OpenRaiser/Intern-Atlas huggingface dataset:
Laplacian-based Cluster-Contractive t-SNE for High Dimensional Data Visualization
Venue: arXiv cs.LG 2022
Year: 2022

Dimensionality reduction techniques aim at representing high-dimensional data in low-dimensional spaces to extract hidden and useful information or facilitate visual understanding and interpretation of the data. However, few of them take into consideration the potential cluster information contained implicitly in the high-dimensional data. In this paper, we propose LaptSNE, a new graph-layout nonlinear dimensionality reduction method based on t-SNE, one of the best techniques for visualizing high-dimensional data as 2D scatter plots. Specifically, LaptSNE leverages the eigenvalue information of the graph Laplacian to shrink the potential clusters in the low-dimensional embedding when learning to preserve the local and global structure from high-dimensional space to low-dimensional space. It is nontrivial to solve the proposed model because the eigenvalues of normalized symmetric Laplacian are functions of the decision variable. We provide a majorization-minimization algorithm with convergence guarantee to solve the optimization problem of LaptSNE and show how to calculate the gradient analytically, which may be of broad interest when considering optimization with Laplacian-composited objective. We evaluate our method by a formal comparison with state-of-the-art methods on seven benchmark datasets, both visually and via established quantitative measurements. The results demonstrate the superiority of our method over baselines such as t-SNE and UMAP. We also provide out-of-sample extension, large-scale extension and mini-batch extension for our LaptSNE to facilitate dimensionality reduction in various scenarios.
Surrogate Modeling of Melt Pool Thermal Field using Deep Learning
Venue: arXiv cs.LG 2022
Year: 2022

Powder-based additive manufacturing has transformed the manufacturing industry over the last decade. In Laser Powder Bed Fusion, a specific part is built in an iterative manner in which two-dimensional cross-sections are formed on top of each other by melting and fusing the proper areas of the powder bed. In this process, the behavior of the melt pool and its thermal field has a very important role in predicting the quality of the manufactured part and its possible defects. However, the simulation of such a complex phenomenon is usually very time-consuming and requires huge computational resources. Flow-3D is one of the software packages capable of executing such simulations using iterative numerical solvers. In this work, we create three datasets of single-trail processes using Flow-3D and use them to train a convolutional neural network capable of predicting the behavior of the three-dimensional thermal field of the melt pool solely by taking three parameters as input: laser power, laser velocity, and time step. The CNN achieves a relative Root Mean Squared Error of 2% to 3% for the temperature field and an average Intersection over Union score of 80% to 90% in predicting the melt pool area. Moreover, since time is included as one of the inputs of the model, the thermal field can be instantly obtained for any arbitrary time step without the need to iterate and compute all the steps
What is Healthy? Generative Counterfactual Diffusion for Lesion Localization
Venue: arXiv cs.CV 2022
Year: 2022

Reducing the requirement for densely annotated masks in medical image segmentation is important due to cost constraints. In this paper, we consider the problem of inferring pixel-level predictions of brain lesions by only using image-level labels for training. By leveraging recent advances in generative diffusion probabilistic models (DPM), we synthesize counterfactuals of "How would a patient appear if X pathology was not present?". The difference image between the observed patient state and the healthy counterfactual can be used for inferring the location of pathology. We generate counterfactuals that correspond to the minimal change of the input such that it is transformed to healthy domain. This requires training with healthy and unhealthy data in DPMs. We improve on previous counterfactual DPMs by manipulating the generation process with implicit guidance along with attention conditioning instead of using classifiers. Code is available at https://github.com/vios-s/Diff-SCM.
Next-generation HPC models for future rotorcraft applications
Venue: arXiv cs.DC 2022
Year: 2022

