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In this paper, we introduce RecallAffectiveMemory, a novel task designed to reconstruct autobiographical memories through audio-visual generation guided by affect extracted from electroencephalogram (EEG) signals. To support this pioneering task, we present the EEG-AffectiveMemory dataset, which encompasses textual descriptions, visuals, music, and EEG recordings collected during memory recall from nine participants. Furthermore, we propose RYM (Recall Your Memory), a three-stage framework for generating synchronized audio-visual contents while maintaining dynamic personal memory affect trajectories. Experimental results indicate that our method can faithfully reconstruct affect-contextualized audio-visual memory across all subjects, both qualitatively and quantitatively, with participants reporting strong affective concordance between their recalled memories and the generated content. Our approaches advance affect decoding research and its practical applications in personalized media creation via neural-based affect comprehension., Comment: Codes and the dataset will be released upon acceptance

Music style transfer, while offering exciting possibilities for personalized music generation, often requires extensive training or detailed textual descriptions. This paper introduces a novel training-free approach leveraging pre-trained Latent Diffusion Models (LDMs). By manipulating the self-attention features of the LDM, we effectively transfer the style of reference music onto content music without additional training. Our method achieves superior style transfer and melody preservation compared to existing methods. This work opens new creative avenues for personalized music generation., Comment: Codes will be released upon acceptance

In distributed optimization, the communication of model updates can be a performance bottleneck. Consequently, gradient compression has been proposed as a means of increasing optimization throughput. In general, due to information loss, compression introduces a penalty on the number of iterations needed to reach a solution. In this work, we investigate how the iteration penalty depends on the interaction between compression and problem structure, in the context of non-convex stochastic optimization. We focus on linear compression schemes, where compression and decompression can be modeled as multiplication with a random matrix. We consider several distributions of matrices, among them random orthogonal matrices and matrices with random Gaussian entries. We find that in each case, the impact of compression on convergence can be quantified in terms of the norm of the Hessian of the objective, using a norm defined by the compression scheme. The analysis reveals that in certain cases, compression performance is related to low-rank structure or other spectral properties of the problem. In these cases, our bounds predict that the penalty introduced by compression is significantly reduced compared to worst-case bounds that only consider the compression level, ignoring problem data. We verify the theoretical findings on several optimization problems, including fine-tuning an image classification model., Comment: 15 pages, 3 figures

High-energy large-scale particle colliders generate data at extraordinary rates. Developing real-time high-throughput data compression algorithms to reduce data volume and meet the bandwidth requirement for storage has become increasingly critical. Deep learning is a promising technology that can address this challenging topic. At the newly constructed sPHENIX experiment at the Relativistic Heavy Ion Collider, a Time Projection Chamber (TPC) serves as the main tracking detector, which records three-dimensional particle trajectories in a volume of a gas-filled cylinder. In terms of occupancy, the resulting data flow can be very sparse reaching $10^{-3}$ for proton-proton collisions. Such sparsity presents a challenge to conventional learning-free lossy compression algorithms, such as SZ, ZFP, and MGARD. In contrast, emerging deep learning-based models, particularly those utilizing convolutional neural networks for compression, have outperformed these conventional methods in terms of compression ratios and reconstruction accuracy. However, research on the efficacy of these deep learning models in handling sparse datasets, like those produced in particle colliders, remains limited. Furthermore, most deep learning models do not adapt their processing speeds to data sparsity, which affects efficiency. To address this issue, we propose a novel approach for TPC data compression via key-point identification facilitated by sparse convolution. Our proposed algorithm, BCAE-VS, achieves a $75\%$ improvement in reconstruction accuracy with a $10\%$ increase in compression ratio over the previous state-of-the-art model. Additionally, BCAE-VS manages to achieve these results with a model size over two orders of magnitude smaller. Lastly, we have experimentally verified that as sparsity increases, so does the model's throughput., Comment: 37 pages, 12 figures, submitted to Journal of Computational Physics

Large-scale international scientific collaborations, such as ATLAS, Belle II, CMS, and DUNE, generate vast volumes of data. These experiments necessitate substantial computational power for varied tasks, including structured data processing, Monte Carlo simulations, and end-user analysis. Centralized workflow and data management systems are employed to handle these demands, but current decision-making processes for data placement and payload allocation are often heuristic and disjointed. This optimization challenge potentially could be addressed using contemporary machine learning methods, such as reinforcement learning, which, in turn, require access to extensive data and an interactive environment. Instead, we propose a generative surrogate modeling approach to address the lack of training data and concerns about privacy preservation. We have collected and processed real-world job submission records, totaling more than two million jobs through 150 days, and applied four generative models for tabular data -- TVAE, CTAGGAN+, SMOTE, and TabDDPM -- to these datasets, thoroughly evaluating their performance. Along with measuring the discrepancy among feature-wise distributions separately, we also evaluate pair-wise feature correlations, distance to closest record, and responses to pre-trained models. Our experiments indicate that SMOTE and TabDDPM can generate similar tabular data, almost indistinguishable from the ground truth. Yet, as a non-learning method, SMOTE ranks the lowest in privacy preservation. As a result, we conclude that the probabilistic-diffusion-model-based TabDDPM is the most suitable generative model for managing job record data., Comment: 8 pages, 5 figures, to be presented in SC24 AI4S Workshop

