Search for: All records

Abstract Phase transitions are typically quantified using order parameters, such as crystal lattice distances and radial distribution functions, which can identify subtle changes in crystalline materials or high‐contrast phases with large structural differences. However, the identification of phases with high complexity, multiscale organization and of complex patterns during the structural fluctuations preceding phase transitions, which are essential for understanding the system pathways between phases, is challenging for those traditional analyses. Here, it is shown that for two model systems— thermotropic liquid crystals and a lyotropic water/surfactant mixtures—graph theoretical (GT) descriptors can successfully identify complex phases combining molecular and nanoscale levels of organization that are hard to characterize with traditional methodologies. Furthermore, the GT descriptors also reveal the pathways between the different phases. Specifically, centrality parameters and node‐based fractal dimension quantify the system behavior preceding the transitions, capturing fluctuation‐induced breakup of aggregates and their long‐range cooperative interactions. GT parameterization can be generalized for a wide range of chemical systems and be instrumental for the growth mechanisms of complex nanostructures. 

Abstract Gels self‐assembled from colloidal nanoparticles (NPs) translate the size‐dependent properties of nanostructures to materials with macroscale volumes. Large spanning networks of NP chains provide high interconnectivity within the material necessary for a wide range of properties from conductivity to viscoelasticity. However, a great challenge for nanoscale engineering of such gels lies in being able to accurately and quantitatively describe their complex non‐crystalline structure that combines order and disorder. The quantitative relationships between the mesoscale structural and material properties of nanostructured gels are currently unknown. Here, it is shown that lead telluride NPs spontaneously self‐assemble into a spanning network hydrogel. By applying graph theory (GT), a method for quantifying the complex structure of the NP gels is established using a topological descriptor of average nodal connectivity that is found to correlate with the gel's mechanical and charge transport properties. GT descriptions make possible the design of non‐crystalline porous materials from a variety of nanoscale components for photonics, catalysis, adsorption, and thermoelectrics. 

Abstract The rampant spread of COVID-19, an infectious disease caused by SARS-CoV-2, all over the world has led to over millions of deaths, and devastated the social, financial and political entities around the world. Without an existing effective medical therapy, vaccines are urgently needed to avoid the spread of this disease. In this study, we propose an in silico deep learning approach for prediction and design of a multi-epitope vaccine (DeepVacPred). By combining the in silico immunoinformatics and deep neural network strategies, the DeepVacPred computational framework directly predicts 26 potential vaccine subunits from the available SARS-CoV-2 spike protein sequence. We further use in silico methods to investigate the linear B-cell epitopes, Cytotoxic T Lymphocytes (CTL) epitopes, Helper T Lymphocytes (HTL) epitopes in the 26 subunit candidates and identify the best 11 of them to construct a multi-epitope vaccine for SARS-CoV-2 virus. The human population coverage, antigenicity, allergenicity, toxicity, physicochemical properties and secondary structure of the designed vaccine are evaluated via state-of-the-art bioinformatic approaches, showing good quality of the designed vaccine. The 3D structure of the designed vaccine is predicted, refined and validated by in silico tools. Finally, we optimize and insert the codon sequence into a plasmid to ensure the cloning and expression efficiency. In conclusion, this proposed artificial intelligence (AI) based vaccine discovery framework accelerates the vaccine design process and constructs a 694aa multi-epitope vaccine containing 16 B-cell epitopes, 82 CTL epitopes and 89 HTL epitopes, which is promising to fight the SARS-CoV-2 viral infection and can be further evaluated in clinical studies. Moreover, we trace the RNA mutations of the SARS-CoV-2 and ensure that the designed vaccine can tackle the recent RNA mutations of the virus. 

Integrating and processing information from various sources or modalities are critical for obtaining a comprehensive and accurate perception of the real world in autonomous systems and cyber-physical systems. Drawing inspiration from neuroscience, we develop the Information-Theoretic Hierarchical Perception (ITHP) model, which utilizes the concept of information bottleneck. Different from most traditional fusion models that incorporate all modalities identically in neural networks, our model designates a prime modality and regards the remaining modalities as detectors in the information pathway, serving to distill the flow of information. Our proposed perception model focuses on constructing an effective and compact information flow by achieving a balance between the minimization of mutual information between the latent state and the input modal state, and the maximization of mutual information between the latent states and the remaining modal states. This approach leads to compact latent state representations that retain relevant information while minimizing redundancy, thereby substantially enhancing the performance of multimodal representation learning. Experimental evaluations on the MUStARD, CMU-MOSI, and CMU-MOSEI datasets demonstrate that our model consistently distills crucial information in multimodal learning scenarios, outperforming state-of-the-art benchmarks. Remarkably, on the CMU-MOSI dataset, ITHP surpasses human-level performance in the multimodal sentiment binary classification task across all evaluation metrics (i.e., Binary Accuracy, F1 Score, Mean Absolute Error, and Pearson Correlation). 

