligence Engineering: a Survey of Concepts and Perspectives
Venue: arXiv cs.AI 2023
Year: 2023

Collectiveness is an important property of many systems--both natural and artificial. By exploiting a large number of individuals, it is often possible to produce effects that go far beyond the capabilities of the smartest individuals, or even to produce intelligent collective behaviour out of not-so-intelligent individuals. Indeed, collective intelligence, namely the capability of a group to act collectively in a seemingly intelligent way, is increasingly often a design goal of engineered computational systems--motivated by recent techno-scientific trends like the Internet of Things, swarm robotics, and crowd computing, just to name a few. For several years, the collective intelligence observed in natural and artificial systems has served as a source of inspiration for engineering ideas, models, and mechanisms. Today, artificial and computational collective intelligence are recognised research topics, spanning various techniques, kinds of target systems, and application domains. However, there is still a lot of fragmentation in the research panorama of the topic within computer science, and the verticality of most communities and contributions makes it difficult to extract the core underlying ideas and frames of reference. The challenge is to identify, place in a common structure, and ultimately connect the different areas and methods addressing intelligent collectives. To address this gap, this paper considers a set of broad scoping questions providing a map of collective intelligence research, mostly by the point of view of computer scientists and engineers. Accordingly, it covers preliminary notions, fundamental concepts, and the main research perspectives, identifying opportunities and challenges for researchers on artificial and computational collective intelligence engineering.
High-performance and Scalable Software-based NVMe Virtualization Mechanism with I/O Queues Passthrough
Venue: arXiv cs.AR 2023
Year: 2023

NVMe(Non-Volatile Memory Express) is an industry standard for solid-state drives (SSDs) that has been widely adopted in data centers. NVMe virtualization is crucial in cloud computing as it allows for virtualized NVMe devices to be used by virtual machines (VMs), thereby improving the utilization of storage resources. However, traditional software-based solutions have flexibility benefits but often come at the cost of performance degradation or high CPU overhead. On the other hand, hardware-assisted solutions offer high performance and low CPU usage, but their adoption is often limited by the need for special hardware support or the requirement for new hardware development. In this paper, we propose LightIOV, a novel software-based NVMe virtualization mechanism that achieves high performance and scalability without consuming valuable CPU resources and without requiring special hardware support. LightIOV can support thousands of VMs on each server. The key idea behind LightIOV is NVMe hardware I/O queues passthrough, which enables VMs to directly access I/O queues of NVMe devices, thus eliminating virtualization overhead and providing near-native performance. Results from our experiments show that LightIOV can provide comparable performance to VFIO, with an IOPS of 97.6%-100.2% of VFIO. Furthermore, in high-density VMs environments, LightIOV achieves 31.4% lower latency than SPDK-Vhost when running 200 VMs, and an improvement of 27.1% in OPS performance in real-world applications.
The Many Publics of Science: Using Altmetrics to Identify Common Communication Channels by Scientific field
Venue: arXiv cs.DL 2023
Year: 2023

Altmetrics have led to new quantitative studies of science through social media interactions. However, there are no models of science communication that respond to the multiplicity of non-academic channels. Using the 3653 authors with the highest volume of altmetrics mentions from the main channels (Twitter, News, Facebook, Wikipedia, Blog, Policy documents, and Peer reviews) to their publications (2016-2020), it has been analyzed where the audiences of each discipline are located. The results evidence the generalities and specificities of these new communication models and the differences between areas. These findings are useful for the development of science communication policies and strategies.
Decoupling anomaly discrimination and representation learning: self-supervised learning for anomaly detection on attributed graph
Venue: arXiv cs.LG 2023
Year: 2023

Anomaly detection on attributed graphs is a crucial topic for its practical application. Existing methods suffer from semantic mixture and imbalance issue because they mainly focus on anomaly discrimination, ignoring representation learning. It conflicts with the assortativity assumption that anomalous nodes commonly connect with normal nodes directly. Additionally, there are far fewer anomalous nodes than normal nodes, indicating a long-tailed data distribution. To address these challenges, a unique algorithm,Decoupled Self-supervised Learning forAnomalyDetection (DSLAD), is proposed in this paper. DSLAD is a self-supervised method with anomaly discrimination and representation learning decoupled for anomaly detection. DSLAD employs bilinear pooling and masked autoencoder as the anomaly discriminators. By decoupling anomaly discrimination and representation learning, a balanced feature space is constructed, in which nodes are more semantically discriminative, as well as imbalance issue can be resolved. Experiments conducted on various six benchmark datasets reveal the effectiveness of DSLAD.
Impact of Power Consumption Models on the Energy Efficiency of Downlink NOMA Systems
Venue: arXiv cs.NI 2023
Year: 2023

While non-orthogonal multiple access (NOMA) improves spectral efficiency, it results in a complexity at the receivers due to successive interference cancellation (SIC). Prior studies on the energy efficiency of NOMA overlook the SIC overhead and rely on simplistic power consumption models (PCM). To fill this gap, we first introduce PCM-$κ$ that accounts for SIC-related power expenditure, where $κ$ represents the average power consumption per SIC layer. Then, to investigate the energy efficiency of NOMA and joint transmission (JT)-CoMP NOMA, we formulate a power allocation problem for maximizing the energy efficiency and consequently propose a global approach running at a centralized entity and a local algorithm running at a base station. We evaluate the energy efficiency using PCM-$κ$ and two PCMs commonly used in the literature. Numerical analysis suggests that using simplistic PCMs leads to a few orders of magnitude overestimation of energy efficiency, especially when the receivers have low rate requirements. Despite the superiority of JT-CoMP NOMA over conventional NOMA in finding a feasible power allocation, the difference in their energy efficiency is only marginal. Moreover, when conventional NOMA is feasible, the optimal solution for JT-CoMP NOMA converges to conventional NOMA and NOMA schemes favour the users with the best channel quality.
Re-Weighted Softmax Cross-Entropy to Control Forgetting in Federated Learning
Venue: arXiv cs.LG 2023
Year: 2023

In Federated Learning, a global model is learned by aggregating model updates computed at a set of independent client nodes, to reduce communication costs multiple gradient steps are performed at each node prior to aggregation. A key challenge in this setting is data heterogeneity across clients resulting in differing local objectives which can lead clients to overly minimize their own local objective, diverging from the global solution. We demonstrate that individual client models experience a catastrophic forgetting with respect to data from other clients and propose an efficient approach that modifies the cross-entropy objective on a per-client basis by re-weighting the softmax logits prior to computing the loss. This approach shields classes outside a client's label set from abrupt representation change and we empirically demonstrate it can alleviate client forgetting and provide consistent improvements to standard federated learning algorithms. Our method is particularly beneficial under the most challenging federated learning settings where data heterogeneity is high and client participation in each round is low.