Quantum machine learning (QML) has recently made significant advancements in various topics. Despite the successes, the safety and interpretability of QML applications have not been thoroughly investigated. This work proposes using Variational Quantum Circuits (VQCs) for activation mapping to enhance model transparency, introducing the Quantum Gradient Class Activation Map (QGrad-CAM). This hybrid quantum-classical computing framework leverages both quantum and classical strengths and gives access to the derivation of an explicit formula of feature map importance. Experimental results demonstrate significant, fine-grained, class-discriminative visual explanations generated across both image and speech datasets., Comment: Submitted to IEEE SiPS 2024

The rapid advancement of quantum computing (QC) and machine learning (ML) has given rise to the burgeoning field of quantum machine learning (QML), aiming to capitalize on the strengths of quantum computing to propel ML forward. Despite its promise, crafting effective QML models necessitates profound expertise to strike a delicate balance between model intricacy and feasibility on Noisy Intermediate-Scale Quantum (NISQ) devices. While complex models offer robust representation capabilities, their extensive circuit depth may impede seamless execution on extant noisy quantum platforms. In this paper, we address this quandary of QML model design by employing deep reinforcement learning to explore proficient QML model architectures tailored for designated supervised learning tasks. Specifically, our methodology involves training an RL agent to devise policies that facilitate the discovery of QML models without predetermined ansatz. Furthermore, we integrate an adaptive mechanism to dynamically adjust the learning objectives, fostering continuous improvement in the agent's learning process. Through extensive numerical simulations, we illustrate the efficacy of our approach within the realm of classification tasks. Our proposed method successfully identifies VQC architectures capable of achieving high classification accuracy while minimizing gate depth. This pioneering approach not only advances the study of AI-driven quantum circuit design but also holds significant promise for enhancing performance in the NISQ era., Comment: Accepted by IEEE International Conference on Quantum Computing and Engineering - QCE 2024

Extreme edge-AI systems, such as those in readout ASICs for radiation detection, must operate under stringent hardware constraints such as micron-level dimensions, sub-milliwatt power, and nanosecond-scale speed while providing clear accuracy advantages over traditional architectures. Finding ideal solutions means identifying optimal AI and ASIC design choices from a design space that has explosively expanded during the merger of these domains, creating non-trivial couplings which together act upon a small set of solutions as constraints tighten. It is impractical, if not impossible, to manually determine ideal choices among possibilities that easily exceed billions even in small-size problems. Existing methods to bridge this gap have leveraged theoretical understanding of hardware to f architecture search. However, the assumptions made in computing such theoretical metrics are too idealized to provide sufficient guidance during the difficult search for a practical implementation. Meanwhile, theoretical estimates for many other crucial metrics (like delay) do not even exist and are similarly variable, dependent on parameters of the process design kit (PDK). To address these challenges, we present a study that employs intelligent search using multi-objective Bayesian optimization, integrating both neural network search and ASIC synthesis in the loop. This approach provides reliable feedback on the collective impact of all cross-domain design choices. We showcase the effectiveness of our approach by finding several Pareto-optimal design choices for effective and efficient neural networks that perform real-time feature extraction from input pulses within the individual pixels of a readout ASIC., Comment: 18 pages, 17 figures

Learning a continuous and reliable representation of physical fields from sparse sampling is challenging and it affects diverse scientific disciplines. In a recent work, we present a novel model called MMGN (Multiplicative and Modulated Gabor Network) with implicit neural networks. In this work, we design additional studies leveraging explainability methods to complement the previous experiments and further enhance the understanding of latent representations generated by the model. The adopted methods are general enough to be leveraged for any latent space inspection. Preliminary results demonstrate the contextual information incorporated in the latent representations and their impact on the model performance. As a work in progress, we will continue to verify our findings and develop novel explainability approaches.

Because protein-protein interactions (PPIs) are crucial to understand living systems, harvesting these data is essential to probe disease development and discern gene/protein functions and biological processes. Some curated datasets contain PPI data derived from the literature and other sources (e.g., IntAct, BioGrid, DIP, and HPRD). However, they are far from exhaustive, and their maintenance is a labor-intensive process. On the other hand, machine learning methods to automate PPI knowledge extraction from the scientific literature have been limited by a shortage of appropriate annotated data. This work presents a unified, multi-source PPI corpora with vetted interaction definitions augmented by binary interaction type labels and a Transformer-based deep learning method that exploits entities' relational context information for relation representation to improve relation classification performance. The model's performance is evaluated on four widely studied biomedical relation extraction datasets, as well as this work's target PPI datasets, to observe the effectiveness of the representation to relation extraction tasks in various data. Results show the model outperforms prior state-of-the-art models. The code and data are available at: https://github.com/BNLNLP/PPI-Relation-Extraction, Comment: 10 pages, 3 figures, 7 tables, 2022 IEEE International Conference on Big Data (Big Data)