Rotorcraft technologies pose great scientific and industrial challenges for numerical computing. As available computational resources approach the exascale, finer scales and therefore more accurate simulations of engineering test cases become accessible. However, shifting legacy workflows and optimizing parallel efficiency and scalability of existing software on new hardware is often demanding. This paper reports preliminary results in CFD and structural dynamics simulations using the T106A Low Pressure Turbine (LPT) blade geometry on Leonardo S.p.A.'s davinci-1 high-performance computing (HPC) facility. Time to solution and scalability are assessed for commercial packages Ansys Fluent, STAR-CCM+, and ABAQUS, and the open-source scientific computing framework PyFR. In direct numerical simulations of compressible fluid flow, normalized time to solution values obtained using PyFR are found to be up to 8 times smaller than those obtained using Fluent and STAR-CCM+. The findings extend to the incompressible case. All models offer weak and strong scaling in tests performed on up to 48 compute nodes, each with 4 Nvidia A100 GPUs. In linear elasticity simulations with ABAQUS, both the iterative solver and the direct solver provide speedup in preliminary scaling tests, with the iterative solver outperforming the direct solver in terms of time-to-solution and memory usage. The results provide a first indication of the potential of HPC architectures in scaling engineering applications towards certification by simulation, and the first step for the Company towards the use of cutting-edge HPC toolkits in the field of Rotorcraft technologies.
ArtFID: Quantitative Evaluation of Neural Style Transfer
Venue: arXiv cs.CV 2022
Year: 2022

The field of neural style transfer has experienced a surge of research exploring different avenues ranging from optimization-based approaches and feed-forward models to meta-learning methods. The developed techniques have not just progressed the field of style transfer, but also led to breakthroughs in other areas of computer vision, such as all of visual synthesis. However, whereas quantitative evaluation and benchmarking have become pillars of computer vision research, the reproducible, quantitative assessment of style transfer models is still lacking. Even in comparison to other fields of visual synthesis, where widely used metrics exist, the quantitative evaluation of style transfer is still lagging behind. To support the automatic comparison of different style transfer approaches and to study their respective strengths and weaknesses, the field would greatly benefit from a quantitative measurement of stylization performance. Therefore, we propose a method to complement the currently mostly qualitative evaluation schemes. We provide extensive evaluations and a large-scale user study to show that the proposed metric strongly coincides with human judgment.
TreeSketchNet: From Sketch To 3D Tree Parameters Generation
Venue: arXiv cs.CV 2022
Year: 2022

3D modeling of non-linear objects from stylized sketches is a challenge even for experts in Computer Graphics (CG). The extrapolation of objects parameters from a stylized sketch is a very complex and cumbersome task. In the present study, we propose a broker system that mediates between the modeler and the 3D modelling software and can transform a stylized sketch of a tree into a complete 3D model. The input sketches do not need to be accurate or detailed, and only need to represent a rudimentary outline of the tree that the modeler wishes to 3D-model. Our approach is based on a well-defined Deep Neural Network (DNN) architecture, we called TreeSketchNet (TSN), based on convolutions and able to generate Weber and Penn parameters that can be interpreted by the modelling software to generate a 3D model of a tree starting from a simple sketch. The training dataset consists of Synthetically-Generated \revision{(SG)} sketches that are associated with Weber-Penn parameters generated by a dedicated Blender modelling software add-on. The accuracy of the proposed method is demonstrated by testing the TSN with both synthetic and hand-made sketches. Finally, we provide a qualitative analysis of our results, by evaluating the coherence of the predicted parameters with several distinguishing features.
Technical Report: Assisting Backdoor Federated Learning with Whole Population Knowledge Alignment
Venue: arXiv cs.AI 2022
Year: 2022

