Bowen Jing

Bowen Jing, Hannes Stärk, Tommi Jaakkola et al. · mit

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible multi-task surrogate models of MD from data. By conditioning on appropriately chosen frames of the trajectory, we show such generative models can be adapted to diverse tasks such as forward simulation, transition path sampling, and trajectory upsampling. By alternatively conditioning on part of the molecular system and inpainting the rest, we also demonstrate the first steps towards dynamics-conditioned molecular design. We validate the full set of these capabilities on tetrapeptide simulations and show that our model can produce reasonable ensembles of protein monomers. Altogether, our work illustrates how generative modeling can unlock value from MD data towards diverse downstream tasks that are not straightforward to address with existing methods or even MD itself. Code is available at https://github.com/bjing2016/mdgen.

Gabriele Corso, Hannes Stärk, Bowen Jing et al. · mit

Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime compared to traditional search-based methods but have yet to offer substantial improvements in accuracy. We instead frame molecular docking as a generative modeling problem and develop DiffDock, a diffusion generative model over the non-Euclidean manifold of ligand poses. To do so, we map this manifold to the product space of the degrees of freedom (translational, rotational, and torsional) involved in docking and develop an efficient diffusion process on this space. Empirically, DiffDock obtains a 38% top-1 success rate (RMSD<2A) on PDBBind, significantly outperforming the previous state-of-the-art of traditional docking (23%) and deep learning (20%) methods. Moreover, while previous methods are not able to dock on computationally folded structures (maximum accuracy 10.4%), DiffDock maintains significantly higher precision (21.7%). Finally, DiffDock has fast inference times and provides confidence estimates with high selective accuracy.

Bowen Jing, Gabriele Corso, Jeffrey Chang et al.

Molecular conformer generation is a fundamental task in computational chemistry. Several machine learning approaches have been developed, but none have outperformed state-of-the-art cheminformatics methods. We propose torsional diffusion, a novel diffusion framework that operates on the space of torsion angles via a diffusion process on the hypertorus and an extrinsic-to-intrinsic score model. On a standard benchmark of drug-like molecules, torsional diffusion generates superior conformer ensembles compared to machine learning and cheminformatics methods in terms of both RMSD and chemical properties, and is orders of magnitude faster than previous diffusion-based models. Moreover, our model provides exact likelihoods, which we employ to build the first generalizable Boltzmann generator. Code is available at https://github.com/gcorso/torsional-diffusion.

Bowen Jing, Ezra Erives, Peter Pao-Huang et al.

Protein structure prediction has reached revolutionary levels of accuracy on single structures, yet distributional modeling paradigms are needed to capture the conformational ensembles and flexibility that underlie biological function. Towards this goal, we develop EigenFold, a diffusion generative modeling framework for sampling a distribution of structures from a given protein sequence. We define a diffusion process that models the structure as a system of harmonic oscillators and which naturally induces a cascading-resolution generative process along the eigenmodes of the system. On recent CAMEO targets, EigenFold achieves a median TMScore of 0.84, while providing a more comprehensive picture of model uncertainty via the ensemble of sampled structures relative to existing methods. We then assess EigenFold's ability to model and predict conformational heterogeneity for fold-switching proteins and ligand-induced conformational change. Code is available at https://github.com/bjing2016/EigenFold.

Hannes Stärk, Bowen Jing, Regina Barzilay et al. · mit

A significant amount of protein function requires binding small molecules, including enzymatic catalysis. As such, designing binding pockets for small molecules has several impactful applications ranging from drug synthesis to energy storage. Towards this goal, we first develop HarmonicFlow, an improved generative process over 3D protein-ligand binding structures based on our self-conditioned flow matching objective. FlowSite extends this flow model to jointly generate a protein pocket's discrete residue types and the molecule's binding 3D structure. We show that HarmonicFlow improves upon state-of-the-art generative processes for docking in simplicity, generality, and average sample quality in pocket-level docking. Enabled by this structure modeling, FlowSite designs binding sites substantially better than baseline approaches.