Detecting abrupt changes in real-time data streams from scientific simulations presents a challenging task, demanding the deployment of accurate and efficient algorithms. Identifying change points in live data stream involves continuous scrutiny of incoming observations for deviations in their statistical characteristics, particularly in high-volume data scenarios. Maintaining a balance between sudden change detection and minimizing false alarms is vital. Many existing algorithms for this purpose rely on known probability distributions, limiting their feasibility. In this study, we introduce the Kernel-based Cumulative Sum (KCUSUM) algorithm, a non-parametric extension of the traditional Cumulative Sum (CUSUM) method, which has gained prominence for its efficacy in online change point detection under less restrictive conditions. KCUSUM splits itself by comparing incoming samples directly with reference samples and computes a statistic grounded in the Maximum Mean Discrepancy (MMD) non-parametric framework. This approach extends KCUSUM's pertinence to scenarios where only reference samples are available, such as atomic trajectories of proteins in vacuum, facilitating the detection of deviations from the reference sample without prior knowledge of the data's underlying distribution. Furthermore, by harnessing MMD's inherent random-walk structure, we can theoretically analyze KCUSUM's performance across various use cases, including metrics like expected delay and mean runtime to false alarms. Finally, we discuss real-world use cases from scientific simulations such as NWChem CODAR and protein folding data, demonstrating KCUSUM's practical effectiveness in online change point detection., Comment: 16 pages. arXiv admin note: text overlap with arXiv:1903.01661

Reliably reconstructing physical fields from sparse sensor data is a challenge that frequently arises in many scientific domains. In practice, the process generating the data often is not understood to sufficient accuracy. Therefore, there is a growing interest in using the deep neural network route to address the problem. This work presents a novel approach that learns a continuous representation of the physical field using implicit neural representations (INRs). Specifically, after factorizing spatiotemporal variability into spatial and temporal components using the separation of variables technique, the method learns relevant basis functions from sparsely sampled irregular data points to develop a continuous representation of the data. In experimental evaluations, the proposed model outperforms recent INR methods, offering superior reconstruction quality on simulation data from a state-of-the-art climate model and a second dataset that comprises ultra-high resolution satellite-based sea surface temperature fields., Comment: 25 pages,21 figures

Ptychography, as a powerful lensless imaging method, has become a popular member of the coherent diffractive imaging family over decades of development. The ability to utilize low-dose X-rays and/or fast scans offers a big advantage in a ptychographic measurement (for example, when measuring radiation-sensitive samples), but results in low-photon statistics, making the subsequent phase retrieval challenging. Here, we demonstrate a dose-efficient automatic differentiation framework for ptychographic reconstruction (DAP) at low-photon statistics and low overlap ratio. As no reciprocal space constraint is required in this DAP framework, the framework, based on various forward models, shows superior performance under these conditions. It effectively suppresses potential artifacts in the reconstructed images, especially for the inherent periodic artifact in a raster scan. We validate the effectiveness and robustness of this method using both simulated and measured datasets., Comment: 26 pages, 5 figures

Quantum federated learning (QFL) can facilitate collaborative learning across multiple clients using quantum machine learning (QML) models, while preserving data privacy. Although recent advances in QFL span different tasks like classification while leveraging several data types, no prior work has focused on developing a QFL framework that utilizes temporal data to approximate functions useful to analyze the performance of distributed quantum sensing networks. In this paper, a novel QFL framework that is the first to integrate quantum long short-term memory (QLSTM) models with temporal data is proposed. The proposed federated QLSTM (FedQLSTM) framework is exploited for performing the task of function approximation. In this regard, three key use cases are presented: Bessel function approximation, sinusoidal delayed quantum feedback control function approximation, and Struve function approximation. Simulation results confirm that, for all considered use cases, the proposed FedQLSTM framework achieves a faster convergence rate under one local training epoch, minimizing the overall computations, and saving 25-33% of the number of communication rounds needed until convergence compared to an FL framework with classical LSTM models., Comment: 20 pages, 9 figures

Computational models are an essential tool for the design, characterization, and discovery of novel materials. Hard computational tasks in materials science stretch the limits of existing high-performance supercomputing centers, consuming much of their simulation, analysis, and data resources. Quantum computing, on the other hand, is an emerging technology with the potential to accelerate many of the computational tasks needed for materials science. In order to do that, the quantum technology must interact with conventional high-performance computing in several ways: approximate results validation, identification of hard problems, and synergies in quantum-centric supercomputing. In this paper, we provide a perspective on how quantum-centric supercomputing can help address critical computational problems in materials science, the challenges to face in order to solve representative use cases, and new suggested directions., Comment: 65 pages, 15 figures; comments welcome

Neural style transfer (NST) has evolved significantly in recent years. Yet, despite its rapid progress and advancement, existing NST methods either struggle to transfer aesthetic information from a style effectively or suffer from high computational costs and inefficiencies in feature disentanglement due to using pre-trained models. This work proposes a lightweight but effective model, AesFA -- Aesthetic Feature-Aware NST. The primary idea is to decompose the image via its frequencies to better disentangle aesthetic styles from the reference image while training the entire model in an end-to-end manner to exclude pre-trained models at inference completely. To improve the network's ability to extract more distinct representations and further enhance the stylization quality, this work introduces a new aesthetic feature: contrastive loss. Extensive experiments and ablations show the approach not only outperforms recent NST methods in terms of stylization quality, but it also achieves faster inference. Codes are available at https://github.com/Sooyyoungg/AesFA., Comment: Accepted by AAAI 2024

