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Shaojie Wang

Publications and source records attributed to Shaojie Wang.

At least 37 records · Page 2Linked to original sources
arXiv2024

Pro-PRIME: A general Temperature-Guided Language model to engineer enhanced Stability and Activity in Proteins

Designing protein mutants of both high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, a deep learning model, which can suggest protein mutants of improved stability and activity without any prior experimental mutagenesis data of the specified protein. Leveraging temperature-aware language modeling, PRIME demonstrated superior predictive power compared to current state-of-the-art models on the public mutagenesis dataset over 283 protein assays. Furthermore, we validated PRIME's predictions on five proteins, examining the top 30-45 single-site mutations' impact on various protein properties, including thermal stability, antigen-antibody binding affinity, and the ability to polymerize non-natural nucleic acid or resilience to extreme alkaline conditions. Remarkably, over 30% of the AI-recommended mutants exhibited superior performance compared to their pre-mutation counterparts across all proteins and desired properties. Moreover, we have developed an efficient, and successful method based on PRIME to rapidly obtain multi-site mutants with enhanced activity and stability. Hence, PRIME demonstrates the general applicability in protein engineering.

q-bio.BM↗
arXiv2024

Unified mesoscale picture of nonlinear generation of zonal flows in toroidal geometry

Recent experimental findings on limit-cycle-oscillations indicate that the nonlinear driving of the turbulent poloidal Reynolds stress to zonal flows is not a significant factor in the toroidal geometry, sparking fundamental controversial issues within the fusion community. By using the global nonlinear gyrokinetic simulations, we propose a unified mesoscale picture of nonlinear driving of zonal flows in the ion-temperature-gradient turbulence. Zonal flows are nonlinearly driven by the turbulent energy flux and the turbulent poloidal Reynolds stress. The turbulent energy flux is not shielded by the toroidal geometry effect in nonlinearly driving zonal flows. The turbulent poloidal Reynolds stress is not shielded on the time scale shorter than the ion bounce period; however, on the time scale longer than the ion bounce period, the turbulent poloidal Reynolds stress is indeed shielded by the toroidal geometry effect.

physics.plasm-ph↗
arXiv2024

SES: Bridging the Gap Between Explainability and Prediction of Graph Neural Networks

Despite the Graph Neural Networks' (GNNs) proficiency in analyzing graph data, achieving high-accuracy and interpretable predictions remains challenging. Existing GNN interpreters typically provide post-hoc explanations disjointed from GNNs' predictions, resulting in misrepresentations. Self-explainable GNNs offer built-in explanations during the training process. However, they cannot exploit the explanatory outcomes to augment prediction performance, and they fail to provide high-quality explanations of node features and require additional processes to generate explainable subgraphs, which is costly. To address the aforementioned limitations, we propose a self-explained and self-supervised graph neural network (SES) to bridge the gap between explainability and prediction. SES comprises two processes: explainable training and enhanced predictive learning. During explainable training, SES employs a global mask generator co-trained with a graph encoder and directly produces crucial structure and feature masks, reducing time consumption and providing node feature and subgraph explanations. In the enhanced predictive learning phase, mask-based positive-negative pairs are constructed utilizing the explanations to compute a triplet loss and enhance the node representations by contrastive learning.

cs.LG↗
arXiv2024

Graph Structure Prompt Learning: A Novel Methodology to Improve Performance of Graph Neural Networks

Graph neural networks (GNNs) are widely applied in graph data modeling. However, existing GNNs are often trained in a task-driven manner that fails to fully capture the intrinsic nature of the graph structure, resulting in sub-optimal node and graph representations. To address this limitation, we propose a novel Graph structure Prompt Learning method (GPL) to enhance the training of GNNs, which is inspired by prompt mechanisms in natural language processing. GPL employs task-independent graph structure losses to encourage GNNs to learn intrinsic graph characteristics while simultaneously solving downstream tasks, producing higher-quality node and graph representations. In extensive experiments on eleven real-world datasets, after being trained by GPL, GNNs significantly outperform their original performance on node classification, graph classification, and edge prediction tasks (up to 10.28%, 16.5%, and 24.15%, respectively). By allowing GNNs to capture the inherent structural prompts of graphs in GPL, they can alleviate the issue of over-smooth and achieve new state-of-the-art performances, which introduces a novel and effective direction for GNN research with potential applications in various domains.