Yunxiang Li, Bowen Jing, Zihan Li et al. · uw

Automatic segmentation of medical images is crucial in modern clinical workflows. The Segment Anything Model (SAM) has emerged as a versatile tool for image segmentation without specific domain training, but it requires human prompts and may have limitations in specific domains. Traditional models like nnUNet perform automatic segmentation during inference and are effective in specific domains but need extensive domain-specific training. To combine the strengths of foundational and domain-specific models, we propose nnSAM, integrating SAM's robust feature extraction with nnUNet's automatic configuration to enhance segmentation accuracy on small datasets. Our nnSAM model optimizes two main approaches: leveraging SAM's feature extraction and nnUNet's domain-specific adaptation, and incorporating a boundary shape supervision loss function based on level set functions and curvature calculations to learn anatomical shape priors from limited data. We evaluated nnSAM on four segmentation tasks: brain white matter, liver, lung, and heart segmentation. Our method outperformed others, achieving the highest DICE score of 82.77% and the lowest ASD of 1.14 mm in brain white matter segmentation with 20 training samples, compared to nnUNet's DICE score of 79.25% and ASD of 1.36 mm. A sample size study highlighted nnSAM's advantage with fewer training samples. Our results demonstrate significant improvements in segmentation performance with nnSAM, showcasing its potential for small-sample learning in medical image segmentation.

Bowen Jing, Gabriele Corso, Renato Berlinghieri et al.

Score-based models generate samples by mapping noise to data (and vice versa) via a high-dimensional diffusion process. We question whether it is necessary to run this entire process at high dimensionality and incur all the inconveniences thereof. Instead, we restrict the diffusion via projections onto subspaces as the data distribution evolves toward noise. When applied to state-of-the-art models, our framework simultaneously improves sample quality -- reaching an FID of 2.17 on unconditional CIFAR-10 -- and reduces the computational cost of inference for the same number of denoising steps. Our framework is fully compatible with continuous-time diffusion and retains its flexible capabilities, including exact log-likelihoods and controllable generation. Code is available at https://github.com/bjing2016/subspace-diffusion.

Bowen Jing, Bonnie Berger, Tommi Jaakkola

The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly accurate single-state predictors such as AlphaFold and ESMFold and fine-tune them under a custom flow matching framework to obtain sequence-conditoned generative models of protein structure called AlphaFlow and ESMFlow. When trained and evaluated on the PDB, our method provides a superior combination of precision and diversity compared to AlphaFold with MSA subsampling. When further trained on ensembles from all-atom MD, our method accurately captures conformational flexibility, positional distributions, and higher-order ensemble observables for unseen proteins. Moreover, our method can diversify a static PDB structure with faster wall-clock convergence to certain equilibrium properties than replicate MD trajectories, demonstrating its potential as a proxy for expensive physics-based simulations. Code is available at https://github.com/bjing2016/alphaflow.

Hannes Stark, Bowen Jing, Chenyu Wang et al. · mit

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that naïve linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in $O(L)$ speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

Siyi Li, Yue Jiang, Bowen Jing et al.

Advancements in 3D modeling,digital display technologies,and the growing availability of digital cultural heritage data have significantly improved the accuracy of heritage depictions and expanded opportunities for analysis.However,while many studies focus on presenting specific cultural heritage figurines,an often overlooked aspect is the visualization of the Terracotta Warriors as a unified entity.This involves concisely representing the distribution of features and their relationships,providing a clear and insightful presentation that engages practitioners, academics,and wider audiences.To tackle the challenges mentioned above,this research seeks to explore the application of AI methods in processing cultural heritage data.It aims to optimize and augment the dataset,analyze the distribution and relationships of various attributes, and interpret the analysis results through visualization techniques.The Terracotta Warriors,among China's most significant cultural heritages and renowned for their abundance,exquisite workmanship,and magnitude,are chosen as a case study.The contribution of this paper is primarily twofold.Firstly,we constructed a dataset of Terracotta Warriors from Pit No.1,detailing the attributes significant for identifying different Terracotta Warriors.Secondly,we employ various AI methods,such as generative adversarial network and random forest,to process and analyze these attributes,followed by visualizing the analysis results for an intuitive presentation.This study introduces a novel scheme for presenting information on a collection of cultural relics,offering a practical case for analyzing and visualizing the Terracotta Warriors'attributes as a whole entity,rather than showcasing individual relics'information in isolation.