A major concern of deep learning models is the large amount of data that is required to build and train them, much of which is reliant on sensitive and personally identifiable information that is vulnerable to access by third parties. Ideas of using the quantum internet to address this issue have been previously proposed, which would enable fast and completely secure online communications. Previous work has yielded a hybrid quantum-classical transfer learning scheme for classical data and communication with a hub-spoke topology. While quantum communication is secure from eavesdrop attacks and no measurements from quantum to classical translation, due to no cloning theorem, hub-spoke topology is not ideal for quantum communication without quantum memory. Here we seek to improve this model by implementing a decentralized ring topology for the federated learning scheme, where each client is given a portion of the entire dataset and only performs training on that set. We also demonstrate the first successful use of quantum weights for quantum federated learning, which allows us to perform our training entirely in quantum.

High-energy large-scale particle colliders produce data at high speed in the order of 1 terabytes per second in nuclear physics and petabytes per second in high-energy physics. Developing real-time data compression algorithms to reduce such data at high throughput to fit permanent storage has drawn increasing attention. Specifically, at the newly constructed sPHENIX experiment at the Relativistic Heavy Ion Collider (RHIC), a time projection chamber is used as the main tracking detector, which records particle trajectories in a volume of a three-dimensional (3D) cylinder. The resulting data are usually very sparse with occupancy around 10.8%. Such sparsity presents a challenge to conventional learning-free lossy compression algorithms, such as SZ, ZFP, and MGARD. The 3D convolutional neural network (CNN)-based approach, Bicephalous Convolutional Autoencoder (BCAE), outperforms traditional methods both in compression rate and reconstruction accuracy. BCAE can also utilize the computation power of graphical processing units suitable for deployment in a modern heterogeneous high-performance computing environment. This work introduces two BCAE variants: BCAE++ and BCAE-2D. BCAE++ achieves a 15% better compression ratio and a 77% better reconstruction accuracy measured in mean absolute error compared with BCAE. BCAE-2D treats the radial direction as the channel dimension of an image, resulting in a 3x speedup in compression throughput. In addition, we demonstrate an unbalanced autoencoder with a larger decoder can improve reconstruction accuracy without significantly sacrificing throughput. Lastly, we observe both the BCAE++ and BCAE-2D can benefit more from using half-precision mode in throughput (76-79% increase) without loss in reconstruction accuracy. The source code and links to data and pretrained models can be found at https://github.com/BNL-DAQ-LDRD/NeuralCompression_v2.

The preservation of privacy is a critical concern in the implementation of artificial intelligence on sensitive training data. There are several techniques to preserve data privacy but quantum computations are inherently more secure due to the no-cloning theorem, resulting in a most desirable computational platform on top of the potential quantum advantages. There have been prior works in protecting data privacy by Quantum Federated Learning (QFL) and Quantum Differential Privacy (QDP) studied independently. However, to the best of our knowledge, no prior work has addressed both QFL and QDP together yet. Here, we propose to combine these privacy-preserving methods and implement them on the quantum platform, so that we can achieve comprehensive protection against data leakage (QFL) and model inversion attacks (QDP). This implementation promises more efficient and secure artificial intelligence. In this paper, we present a successful implementation of these privacy-preservation methods by performing the binary classification of the Cats vs Dogs dataset. Using our quantum-classical machine learning model, we obtained a test accuracy of over 0.98, while maintaining epsilon values less than 1.3. We show that federated differentially private training is a viable privacy preservation method for quantum machine learning on Noisy Intermediate-Scale Quantum (NISQ) devices., Comment: 5 pages, 7 figures

In the upcoming decade, deep learning may revolutionize the natural sciences, enhancing our capacity to model and predict natural occurrences. This could herald a new era of scientific exploration, bringing significant advancements across sectors from drug development to renewable energy. To answer this call, we present DeepSpeed4Science initiative (deepspeed4science.ai) which aims to build unique capabilities through AI system technology innovations to help domain experts to unlock today's biggest science mysteries. By leveraging DeepSpeed's current technology pillars (training, inference and compression) as base technology enablers, DeepSpeed4Science will create a new set of AI system technologies tailored for accelerating scientific discoveries by addressing their unique complexity beyond the common technical approaches used for accelerating generic large language models (LLMs). In this paper, we showcase the early progress we made with DeepSpeed4Science in addressing two of the critical system challenges in structural biology research.