Backpropagation (BP) has been a successful optimization technique for deep learning models. However, its limitations, such as backward- and update-locking, and its biological implausibility, hinder the concurrent updating of layers and do not mimic the local learning processes observed in the human brain. To address these issues, recent research has suggested using local error signals to asynchronously train network blocks. However, this approach often involves extensive trial-and-error iterations to determine the best configuration for local training. This includes decisions on how to decouple network blocks and which auxiliary networks to use for each block. In our work, we introduce a novel BP-free approach: a block-wise BP-free (BWBPF) neural network that leverages local error signals to optimize distinct sub-neural networks separately, where the global loss is only responsible for updating the output layer. The local error signals used in the BP-free model can be computed in parallel, enabling a potential speed-up in the weight update process through parallel implementation. Our experimental results consistently show that this approach can identify transferable decoupled architectures for VGG and ResNet variations, outperforming models trained with end-to-end backpropagation and other state-of-the-art block-wise learning techniques on datasets such as CIFAR-10 and Tiny-ImageNet. The code is released at https://github.com/Belis0811/BWBPF. 

Malware represents a significant security concern in today’s digital landscape, as it can destroy or disable operating systems, steal sensitive user information, and occupy valuable disk space. However, current malware detection methods, such as static-based and dynamic-based approaches, struggle to identify newly developed ("zero-day") malware and are limited by customized virtual machine (VM) environments. To overcome these limitations, we propose a novel malware detection approach that leverages deep learning, mathematical techniques, and network science. Our approach focuses on static and dynamic analysis and utilizes the Low-Level Virtual Machine (LLVM) to profile applications within a complex network. The generated network topologies are input into the GraphSAGE architecture to efficiently distinguish between benign and malicious software applications, with the operation names denoted as node features. Importantly, the GraphSAGE models analyze the network’s topological geometry to make predictions, enabling them to detect state-of-the-art malware and prevent potential damage during execution in a VM. To evaluate our approach, we conduct a study on a dataset comprising source code from 24,376 applications, specifically written in C/C++, sourced directly from widely-recognized malware and various types of benign software. The results show a high detection performance with an Area Under the Receiver Operating Characteristic Curve (AUROC) of 99.85%. Our approach marks a substantial improvement in malware detection, providing a notably more accurate and efficient solution when compared to current state-of-the-art malware detection methods. The code is released at https://github.com/HantangZhang/MGN. 

The gap between chronological age (CA) and biological brain age, as estimated from magnetic resonance images (MRIs), reflects how individual patterns of neuroanatomic aging deviate from their typical trajectories. MRI-derived brain age (BA) estimates are often obtained using deep learning models that may perform relatively poorly on new data or that lack neuroanatomic interpretability. This study introduces a convolutional neural network (CNN) to estimate BA after training on the MRIs of 4,681 cognitively normal (CN) participants and testing on 1,170 CN participants from an independent sample. BA estimation errors are notably lower than those of previous studies. At both individual and cohort levels, the CNN provides detailed anatomic maps of brain aging patterns that reveal sex dimorphisms and neurocognitive trajectories in adults with mild cognitive impairment (MCI, N  = 351) and Alzheimer’s disease (AD, N  = 359). In individuals with MCI (54% of whom were diagnosed with dementia within 10.9 y from MRI acquisition), BA is significantly better than CA in capturing dementia symptom severity, functional disability, and executive function. Profiles of sex dimorphism and lateralization in brain aging also map onto patterns of neuroanatomic change that reflect cognitive decline. Significant associations between BA and neurocognitive measures suggest that the proposed framework can map, systematically, the relationship between aging-related neuroanatomy changes in CN individuals and in participants with MCI or AD. Early identification of such neuroanatomy changes can help to screen individuals according to their AD risk. 

Time-evolution of partial differential equations is the key to model several dynamical processes, events forecasting but the operators associated with such problems are non-linear. We propose a Padé approximation based exponential neural operator scheme for efficiently learning the map between a given initial condition and activities at a later time. The multiwavelets bases are used for space discretization. By explicitly embedding the exponential operators in the model, we reduce the training parameters and make it more data-efficient which is essential in dealing with scarce real-world datasets. The Padé exponential operator uses a to model the non-linearity compared to recent neural operators that rely on using multiple linear operator layers in succession. We show theoretically that the gradients associated with the recurrent Padé network are bounded across the recurrent horizon. We perform experiments on non-linear systems such as Korteweg-de Vries (KdV) and Kuramoto–Sivashinsky (KS) equations to show that the proposed approach achieves the best performance and at the same time is data-efficient. We also show that urgent real-world problems like Epidemic forecasting (for example, COVID-19) can be formulated as a 2D time-varying operator problem. The proposed Padé exponential operators yield better prediction results ( better MAE than best neural operator (non-neural operator deep learning model)) compared to state-of-the-art forecasting models. 

We present a policy gradient method for Multi-Objective Reinforcement Learning under unknown, linear preferences. By enforcing Pareto stationarity, a first-order condition for Pareto optimality, we are able to design a simple policy gradient algorithm that approximates the Pareto front and infers the unknown preferences. Our method relies on a projected gradient descent solver that identifies common ascent directions for all objectives. Leveraging the solution of that solver, we introduce Pareto Policy Adaptation (PPA), a loss function that adapts the policy to be optimal with respect to any distribution over preferences. PPA uses implicit differentiation to back-propagate the loss gradient bypassing the operations of the projected gradient descent solver. Our approach is straightforward, easy to implement and can be used with all existing policy gradient and actor-critic methods. We evaluate our method in a series of reinforcement learning tasks