Weiche Hsieh, Ziqian Bi, Chuanqi Jiang et al.

Explainable Artificial Intelligence (XAI) addresses the growing need for transparency and interpretability in AI systems, enabling trust and accountability in decision-making processes. This book offers a comprehensive guide to XAI, bridging foundational concepts with advanced methodologies. It explores interpretability in traditional models such as Decision Trees, Linear Regression, and Support Vector Machines, alongside the challenges of explaining deep learning architectures like CNNs, RNNs, and Large Language Models (LLMs), including BERT, GPT, and T5. The book presents practical techniques such as SHAP, LIME, Grad-CAM, counterfactual explanations, and causal inference, supported by Python code examples for real-world applications. Case studies illustrate XAI's role in healthcare, finance, and policymaking, demonstrating its impact on fairness and decision support. The book also covers evaluation metrics for explanation quality, an overview of cutting-edge XAI tools and frameworks, and emerging research directions, such as interpretability in federated learning and ethical AI considerations. Designed for a broad audience, this resource equips readers with the theoretical insights and practical skills needed to master XAI. Hands-on examples and additional resources are available at the companion GitHub repository: https://github.com/Echoslayer/XAI_From_Classical_Models_to_LLMs.

Bowen Jing, Ruiyang Hao, Weitao Zhou et al.

Generating safety-critical driving scenarios requires understanding why dangerous interactions arise, rather than merely forcing collisions. However, existing methods rely on heuristic adversarial agent selection and unstructured perturbations, lacking explicit modeling of interaction dependencies and thus exhibiting a realism--adversarial trade-off. We present CounterScene, a framework that endows closed-loop generative BEV world models with structured counterfactual reasoning for safety-critical scenario generation. Given a safe scene, CounterScene asks: what if the causally critical agent had behaved differently? To answer this, we introduce causal adversarial agent identification to identify the critical agent and classify conflict types, and develop a conflict-aware interactive world model in which a causal interaction graph is used to explicitly model dynamic inter-agent dependencies. Building on this structure, stage-adaptive counterfactual guidance performs minimal interventions on the identified agent, removing its spatial and temporal safety margins while allowing risk to emerge through natural interaction propagation. Extensive experiments on nuScenes demonstrate that CounterScene achieves the strongest adversarial effectiveness while maintaining superior trajectory realism across all horizons, improving long-horizon collision rate from 12.3% to 22.7% over the strongest baseline with better realism (ADE 1.88 vs.2.09). Notably, this advantage further widens over longer rollouts, and CounterScene generalizes zero-shot to nuPlan with state-of-the-art realism.

Bowen Jing, Tommi Jaakkola, Bonnie Berger

Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can accelerate this process by learning a scoring function with a functional form that allows for more rapid optimization. Specifically, we define the scoring function to be the cross-correlation of multi-channel ligand and protein scalar fields parameterized by equivariant graph neural networks, enabling rapid optimization over rigid-body degrees of freedom with fast Fourier transforms. The runtime of our approach can be amortized at several levels of abstraction, and is particularly favorable for virtual screening settings with a common binding pocket. We benchmark our scoring functions on two simplified docking-related tasks: decoy pose scoring and rigid conformer docking. Our method attains similar but faster performance on crystal structures compared to the widely-used Vina and Gnina scoring functions, and is more robust on computationally predicted structures. Code is available at https://github.com/bjing2016/scalar-fields.

Ezra Erives, Bowen Jing, Peter Holderrieth et al.

Annealing-based neural samplers seek to amortize sampling from unnormalized distributions by training neural networks to transport a family of densities interpolating from source to target. A crucial design choice in the training phase of such samplers is the proposal distribution by which locations are generated at which to evaluate the loss. Previous work has obtained such a proposal distribution by combining a partially learned transport with annealed Langevin dynamics. However, isolated modes and other pathological properties of the annealing path imply that such proposals achieve insufficient exploration and thereby lower performance post training. To remedy this, we propose continuously tempered diffusion samplers, which leverage exploration techniques developed in the context of molecular dynamics to improve proposal distributions. Specifically, a family of distributions across different temperatures is introduced to lower energy barriers at higher temperatures and drive exploration at the lower temperature of interest. We empirically validate improved sampler performance driven by extended exploration. Code is available at https://github.com/eje24/ctds.