Electrochemical degradation of solid electrolytes is a major roadblock in the development of solid-state batteries, and the formed solid-solid interphase (SSI) plays a key role in the performance of solid-state batteries. In this study, by combining experimental X-ray absorption spectroscopy (XAS) measurements, first-principles simulations, and unsupervised machine learning, we have unraveled the atomic-scale oxidative degradation mechanisms of sulfide electrolytes at the interface using the baseline Li3PS4 (LPS) electrolyte as a model system. The degradation begins with a decrease of Li neighbor affinity to S atoms upon initial delithiation, followed by the formation of S-S bonds as the PS4 tetrahedron deforms. After the first delithiation cycle, the PS4 motifs become strongly distorted and PS3 motifs start to form. Spectral fingerprints of the local structural evolution are identified, which correspond to the main peak broadening and the peak shifting to a higher energy by about 2.5 eV in P K-edge XAS and a new peak emerging at 2473 eV in S K-edge XAS during delithiation. The spectral fingerprints serve as a proxy for the electrochemical stability of phosphorus sulfide solid electrolytes beyond LPS, as demonstrated in argyrodite Li6PS5Cl. We observed that the strong distortion and destruction of PS4 tetrahedra and the formation of S-S bonds are correlated with an increased interfacial impedance. To the best of our knowledge, this study showcases the first atomic-scale insights into the oxidative degradation mechanism of the LPS electrolyte, which can provide guidance for controlling macroscopic reactions through microstructural engineering and, more generally, can advance the rational design of sulfide electrolytes.

While deep neural networks (DNNs) have revolutionized many fields, their fragility to carefully designed adversarial attacks impedes the usage of DNNs in safety-critical applications. In this paper, we strive to explore the robust features which are not affected by the adversarial perturbations, i.e., invariant to the clean image and its adversarial examples, to improve the model's adversarial robustness. Specifically, we propose a feature disentanglement model to segregate the robust features from non-robust features and domain specific features. The extensive experiments on four widely used datasets with different attacks demonstrate that robust features obtained from our model improve the model's adversarial robustness compared to the state-of-the-art approaches. Moreover, the trained domain discriminator is able to identify the domain specific features from the clean images and adversarial examples almost perfectly. This enables adversarial example detection without incurring additional computational costs. With that, we can also specify different classifiers for clean images and adversarial examples, thereby avoiding any drop in clean image accuracy., Comment: 12 pages, 8 figures

Domain Generalization (DG) aims to learn a generalizable model on the unseen target domain by only training on the multiple observed source domains. Although a variety of DG methods have focused on extracting domain-invariant features, the domain-specific class-relevant features have attracted attention and been argued to benefit generalization to the unseen target domain. To take into account the class-relevant domain-specific information, in this paper we propose an Information theory iNspired diSentanglement and pURification modEl (INSURE) to explicitly disentangle the latent features to obtain sufficient and compact (necessary) class-relevant feature for generalization to the unseen domain. Specifically, we first propose an information theory inspired loss function to ensure the disentangled class-relevant features contain sufficient class label information and the other disentangled auxiliary feature has sufficient domain information. We further propose a paired purification loss function to let the auxiliary feature discard all the class-relevant information and thus the class-relevant feature will contain sufficient and compact (necessary) class-relevant information. Moreover, instead of using multiple encoders, we propose to use a learnable binary mask as our disentangler to make the disentanglement more efficient and make the disentangled features complementary to each other. We conduct extensive experiments on four widely used DG benchmark datasets including PACS, OfficeHome, TerraIncognita, and DomainNet. The proposed INSURE outperforms the state-of-art methods. We also empirically show that domain-specific class-relevant features are beneficial for domain generalization., Comment: 10 pages, 4 figures

We present an extensible method for identifying semantic points to reverse engineer (i.e. extract the values of) data charts, particularly those in scientific articles. Our method uses a point proposal network (akin to region proposal networks for object detection) to directly predict the position of points of interest in a chart, and it is readily extensible to multiple chart types and chart elements. We focus on complex bar charts in the scientific literature, on which our model is able to detect salient points with an accuracy of 0.8705 F1 (@1.5-cell max deviation); it achieves 0.9810 F1 on synthetically-generated charts similar to those used in prior works. We also explore training exclusively on synthetic data with novel augmentations, reaching surprisingly competent performance in this way (0.6621 F1) on real charts with widely varying appearance, and we further demonstrate our unchanged method applied directly to synthetic pie charts (0.8343 F1). Datasets, trained models, and evaluation code are available at https://github.com/BNLNLP/PPN_model.

The challenge of optimal design of experiments (DOE) pervades materials science, physics, chemistry, and biology. Bayesian optimization has been used to address this challenge in vast sample spaces, although it requires framing experimental campaigns through the lens of maximizing some observable. This framing is insufficient for epistemic research goals that seek to comprehensively analyze a sample space, without an explicit scalar objective (e.g., the characterization of a wafer or sample library). In this work, we propose a flexible formulation of scientific value that recasts a dataset of input conditions and higher-dimensional observable data into a continuous, scalar metric. Intuitively, the scientific value function measures where observables change significantly, emulating the perspective of experts driving an experiment, and can be used in collaborative analysis tools or as an objective for optimization techniques. We demonstrate this technique by exploring simulated phase boundaries from different observables, autonomously driving a variable temperature measurement of a ferroelectric material, and providing feedback from a nanoparticle synthesis campaign. The method is seamlessly compatible with existing optimization tools, can be extended to multi-modal and multi-fidelity experiments, and can integrate existing models of an experimental system. Because of its flexibility, it can be deployed in a range of experimental settings for autonomous or accelerated experiments.