Due to the distributed nature of Federated Learning (FL), researchers have uncovered that FL is vulnerable to backdoor attacks, which aim at injecting a sub-task into the FL without corrupting the performance of the main task. Single-shot backdoor attack achieves high accuracy on both the main task and backdoor sub-task when injected at the FL model convergence. However, the early-injected single-shot backdoor attack is ineffective because: (1) the maximum backdoor effectiveness is not reached at injection because of the dilution effect from normal local updates; (2) the backdoor effect decreases quickly as the backdoor will be overwritten by the newcoming normal local updates. In this paper, we strengthen the early-injected single-shot backdoor attack utilizing FL model information leakage. We show that the FL convergence can be expedited if the client trains on a dataset that mimics the distribution and gradients of the whole population. Based on this observation, we proposed a two-phase backdoor attack, which includes a preliminary phase for the subsequent backdoor attack. In the preliminary phase, the attacker-controlled client first launches a whole population distribution inference attack and then trains on a locally crafted dataset that is aligned with both the gradient and inferred distribution. Benefiting from the preliminary phase, the later injected backdoor achieves better effectiveness as the backdoor effect will be less likely to be diluted by the normal model updates. Extensive experiments are conducted on MNIST dataset under various data heterogeneity settings to evaluate the effectiveness of the proposed backdoor attack. Results show that the proposed backdoor outperforms existing backdoor attacks in both success rate and longevity, even when defense mechanisms are in place.
Unsteady aerodynamic modeling of Aerobat using lifting line theory and Wagner's function
Venue: arXiv cs.RO 2022
Year: 2022

Flying animals possess highly complex physical characteristics and are capable of performing agile maneuvers using their wings. The flapping wings generate complex wake structures that influence the aerodynamic forces, which can be difficult to model. While it is possible to model these forces using fluid-structure interaction, it is very computationally expensive and difficult to formulate. In this paper, we follow a simpler approach by deriving the aerodynamic forces using a relatively small number of states and presenting them in a simple state-space form. The formulation utilizes Prandtl's lifting line theory and Wagner's function to determine the unsteady aerodynamic forces acting on the wing in a simulation, which then are compared to experimental data of the bat-inspired robot called the Aerobat. The simulated trailing-edge vortex shedding can be evaluated from this model, which then can be analyzed for a wake-based gait design approach to improve the aerodynamic performance of the robot.
Fine-Tuning BERT for Automatic ADME Semantic Labeling in FDA Drug Labeling to Enhance Product-Specific Guidance Assessment
Venue: arXiv cs.CL 2022
Year: 2022

Product-specific guidances (PSGs) recommended by the United States Food and Drug Administration (FDA) are instrumental to promote and guide generic drug product development. To assess a PSG, the FDA assessor needs to take extensive time and effort to manually retrieve supportive drug information of absorption, distribution, metabolism, and excretion (ADME) from the reference listed drug labeling. In this work, we leveraged the state-of-the-art pre-trained language models to automatically label the ADME paragraphs in the pharmacokinetics section from the FDA-approved drug labeling to facilitate PSG assessment. We applied a transfer learning approach by fine-tuning the pre-trained Bidirectional Encoder Representations from Transformers (BERT) model to develop a novel application of ADME semantic labeling, which can automatically retrieve ADME paragraphs from drug labeling instead of manual work. We demonstrated that fine-tuning the pre-trained BERT model can outperform the conventional machine learning techniques, achieving up to 11.6% absolute F1 improvement. To our knowledge, we were the first to successfully apply BERT to solve the ADME semantic labeling task. We further assessed the relative contribution of pre-training and fine-tuning to the overall performance of the BERT model in the ADME semantic labeling task using a series of analysis methods such as attention similarity and layer-based ablations. Our analysis revealed that the information learned via fine-tuning is focused on task-specific knowledge in the top layers of the BERT, whereas the benefit from the pre-trained BERT model is from the bottom layers.
Versatile Weight Attack via Flipping Limited Bits
Venue: arXiv cs.CR 2022
Year: 2022