Yichao Zhang, Ningyuan Deng, Xinyuan Song et al.

After AlphaFold won the Nobel Prize, protein prediction with deep learning once again became a hot topic. We comprehensively explore advanced deep learning methods applied to protein structure prediction and design. It begins by examining recent innovations in prediction architectures, with detailed discussions on improvements such as diffusion based frameworks and novel pairwise attention modules. The text analyses key components including structure generation, evaluation metrics, multiple sequence alignment processing, and network architecture, thereby illustrating the current state of the art in computational protein modelling. Subsequent chapters focus on practical applications, presenting case studies that range from individual protein predictions to complex biomolecular interactions. Strategies for enhancing prediction accuracy and integrating deep learning techniques with experimental validation are thoroughly explored. The later sections review the industry landscape of protein design, highlighting the transformative role of artificial intelligence in biotechnology and discussing emerging market trends and future challenges. Supplementary appendices provide essential resources such as databases and open source tools, making this volume a valuable reference for researchers and students.

Bowen Jing, Stephan Eismann, Pratham N. Soni et al.

Representing and reasoning about 3D structures of macromolecules is emerging as a distinct challenge in machine learning. Here, we extend recent work on geometric vector perceptrons and apply equivariant graph neural networks to a wide range of tasks from structural biology. Our method outperforms all reference architectures on three out of eight tasks in the ATOM3D benchmark, is tied for first on two others, and is competitive with equivariant networks using higher-order representations and spherical harmonic convolutions. In addition, we demonstrate that transfer learning can further improve performance on certain downstream tasks. Code is available at https://github.com/drorlab/gvp-pytorch.

Raphael J. L. Townshend, Martin Vögele, Patricia Suriana et al.

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their widespread adoption in the biomolecular domain has been limited by a lack of either systematic performance benchmarks or a unified toolkit for interacting with molecular data. To address this, we present ATOM3D, a collection of both novel and existing benchmark datasets spanning several key classes of biomolecules. We implement several classes of three-dimensional molecular learning methods for each of these tasks and show that they consistently improve performance relative to methods based on one- and two-dimensional representations. The specific choice of architecture proves to be critical for performance, with three-dimensional convolutional networks excelling at tasks involving complex geometries, graph networks performing well on systems requiring detailed positional information, and the more recently developed equivariant networks showing significant promise. Our results indicate that many molecular problems stand to gain from three-dimensional molecular learning, and that there is potential for improvement on many tasks which remain underexplored. To lower the barrier to entry and facilitate further developments in the field, we also provide a comprehensive suite of tools for dataset processing, model training, and evaluation in our open-source atom3d Python package. All datasets are available for download from https://www.atom3d.ai .

Bowen Jing, Stephan Eismann, Patricia Suriana et al.

Learning on 3D structures of large biomolecules is emerging as a distinct area in machine learning, but there has yet to emerge a unifying network architecture that simultaneously leverages the graph-structured and geometric aspects of the problem domain. To address this gap, we introduce geometric vector perceptrons, which extend standard dense layers to operate on collections of Euclidean vectors. Graph neural networks equipped with such layers are able to perform both geometric and relational reasoning on efficient and natural representations of macromolecular structure. We demonstrate our approach on two important problems in learning from protein structure: model quality assessment and computational protein design. Our approach improves over existing classes of architectures, including state-of-the-art graph-based and voxel-based methods. We release our code at https://github.com/drorlab/gvp.

Ruiyang Hao, Bowen Jing, Haibao Yu et al.

Personalization, while extensively studied in conventional autonomous driving pipelines, has been largely overlooked in the context of end-to-end autonomous driving (E2EAD), despite its critical role in fostering user trust, safety perception, and real-world adoption. A primary bottleneck is the absence of large-scale real-world datasets that systematically capture driving preferences, severely limiting the development and evaluation of personalized E2EAD models. In this work, we introduce the first large-scale real-world dataset explicitly curated for personalized E2EAD, integrating comprehensive scene topology with rich dynamic context derived from agent dynamics and semantics inferred via a fine-tuned vision-language model (VLM). We propose a hybrid annotation pipeline that combines behavioral analysis, rule-and-distribution-based heuristics, and subjective semantic modeling guided by VLM reasoning, with final refinement through human-in-the-loop verification. Building upon this dataset, we introduce the first standardized benchmark for systematically evaluating personalized E2EAD models. Empirical evaluations on state-of-the-art architectures demonstrate that incorporating personalized driving preferences significantly improves behavioral alignment with human demonstrations.