cs.LG↗
arXiv2024

Gyrokinetic simulation of the spontaneous toroidal rotation of plasma in a stochastic magnetic field

Since the DIII-D resonant magnetic perturbation experiment [Nucl. Fusion $\bm{59}$, 126010 (2019)] suggests that the neoclassical toroidal viscosity due to the collisional effects associated with the non-resonant magnetic perturbations is not enough to explain the observed toroidal rotation, it is of interest to investigate the toroidal rotation induced by the anomalous diffusion due to the resonant magnetic perturbations. Gyrokinetic simulation of the toroidal rotation of plasma in a stochastic magnetic field is carried out to investigate the resonant magnetic perturbations effects on toroidal rotation. The simulation results suggest that, in a stochastic magnetic field, resonant magnetic perturbations drive the plasma to toroidally rotate through the ambipolar radial electric field. It is found that this spontaneous flow driven on the time scale less than an ion-ion collision time is the parallel return flow of the $\bm{E}_r\times\bm{B}_0$ drift, which is due to the the ambipolar radial electric field induced by the non-ambipolar radial diffusion in the stochastic magnetic field. Collisional effect changes the plasma toroidal rotation from the return flow to the rigid-body flow after a few ion-ion collision times. The toroidal rotation observed in DIII-D resonant magnetic perturbation experiment [Nucl. Fusion $\bm{59}$, 126010 (2019)], can be explained by the rigid-body rotation driven by the ambipolar radial electric field generated by the stochastic magnetic field layer.

physics.plasm-ph↗
arXiv2024

Numerical dissipation induced by the low-pass filtering in nonlinear gyrokinetic simulations

De-aliasing is an essential procedure for eliminating the aliasing error in nonlinear simulations, such as nonlinear gyrokinetic turbulence simulations. An ideal approach to de-aliasing in the periodic dimension is Fourier truncation. Finite difference low-pass filtering applied in the non-periodic direction strongly dampens aliasing modes. At the same time, it induces numerical dissipation in the region of the physically realistic solution. It is shown analytically that the long-wave dissipation coefficient is proportional to the (Np-3) power of the wavenumber under desirable constraints satisfying the highest order accuracy, where Np is the number of filter points. Numerical results after applying the optimised low-pass filtering to the nonlinear gyrokinetic turbulence simulation suggest that the nine-point format preserves intact mesoscopic zonal structures in Tokamak plasmas, and is therefore suitable for long-time nonlinear turbulence simulations.

physics.plasm-ph↗
arXiv2023

A bioinspired three-stage model for camouflaged object detection

Camouflaged objects are typically assimilated into their backgrounds and exhibit fuzzy boundaries. The complex environmental conditions and the high intrinsic similarity between camouflaged targets and their surroundings pose significant challenges in accurately locating and segmenting these objects in their entirety. While existing methods have demonstrated remarkable performance in various real-world scenarios, they still face limitations when confronted with difficult cases, such as small targets, thin structures, and indistinct boundaries. Drawing inspiration from human visual perception when observing images containing camouflaged objects, we propose a three-stage model that enables coarse-to-fine segmentation in a single iteration. Specifically, our model employs three decoders to sequentially process subsampled features, cropped features, and high-resolution original features. This proposed approach not only reduces computational overhead but also mitigates interference caused by background noise. Furthermore, considering the significance of multi-scale information, we have designed a multi-scale feature enhancement module that enlarges the receptive field while preserving detailed structural cues. Additionally, a boundary enhancement module has been developed to enhance performance by leveraging boundary information. Subsequently, a mask-guided fusion module is proposed to generate fine-grained results by integrating coarse prediction maps with high-resolution feature maps. Our network surpasses state-of-the-art CNN-based counterparts without unnecessary complexities. Upon acceptance of the paper, the source code will be made publicly available at https://github.com/clelouch/BTSNet.