To explore the vulnerability of deep neural networks (DNNs), many attack paradigms have been well studied, such as the poisoning-based backdoor attack in the training stage and the adversarial attack in the inference stage. In this paper, we study a novel attack paradigm, which modifies model parameters in the deployment stage. Considering the effectiveness and stealthiness goals, we provide a general formulation to perform the bit-flip based weight attack, where the effectiveness term could be customized depending on the attacker's purpose. Furthermore, we present two cases of the general formulation with different malicious purposes, i.e., single sample attack (SSA) and triggered samples attack (TSA). To this end, we formulate this problem as a mixed integer programming (MIP) to jointly determine the state of the binary bits (0 or 1) in the memory and learn the sample modification. Utilizing the latest technique in integer programming, we equivalently reformulate this MIP problem as a continuous optimization problem, which can be effectively and efficiently solved using the alternating direction method of multipliers (ADMM) method. Consequently, the flipped critical bits can be easily determined through optimization, rather than using a heuristic strategy. Extensive experiments demonstrate the superiority of SSA and TSA in attacking DNNs.
Machine Learning to Predict the Antimicrobial Activity of Cold Atmospheric Plasma-Activated Liquids
Venue: arXiv cs.LG 2022
Year: 2022

Plasma is defined as the fourth state of matter and non-thermal plasma can be produced at atmospheric pressure under a high electrical field. The strong and broad-spectrum antimicrobial effect of plasma-activated liquids (PALs) is now well known. The proven applicability of machine learning (ML) in the medical field is encouraging for its application in the field of plasma medicine as well. Thus, ML applications on PALs could present a new perspective to better understand the influences of various parameters on their antimicrobial effects. In this paper, comparative supervised ML models are presented by using previously obtained data to qualitatively predict the in vitro antimicrobial activity of PALs. A literature search was performed and data is collected from 33 relevant articles. After the required preprocessing steps, two supervised ML methods, namely classification, and regression are applied to data to obtain microbial inactivation (MI) predictions. For classification, MI is labeled in four categories and for regression, MI is used as a continuous variable. Two different robust cross-validation strategies are conducted for classification and regression models to evaluate the proposed method; repeated stratified k-fold cross-validation and k-fold cross-validation, respectively. We also investigate the effect of different features on models. The results demonstrated that the hyperparameter-optimized Random Forest Classifier (oRFC) and Random Forest Regressor (oRFR) provided better results than other models for the classification and regression, respectively. Finally, the best test accuracy of 82.68% for oRFC and R2 of 0.75 for the oRFR are obtained. ML techniques could contribute to a better understanding of plasma parameters that have a dominant role in the desired antimicrobial effect. Furthermore, such findings may contribute to the definition of a plasma dose in the future.
AGAPECert: An Auditable, Generalized, Automated, Privacy-Enabling Certification Framework with Oblivious Smart Contracts
Venue: arXiv cs.CR 2022
Year: 2022

This paper introduces AGAPECert, an Auditable, Generalized, Automated, Privacy-Enabling, Certification framework capable of performing auditable computation on private data and reporting real-time aggregate certification status without disclosing underlying private data. AGAPECert utilizes a novel mix of trusted execution environments, blockchain technologies, and a real-time graph-based API standard to provide automated, oblivious, and auditable certification. Our technique allows a privacy-conscious data owner to run pre-approved Oblivious Smart Contract code in their own environment on their own private data to produce Private Automated Certifications. These certifications are verifiable, purely functional transformations of the available data, enabling a third party to trust that the private data must have the necessary properties to produce the resulting certification. Recently, a multitude of solutions for certification and traceability in supply chains have been proposed. These often suffer from significant privacy issues because they tend to take a" shared, replicated database" approach: every node in the network has access to a copy of all relevant data and contract code to guarantee the integrity and reach consensus, even in the presence of malicious nodes. In these contexts of certifications that require global coordination, AGAPECert can include a blockchain to guarantee ordering of events, while keeping a core privacy model where private data is not shared outside of the data owner's own platform. AGAPECert contributes an open-source certification framework that can be adopted in any regulated environment to keep sensitive data private while enabling a trusted automated workflow.
Pinned Distance Sets Using Effective Dimension
Venue: arXiv cs.CC 2022
Year: 2022

In this paper, we use algorithmic tools, effective dimension and Kolmogorov complexity, to study the fractal dimension of distance sets. We show that, for any analytic set $E\subseteq\R^2$ of Hausdorff dimension strictly greater than one, the \textit{pinned distance set} of $E$, $Δ_x E$, has Hausdorff dimension of at least $\frac{3}{4}$, for all points $x$ outside a set of Hausdorff dimension at most one. This improves the best known bounds when the dimension of $E$ is close to one.
Live Stream Temporally Embedded 3D Human Body Pose and Shape Estimation
Venue: arXiv cs.CV 2022
Year: 2022