Haibao Yu, Kuntao Xiao, Jiahang Wang et al.

High-fidelity visual reconstruction and novel-view synthesis are essential for realistic closed-loop evaluation in autonomous driving. While 4D Gaussian Splatting (4DGS) offers a promising balance of accuracy and efficiency, existing per-scene optimization methods require costly iterative refinement, rendering them unscalable for extensive urban environments. Conversely, current feed-forward approaches often suffer from degraded photometric quality. To address these limitations, we propose ReconDrive, a feed-forward framework that leverages and extends the 3D foundation model VGGT for rapid, high-fidelity 4DGS generation. Our architecture introduces two core adaptations to tailor the foundation model to dynamic driving scenes: (1) Hybrid Gaussian Prediction Heads, which decouple the regression of spatial coordinates and appearance attributes to overcome the photometric deficiencies inherent in generalized foundation features; and (2) a Static-Dynamic 4D Composition strategy that explicitly captures temporal motion via velocity modeling to represent complex dynamic environments. Benchmarked on nuScenes, ReconDrive significantly outperforms existing feed-forward baselines in reconstruction, novel-view synthesis, and 3D perception. It achieves performance competitive with per-scene optimization while being orders of magnitude faster, providing a scalable and practical solution for realistic driving simulation.

Bowen Jing, Bonnie Berger, Tommi Jaakkola

Advances in deep learning have opened an era of abundant and accurate predicted protein structures; however, similar progress in protein ensembles has remained elusive. This review highlights several recent research directions towards AI-based predictions of protein ensembles, including coarse-grained force fields, generative models, multiple sequence alignment perturbation methods, and modeling of ensemble descriptors. An emphasis is placed on realistic assessments of the technological maturity of current methods, the strengths and weaknesses of broad families of techniques, and promising machine learning frameworks at an early stage of development. We advocate for "closing the loop" between model training, simulation, and inference to overcome challenges in training data availability and to enable the next generation of models.

Mihir Bafna, Bowen Jing, Bonnie Berger

Many methods have been developed to predict static protein structures, however understanding the dynamics of protein structure is essential for elucidating biological function. While molecular dynamics (MD) simulations remain the in silico gold standard, its high computational cost limits scalability. We present DynaProt, a lightweight, SE(3)-invariant framework that predicts rich descriptors of protein dynamics directly from static structures. By casting the problem through the lens of multivariate Gaussians, DynaProt estimates dynamics at two complementary scales: (1) per-residue marginal anisotropy as $3 \times 3$ covariance matrices capturing local flexibility, and (2) joint scalar covariances encoding pairwise dynamic coupling across residues. From these dynamics outputs, DynaProt achieves high accuracy in predicting residue-level flexibility (RMSF) and, remarkably, enables reasonable reconstruction of the full covariance matrix for fast ensemble generation. Notably, it does so using orders of magnitude fewer parameters than prior methods. Our results highlight the potential of direct protein dynamics prediction as a scalable alternative to existing methods.

Tianyang Wang, Ziqian Bi, Yichao Zhang et al.

Deep learning has transformed AI applications but faces critical security challenges, including adversarial attacks, data poisoning, model theft, and privacy leakage. This survey examines these vulnerabilities, detailing their mechanisms and impact on model integrity and confidentiality. Practical implementations, including adversarial examples, label flipping, and backdoor attacks, are explored alongside defenses such as adversarial training, differential privacy, and federated learning, highlighting their strengths and limitations. Advanced methods like contrastive and self-supervised learning are presented for enhancing robustness. The survey concludes with future directions, emphasizing automated defenses, zero-trust architectures, and the security challenges of large AI models. A balanced approach to performance and security is essential for developing reliable deep learning systems.