Fast screening of drug molecules based on the ligand binding affinity is an important step in the drug discovery pipeline. Graph neural fingerprint is a promising method for developing molecular docking surrogates with high throughput and great fidelity. In this study, we built a COVID-19 drug docking dataset of about 300,000 drug candidates on 23 coronavirus protein targets. With this dataset, we trained graph neural fingerprint docking models for high-throughput virtual COVID-19 drug screening. The graph neural fingerprint models yield high prediction accuracy on docking scores with the mean squared error lower than $0.21$ kcal/mol for most of the docking targets, showing significant improvement over conventional circular fingerprint methods. To make the neural fingerprints transferable for unknown targets, we also propose a transferable graph neural fingerprint method trained on multiple targets. With comparable accuracy to target-specific graph neural fingerprint models, the transferable model exhibits superb training and data efficiency. We highlight that the impact of this study extends beyond COVID-19 dataset, as our approach for fast virtual ligand screening can be easily adapted and integrated into a general machine learning-accelerated pipeline to battle future bio-threats., Comment: 8 pages, 5 figures, 2 tables, accepted by ICLMA2023

Understanding protein interactions and pathway knowledge is crucial for unraveling the complexities of living systems and investigating the underlying mechanisms of biological functions and complex diseases. While existing databases provide curated biological data from literature and other sources, they are often incomplete and their maintenance is labor-intensive, necessitating alternative approaches. In this study, we propose to harness the capabilities of large language models to address these issues by automatically extracting such knowledge from the relevant scientific literature. Toward this goal, in this work, we investigate the effectiveness of different large language models in tasks that involve recognizing protein interactions, identifying genes associated with pathways affected by low-dose radiation, and gene regulatory relations. We thoroughly evaluate the performance of various models, highlight the significant findings, and discuss both the future opportunities and the remaining challenges associated with this approach. The code and data are available at: https://github.com/boxorange/BioIE-LLM

Modeling spatiotemporal brain dynamics from high-dimensional data, such as functional Magnetic Resonance Imaging (fMRI), is a formidable task in neuroscience. Existing approaches for fMRI analysis utilize hand-crafted features, but the process of feature extraction risks losing essential information in fMRI scans. To address this challenge, we present SwiFT (Swin 4D fMRI Transformer), a Swin Transformer architecture that can learn brain dynamics directly from fMRI volumes in a memory and computation-efficient manner. SwiFT achieves this by implementing a 4D window multi-head self-attention mechanism and absolute positional embeddings. We evaluate SwiFT using multiple large-scale resting-state fMRI datasets, including the Human Connectome Project (HCP), Adolescent Brain Cognitive Development (ABCD), and UK Biobank (UKB) datasets, to predict sex, age, and cognitive intelligence. Our experimental outcomes reveal that SwiFT consistently outperforms recent state-of-the-art models. Furthermore, by leveraging its end-to-end learning capability, we show that contrastive loss-based self-supervised pre-training of SwiFT can enhance performance on downstream tasks. Additionally, we employ an explainable AI method to identify the brain regions associated with sex classification. To our knowledge, SwiFT is the first Swin Transformer architecture to process dimensional spatiotemporal brain functional data in an end-to-end fashion. Our work holds substantial potential in facilitating scalable learning of functional brain imaging in neuroscience research by reducing the hurdles associated with applying Transformer models to high-dimensional fMRI., Comment: NeurIPS 2023

Quantum computers offer an intriguing path for a paradigmatic change of computing in the natural sciences and beyond, with the potential for achieving a so-called quantum advantage, namely a significant (in some cases exponential) speed-up of numerical simulations. The rapid development of hardware devices with various realizations of qubits enables the execution of small scale but representative applications on quantum computers. In particular, the high-energy physics community plays a pivotal role in accessing the power of quantum computing, since the field is a driving source for challenging computational problems. This concerns, on the theoretical side, the exploration of models which are very hard or even impossible to address with classical techniques and, on the experimental side, the enormous data challenge of newly emerging experiments, such as the upgrade of the Large Hadron Collider. In this roadmap paper, led by CERN, DESY and IBM, we provide the status of high-energy physics quantum computations and give examples for theoretical and experimental target benchmark applications, which can be addressed in the near future. Having the IBM 100 x 100 challenge in mind, where possible, we also provide resource estimates for the examples given using error mitigated quantum computing.

Accurate classification of molecular chemical motifs from experimental measurement is an important problem in molecular physics, chemistry and biology. In this work, we present neural network ensemble classifiers for predicting the presence (or lack thereof) of 41 different chemical motifs on small molecules from simulated C, N and O K-edge X-ray absorption near-edge structure (XANES) spectra. Our classifiers not only reach a maximum average class-balanced accuracy of 0.99 but also accurately quantify uncertainty. We also show that including multiple XANES modalities improves predictions notably on average, demonstrating a "multi-modal advantage" over any single modality. In addition to structure refinement, our approach can be generalized for broad applications with molecular design pipelines.