cs.CV↗
arXiv2022

Adversarial Robustness of Deep Sensor Fusion Models

We experimentally study the robustness of deep camera-LiDAR fusion architectures for 2D object detection in autonomous driving. First, we find that the fusion model is usually both more accurate, and more robust against single-source attacks than single-sensor deep neural networks. Furthermore, we show that without adversarial training, early fusion is more robust than late fusion, whereas the two perform similarly after adversarial training. However, we note that single-channel adversarial training of deep fusion is often detrimental even to robustness. Moreover, we observe cross-channel externalities, where single-channel adversarial training reduces robustness to attacks on the other channel. Additionally, we observe that the choice of adversarial model in adversarial training is critical: using attacks restricted to cars' bounding boxes is more effective in adversarial training and exhibits less significant cross-channel externalities. Finally, we find that joint-channel adversarial training helps mitigate many of the issues above, but does not significantly boost adversarial robustness.

cs.CV↗
arXiv2021

PROVES: Establishing Image Provenance using Semantic Signatures

Modern AI tools, such as generative adversarial networks, have transformed our ability to create and modify visual data with photorealistic results. However, one of the deleterious side-effects of these advances is the emergence of nefarious uses in manipulating information in visual data, such as through the use of deep fakes. We propose a novel architecture for preserving the provenance of semantic information in images to make them less susceptible to deep fake attacks. Our architecture includes semantic signing and verification steps. We apply this architecture to verifying two types of semantic information: individual identities (faces) and whether the photo was taken indoors or outdoors. Verification accounts for a collection of common image transformation, such as translation, scaling, cropping, and small rotations, and rejects adversarial transformations, such as adversarially perturbed or, in the case of face verification, swapped faces. Experiments demonstrate that in the case of provenance of faces in an image, our approach is robust to black-box adversarial transformations (which are rejected) as well as benign transformations (which are accepted), with few false negatives and false positives. Background verification, on the other hand, is susceptible to black-box adversarial examples, but becomes significantly more robust after adversarial training.

cs.CV↗
arXiv2021

Improve CAM with Auto-adapted Segmentation and Co-supervised Augmentation

Weakly Supervised Object Localization (WSOL) methods generate both classification and localization results by learning from only image category labels. Previous methods usually utilize class activation map (CAM) to obtain target object regions. However, most of them only focus on improving foreground object parts in CAM, but ignore the important effect of its background contents. In this paper, we propose a confidence segmentation (ConfSeg) module that builds confidence score for each pixel in CAM without introducing additional hyper-parameters. The generated sample-specific confidence mask is able to indicate the extent of determination for each pixel in CAM, and further supervises additional CAM extended from internal feature maps. Besides, we introduce Co-supervised Augmentation (CoAug) module to capture feature-level representation for foreground and background parts in CAM separately. Then a metric loss is applied at batch sample level to augment distinguish ability of our model, which helps a lot to localize more related object parts. Our final model, CSoA, combines the two modules and achieves superior performance, e.g. $37.69\%$ and $48.81\%$ Top-1 localization error on CUB-200 and ILSVRC datasets, respectively, which outperforms all previous methods and becomes the new state-of-the-art.

cs.CV↗
arXiv2020

Spontaneous spin-up induced by turbulence-driven topological transition of orbits in a tokamak plasma

Spontaneous spin-up are widely observed in tokamak plasmas, which is crucially important for plasma confinement. A kinetic theory is proposed to show that a toroidal rotation of core plasma is induced by the topological transition of orbits driven by turbulent diffusion in a collisionless tokamak plasma. The theoretical prediction agrees well with the well-known Rice-scaling of intrinsic core plasma flow. This new theory predicts an intrinsic core parallel flow of $\sim 100km/s$ for the International Thermonuclear Experimental Reactor.