Ezra Erives, Bowen Jing, Tommi Jaakkola

Approximations in computing model likelihoods with continuous normalizing flows (CNFs) hinder the use of these models for importance sampling of Boltzmann distributions, where exact likelihoods are required. In this work, we present Verlet flows, a class of CNFs on an augmented state-space inspired by symplectic integrators from Hamiltonian dynamics. When used with carefully constructed Taylor-Verlet integrators, Verlet flows provide exact-likelihood generative models which generalize coupled flow architectures from a non-continuous setting while imposing minimal expressivity constraints. On experiments over toy densities, we demonstrate that the variance of the commonly used Hutchinson trace estimator is unsuitable for importance sampling, whereas Verlet flows perform comparably to full autograd trace computations while being significantly faster.

Bowen Jing, Yang Cui, Tianpeng Huang

In the era of large language model, relation extraction (RE) plays an important role in information extraction through the transformation of unstructured raw text into structured data (Wadhwa et al., 2023). In this paper, we systematically compare the performance of deep supervised learning approaches without transformers and those with transformers. We used a series of non-transformer architectures such as PA-LSTM(Zhang et al., 2017), C-GCN(Zhang et al., 2018), and AGGCN(attention guide GCN)(Guo et al., 2019), and a series of transformer architectures such as BERT, RoBERTa, and R-BERT(Wu and He, 2019). Our comparison included traditional metrics like micro F1, as well as evaluations in different scenarios, varying sentence lengths, and different percentages of the dataset for training. Our experiments were conducted on TACRED, TACREV, and RE-TACRED. The results show that transformer-based models outperform non-transformer models, achieving micro F1 scores of 80-90% compared to 64-67% for non-transformer models. Additionally, we briefly review the research journey in supervised relation classification and discuss the role and current status of large language models (LLMs) in relation extraction.

Junhao Song, Yichao Zhang, Ziqian Bi et al.

Generative Adversarial Networks (GAN) have greatly influenced the development of computer vision and artificial intelligence in the past decade and also connected art and machine intelligence together. This book begins with a detailed introduction to the fundamental principles and historical development of GANs, contrasting them with traditional generative models and elucidating the core adversarial mechanisms through illustrative Python examples. The text systematically addresses the mathematical and theoretical underpinnings including probability theory, statistics, and game theory providing a solid framework for understanding the objectives, loss functions, and optimisation challenges inherent to GAN training. Subsequent chapters review classic variants such as Conditional GANs, DCGANs, InfoGAN, and LAPGAN before progressing to advanced training methodologies like Wasserstein GANs, GANs with gradient penalty, least squares GANs, and spectral normalisation techniques. The book further examines architectural enhancements and task-specific adaptations in generators and discriminators, showcasing practical implementations in high resolution image generation, artistic style transfer, video synthesis, text to image generation and other multimedia applications. The concluding sections offer insights into emerging research trends, including self-attention mechanisms, transformer-based generative models, and a comparative analysis with diffusion models, thus charting promising directions for future developments in both academic and applied settings.

Bowen Jing, Jing Wang

Rationale and Objectives: Early prediction of pathological complete response (pCR) can facilitate personalized treatment for breast cancer patients. To improve prediction accuracy at the early time point of neoadjuvant chemotherapy, we proposed a two-stage dual-task learning strategy to train a deep neural network for early prediction of pCR using early-treatment magnetic resonance images. Methods: We developed and validated the two-stage dual-task learning strategy using the dataset from the national-wide, multi-institutional I-SPY2 clinical trial, which included dynamic contrast-enhanced magnetic resonance images acquired at three time points: pretreatment (T0), after 3 weeks (T1), and after 12 weeks of treatment (T2). First, we trained a convolutional long short-term memory network to predict pCR and extract the latent space image features at T2. At the second stage, we trained a dual-task network to simultaneously predict pCR and the image features at T2 using images from T0 and T1. This allowed us to predict pCR earlier without using images from T2. Results: The conventional single-stage single-task strategy gave an area under the receiver operating characteristic curve (AUROC) of 0.799 for pCR prediction using all the data at time points T0 and T1. By using the proposed two-stage dual-task learning strategy, the AUROC was improved to 0.820. Conclusions: The proposed two-stage dual-task learning strategy can improve model performance significantly (p=0.0025) for predicting pCR at the early stage (3rd week) of neoadjuvant chemotherapy. The early prediction model can potentially help physicians to intervene early and develop personalized plans at the early stage of chemotherapy.