Deciding how to optimally deploy sensors in a large, complex, and spatially extended structure is critical to ensure that the surface pressure field is accurately captured for subsequent analysis and design. In some cases, reconstruction of missing data is required in downstream tasks such as the development of digital twins. This paper presents a data-driven sparse sensor selection algorithm, aiming to provide the most information contents for reconstructing aerodynamic characteristics of wind pressures over tall building structures parsimoniously. The algorithm first fits a set of basis functions to the training data, then applies a computationally efficient QR algorithm that ranks existing pressure sensors in order of importance based on the state reconstruction to this tailored basis. The findings of this study show that the proposed algorithm successfully reconstructs the aerodynamic characteristics of tall buildings from sparse measurement locations, generating stable and optimal solutions across a range of conditions. As a result, this study serves as a promising first step toward leveraging the success of data-driven and machine learning algorithms to supplement traditional genetic algorithms currently used in wind engineering., Comment: 31 pages, 19 figures

An unpaired image-to-image (I2I) translation technique seeks to find a mapping between two domains of data in a fully unsupervised manner. While initial solutions to the I2I problem were provided by generative adversarial neural networks (GANs), diffusion models (DMs) currently hold the state-of-the-art status on the I2I translation benchmarks in terms of Frechet inception distance (FID). Yet, DMs suffer from limitations, such as not using data from the source domain during the training or maintaining consistency of the source and translated images only via simple pixel-wise errors. This work improves a recent UVCGAN model and equips it with modern advancements in model architectures and training procedures. The resulting revised model significantly outperforms other advanced GAN- and DM-based competitors on a variety of benchmarks. In the case of Male-to-Female translation of CelebA, the model achieves more than 40% improvement in FID score compared to the state-of-the-art results. This work also demonstrates the ineffectiveness of the pixel-wise I2I translation faithfulness metrics and suggests their revision. The code and trained models are available at https://github.com/LS4GAN/uvcgan2

Numerical simulation of non-linear partial differential equations plays a crucial role in modeling physical science and engineering phenomena, such as weather, climate, and aerodynamics. Recent Machine Learning (ML) models trained on low-resolution spatio-temporal signals have shown new promises in capturing important dynamics in high-resolution signals, under the condition that the models can effectively recover the missing details. However, this study shows that significant information is often lost in the low-resolution down-sampled features. To address such issues, we propose a new approach, namely Temporal Stencil Modeling (TSM), which combines the strengths of advanced time-series sequence modeling (with the HiPPO features) and state-of-the-art neural PDE solvers (with learnable stencil modeling). TSM aims to recover the lost information from the PDE trajectories and can be regarded as a temporal generalization of classic finite volume methods such as WENO. Our experimental results show that TSM achieves the new state-of-the-art simulation accuracy for 2-D incompressible Navier-Stokes turbulent flows: it significantly outperforms the previously reported best results by 19.9% in terms of the highly-correlated duration time and reduces the inference latency into 80%. We also show a strong generalization ability of the proposed method to various out-of-distribution turbulent flow settings. Our code is available at "https://github.com/Edward-Sun/TSM-PDE".

X-ray absorption spectroscopy (XAS) is a premier technique for materials characterization, providing key information about the local chemical environment of the absorber atom. In this work, we develop a database of sulfur K-edge XAS spectra of crystalline and amorphous lithium thiophosphate materials based on the atomic structures reported in Chem. Mater., 34, 6702 (2022). The XAS database is based on simulations using the excited electron and core-hole pseudopotential approach implemented in the Vienna Ab initio Simulation Package. Our database contains 2681 S K-edge XAS spectra for 66 crystalline and glassy structure models, making it the largest collection of first-principles computational XAS spectra for glass/ceramic lithium thiophosphates to date. This database can be used to correlate S spectral features with distinct S species based on their local coordination and short-range ordering in sulfide-based solid electrolytes. The data is openly distributed via the Materials Cloud, allowing researchers to access it for free and use it for further analysis, such as spectral fingerprinting, matching with experiments, and developing machine learning models., Comment: 11 pages, 3 figures, 1 table

There are various sources of ionizing radiation exposure, where medical exposure for radiation therapy or diagnosis is the most common human-made source. Understanding how gene expression is modulated after ionizing radiation exposure and investigating the presence of any dose-dependent gene expression patterns have broad implications for health risks from radiotherapy, medical radiation diagnostic procedures, as well as other environmental exposure. In this paper, we perform a comprehensive pathway-based analysis of gene expression profiles in response to low-dose radiation exposure, in order to examine the potential mechanism of gene regulation underlying such responses. To accomplish this goal, we employ a statistical framework to determine whether a specific group of genes belonging to a known pathway display coordinated expression patterns that are modulated in a manner consistent with the radiation level. Findings in our study suggest that there exist complex yet consistent signatures that reflect the molecular response to radiation exposure, which differ between low-dose and high-dose radiation., Comment: 9 pages, 6 figures