physics.plasm-ph↗
arXiv2019

Weakly Supervised Localization Using Background Images

Weakly Supervised Object Localization (WSOL) methodsusually rely on fully convolutional networks in order to ob-tain class activation maps(CAMs) of targeted labels. How-ever, these networks always highlight the most discriminativeparts to perform the task, the located areas are much smallerthan entire targeted objects. In this work, we propose a novelend-to-end model to enlarge CAMs generated from classifi-cation models, which can localize targeted objects more pre-cisely. In detail, we add an additional module in traditionalclassification networks to extract foreground object propos-als from images without classifying them into specific cate-gories. Then we set these normalized regions as unrestrictedpixel-level mask supervision for the following classificationtask. We collect a set of images defined as Background ImageSet from the Internet. The number of them is much smallerthan the targeted dataset but surprisingly well supports themethod to extract foreground regions from different pictures.The region extracted is independent from classification task,where the extracted region in each image covers almost en-tire object rather than just a significant part. Therefore, theseregions can serve as masks to supervise the response mapgenerated from classification models to become larger andmore precise. The method achieves state-of-the-art results onCUB-200-2011 in terms of Top-1 and Top-5 localization er-ror while has a competitive result on ILSVRC2016 comparedwith other approaches.

cs.CV↗
arXiv2018

How to Make a BLT Sandwich? Learning to Reason towards Understanding Web Instructional Videos

Understanding web instructional videos is an essential branch of video understanding in two aspects. First, most existing video methods focus on short-term actions for a-few-second-long video clips; these methods are not directly applicable to long videos. Second, unlike unconstrained long videos, e.g., movies, instructional videos are more structured in that they have step-by-step procedure constraining the understanding task. In this paper, we study reasoning on instructional videos via question-answering (QA). Surprisingly, it has not been an emphasis in the video community despite its rich applications. We thereby introduce YouQuek, an annotated QA dataset for instructional videos based on the recent YouCook2. The questions in YouQuek are not limited to cues on one frame but related to logical reasoning in the temporal dimension. Observing the lack of effective representations for modeling long videos, we propose a set of carefully designed models including a novel Recurrent Graph Convolutional Network (RGCN) that captures both temporal order and relation information. Furthermore, we study multiple modalities including description and transcripts for the purpose of boosting video understanding. Extensive experiments on YouQuek suggest that RGCN performs the best in terms of QA accuracy and a better performance is gained by introducing human annotated description.

cs.CV↗
arXiv2018

GAN-EM: GAN based EM learning framework

Expectation maximization (EM) algorithm is to find maximum likelihood solution for models having latent variables. A typical example is Gaussian Mixture Model (GMM) which requires Gaussian assumption, however, natural images are highly non-Gaussian so that GMM cannot be applied to perform clustering task on pixel space. To overcome such limitation, we propose a GAN based EM learning framework that can maximize the likelihood of images and estimate the latent variables with only the constraint of L-Lipschitz continuity. We call this model GAN-EM, which is a framework for image clustering, semi-supervised classification and dimensionality reduction. In M-step, we design a novel loss function for discriminator of GAN to perform maximum likelihood estimation (MLE) on data with soft class label assignments. Specifically, a conditional generator captures data distribution for $K$ classes, and a discriminator tells whether a sample is real or fake for each class. Since our model is unsupervised, the class label of real data is regarded as latent variable, which is estimated by an additional network (E-net) in E-step. The proposed GAN-EM achieves state-of-the-art clustering and semi-supervised classification results on MNIST, SVHN and CelebA, as well as comparable quality of generated images to other recently developed generative models.

cs.LG↗
arXiv2018

In-Out impurity density asymmetry due to the Coriolis force in a rotating tokamak plasma

The effect of the Coriolis force due to the impurity toroidal and poloidal rotation on the in-out impurity density asymmetry in a rotating tokamak plasma is identified. The in-out impurity density asymmetry can be induced by the Coriolis force with q*v_theta_z*omega_z, in this case, when moving along the magnetic field line from the outboard side to the inboard side in a magnetic flux surface, one sees a positive Coriolis force. The proposed theory is consistent with the ASDEX Upgrade experimental observations.

physics.plasm-ph↗
arXiv2015

Transport equation for plasmas in a stationary-homogeneous turbulence

For a plasma in a stationary homogeneous turbulence, the Fokker-Planck equation is derived from the nonlinear Vlasov equation by introducing the entropy principle. The ensemble average in evaluating the kinetic diffusion tensor, whose symmetry has been proved, can be computed in a straightforward way when the fluctuating particle trajectories are provided. As an application, it has been shown that a mean electric filed can drive a particle flux through the Stokes-Einstein relation, independent of the details of turbulence.

physics.plasm-ph↗