3D Human body pose and shape estimation within a temporal sequence can be quite critical for understanding human behavior. Despite the significant progress in human pose estimation in the recent years, which are often based on single images or videos, human motion estimation on live stream videos is still a rarely-touched area considering its special requirements for real-time output and temporal consistency. To address this problem, we present a temporally embedded 3D human body pose and shape estimation (TePose) method to improve the accuracy and temporal consistency of pose estimation in live stream videos. TePose uses previous predictions as a bridge to feedback the error for better estimation in the current frame and to learn the correspondence between data frames and predictions in the history. A multi-scale spatio-temporal graph convolutional network is presented as the motion discriminator for adversarial training using datasets without any 3D labeling. We propose a sequential data loading strategy to meet the special start-to-end data processing requirement of live stream. We demonstrate the importance of each proposed module with extensive experiments. The results show the effectiveness of TePose on widely-used human pose benchmarks with state-of-the-art performance.
$p$-DkNN: Out-of-Distribution Detection Through Statistical Testing of Deep Representations
Venue: arXiv cs.LG 2022
Year: 2022

The lack of well-calibrated confidence estimates makes neural networks inadequate in safety-critical domains such as autonomous driving or healthcare. In these settings, having the ability to abstain from making a prediction on out-of-distribution (OOD) data can be as important as correctly classifying in-distribution data. We introduce $p$-DkNN, a novel inference procedure that takes a trained deep neural network and analyzes the similarity structures of its intermediate hidden representations to compute $p$-values associated with the end-to-end model prediction. The intuition is that statistical tests performed on latent representations can serve not only as a classifier, but also offer a statistically well-founded estimation of uncertainty. $p$-DkNN is scalable and leverages the composition of representations learned by hidden layers, which makes deep representation learning successful. Our theoretical analysis builds on Neyman-Pearson classification and connects it to recent advances in selective classification (reject option). We demonstrate advantageous trade-offs between abstaining from predicting on OOD inputs and maintaining high accuracy on in-distribution inputs. We find that $p$-DkNN forces adaptive attackers crafting adversarial examples, a form of worst-case OOD inputs, to introduce semantically meaningful changes to the inputs.
Ethics for social robotics: A critical analysis
Venue: arXiv cs.CY 2022
Year: 2022

Social robotics development for the practice of care and European prospects to incorporate these AI-based systems in institutional healthcare contexts call for an urgent ethical reflection to (re)configurate our practical life according to human values and rights. Despite the growing attention to the ethical implications of social robotics, the current debate on one of its central branches, social assistive robotics (SAR), rests upon an impoverished ethical approach. This paper presents and examines some tendencies of this prevailing approach, which have been identified as a result of a critical literature review. Based on this analysis of a representative case of how ethical reflection is being led towards social robotics, some future research lines are outlined, which may help reframe and deepen in its ethical implications.
Rank and pairs of Rank and Dimension of Kernel of $\mathbb{Z}_p\mathbb{Z}_{p^2}$-linear codes
Venue: arXiv cs.IT 2022
Year: 2022

A code $C$ is called $\mathbb{Z}_p\mathbb{Z}_{p^2}$-linear if it is the Gray image of a $\mathbb{Z}_p\mathbb{Z}_{p^2}$-additive code. For any prime number $p$ larger than $3$, the bounds of the rank of $\mathbb{Z}_p\mathbb{Z}_{p^2}$-linear codes are given. For each value of the rank and the pairs of rank and the dimension of the kernel of $\mathbb{Z}_p\mathbb{Z}_{p^2}$-linear codes, we give detailed construction of the corresponding codes. Finally, as an example, the rank and the dimension of the kernel of $\mathbb{Z}_5\mathbb{Z}_{25}$-linear codes are studied.