Optical astronomical images are strongly affected by the point spread function (PSF) of the optical system and the atmosphere (seeing) which blurs the observed image. The amount of blurring depends both on the observed band, and on the atmospheric conditions during observation. A typical astronomical image will likely have a unique PSF, that is non-circular and different in different bands. At the same time, observations of known stars also give us an accurate determination of this PSF. Therefore, any serious candidate for production analysis of astronomical images must take the known PSF into account during the image analysis. So far, the majority of applications of neural networks (NN) to astronomical image analysis have ignored this problem by assuming a fixed PSF in training and validation. We present a neural-network based deconvolution algorithm based on Deep Wiener Deconvolution Network (DWDN). This algorithm belongs to a class of non-blind deconvolution algorithms, since it assumes the PSF shape is known. We study the performance of different versions of this algorithm under realistic observational conditions in terms of the recovery of the most relevant astronomical quantities such as colors, ellipticities and orientations. We investigate custom loss functions that optimize the recovery of astronomical quantities with mixed results., Comment: 15 pages, 7 figures. Accepted for publication in the Open Journal of Astrophysics

As machine learning (ML) methods continue to be applied to a broad scope of problems in the physical sciences, uncertainty quantification is becoming correspondingly more important for their robust application. Uncertainty aware machine learning methods have been used in select applications, but largely for scalar properties. In this work, we showcase an exemplary study in which neural network ensembles are used to predict the X-ray absorption spectra of small molecules, as well as their point-wise uncertainty, from local atomic environments. The performance of the resulting surrogate clearly demonstrates quantitative correlation between errors relative to ground truth and the predicted uncertainty estimates. Significantly, the model provides an upper bound on the expected error. Specifically, an important quality of this uncertainty-aware model is that it can indicate when the model is predicting on out-of-sample data. This allows for its integration with large scale sampling of structures together with active learning or other techniques for structure refinement. Additionally, our models can be generalized to larger molecules than those used for training, and also successfully track uncertainty due to random distortions in test molecules. While we demonstrate this workflow on a specific example, ensemble learning is completely general. We believe it could have significant impact on ML-enabled forward modeling of a broad array of molecular and materials properties., Comment: 24 pages, 16 figures

DUNE, like other HEP experiments, faces a challenge related to matching execution patterns of our production simulation and data processing software to the limitations imposed by modern high-performance computing facilities. In order to efficiently exploit these new architectures, particularly those with high CPU core counts and GPU accelerators, our existing software execution models require adaptation. In addition, the large size of individual units of raw data from the far detector modules pose an additional challenge somewhat unique to DUNE. Here we describe some of these problems and how we begin to solve them today with existing software frameworks and toolkits. We also describe ways we may leverage these existing software architectures to attack remaining problems going forward. This whitepaper is a contribution to the Computational Frontier of Snowmass21., Comment: This whitepaper is a contribution to the Computational Frontier of Snowmass21

Unpaired image-to-image translation has broad applications in art, design, and scientific simulations. One early breakthrough was CycleGAN that emphasizes one-to-one mappings between two unpaired image domains via generative-adversarial networks (GAN) coupled with the cycle-consistency constraint, while more recent works promote one-to-many mapping to boost diversity of the translated images. Motivated by scientific simulation and one-to-one needs, this work revisits the classic CycleGAN framework and boosts its performance to outperform more contemporary models without relaxing the cycle-consistency constraint. To achieve this, we equip the generator with a Vision Transformer (ViT) and employ necessary training and regularization techniques. Compared to previous best-performing models, our model performs better and retains a strong correlation between the original and translated image. An accompanying ablation study shows that both the gradient penalty and self-supervised pre-training are crucial to the improvement. To promote reproducibility and open science, the source code, hyperparameter configurations, and pre-trained model are available at https://github.com/LS4GAN/uvcgan., Comment: Accepted by WACV2023, contains 5 pages, 2 figures, 2 tables

This work proposes a deep learning-based emulator for the efficient computation of the coupled viscous Burgers' equation with random initial conditions. In a departure from traditional data-driven deep learning approaches, the proposed emulator does not require a classical numerical solver to collect training data. Instead, it makes direct use of the problem's physics. Specifically, the model emulates a second-order finite difference solver, i.e., the Crank-Nicolson scheme in learning dynamics. A systematic case study is conducted to examine the model's prediction performance, generalization ability, and computational efficiency. The computed results are graphically represented and compared to those of state-of-the-art numerical solvers., Comment: 23 pages, 8 figures

Since model bias and associated initialization shock are serious shortcomings that reduce prediction skills in state-of-the-art decadal climate prediction efforts, we pursue a complementary machine-learning-based approach to climate prediction. The example problem setting we consider consists of predicting natural variability of the North Atlantic sea surface temperature on the interannual timescale in the pre-industrial control simulation of the Community Earth System Model (CESM2). While previous works have considered the use of recurrent networks such as convolutional LSTMs and reservoir computing networks in this and other similar problem settings, we currently focus on the use of feedforward convolutional networks. In particular, we find that a feedforward convolutional network with a Densenet architecture is able to outperform a convolutional LSTM in terms of predictive skill. Next, we go on to consider a probabilistic formulation of the same network based on Stein variational gradient descent and find that in addition to providing useful measures of predictive uncertainty, the probabilistic (Bayesian) version improves on its deterministic counterpart in terms of predictive skill. Finally, we characterize the reliability of the ensemble of ML models obtained in the probabilistic setting by using analysis tools developed in the context of ensemble numerical weather prediction., Comment: 32 pages, 12 figures