Weiche Hsieh, Ziqian Bi, Keyu Chen et al.

Advancements in artificial intelligence, machine learning, and deep learning have catalyzed the transformation of big data analytics and management into pivotal domains for research and application. This work explores the theoretical foundations, methodological advancements, and practical implementations of these technologies, emphasizing their role in uncovering actionable insights from massive, high-dimensional datasets. The study presents a systematic overview of data preprocessing techniques, including data cleaning, normalization, integration, and dimensionality reduction, to prepare raw data for analysis. Core analytics methodologies such as classification, clustering, regression, and anomaly detection are examined, with a focus on algorithmic innovation and scalability. Furthermore, the text delves into state-of-the-art frameworks for data mining and predictive modeling, highlighting the role of neural networks, support vector machines, and ensemble methods in tackling complex analytical challenges. Special emphasis is placed on the convergence of big data with distributed computing paradigms, including cloud and edge computing, to address challenges in storage, computation, and real-time analytics. The integration of ethical considerations, including data privacy and compliance with global standards, ensures a holistic perspective on data management. Practical applications across healthcare, finance, marketing, and policy-making illustrate the real-world impact of these technologies. Through comprehensive case studies and Python-based implementations, this work equips researchers, practitioners, and data enthusiasts with the tools to navigate the complexities of modern data analytics. It bridges the gap between theory and practice, fostering the development of innovative solutions for managing and leveraging data in the era of artificial intelligence.

Stephan Eismann, Patricia Suriana, Bowen Jing et al.

Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate structural model among a large pool of candidates, a task addressed in model quality assessment. Here, we present a novel deep learning approach to assess the quality of a protein model. Our network builds on a point-based representation of the atomic structure and rotation-equivariant convolutions at different levels of structural resolution. These combined aspects allow the network to learn end-to-end from entire protein structures. Our method achieves state-of-the-art results in scoring protein models submitted to recent rounds of CASP, a blind prediction community experiment. Particularly striking is that our method does not use physics-inspired energy terms and does not rely on the availability of additional information (beyond the atomic structure of the individual protein model), such as sequence alignments of multiple proteins.

Bowen Jing, Vinay Prabhu, Angela Gu et al.

A desireable property of accelerometric gait-based identification systems is robustness to new device orientations presented by users during testing but unseen during the training phase. However, traditional Convolutional neural networks (CNNs) used in these systems compensate poorly for such transformations. In this paper, we target this problem by introducing Quaternion CNN, a network architecture which is intrinsically layer-wise equivariant and globally invariant under 3D rotations of an array of input vectors. We show empirically that this network indeed significantly outperforms a traditional CNN in a multi-user rotation-invariant gait classification setting .Lastly, we demonstrate how the kernels learned by this QCNN can also be visualized as basis-independent but origin- and chirality-dependent trajectory fragments in the euclidean space, thus yielding a novel mode of feature visualization and extraction.

Stephan Eismann, Raphael J. L. Townshend, Nathaniel Thomas et al.

Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural features to distinguish accurate structural models from less accurate ones. This raises the question of whether it is possible to learn characteristics of accurate models directly from atomic coordinates of protein complexes, with no prior assumptions. Here we introduce a machine learning method that learns directly from the 3D positions of all atoms to identify accurate models of protein complexes, without using any pre-computed physics-inspired or statistical terms. Our neural network architecture combines multiple ingredients that together enable end-to-end learning from molecular structures containing tens of thousands of atoms: a point-based representation of atoms, equivariance with respect to rotation and translation, local convolutions, and hierarchical subsampling operations. When used in combination with previously developed scoring functions, our network substantially improves the identification of accurate structural models among a large set of possible models. Our network can also be used to predict the accuracy of a given structural model in absolute terms. The architecture we present is readily applicable to other tasks involving learning on 3D structures of large atomic systems.

Bowen Jing, Ethan A. Chi, Jillian Tang

Generative models of graphs are well-known, but many existing models are limited in scalability and expressivity. We present a novel sequential graphical variational autoencoder operating directly on graphical representations of data. In our model, the encoding and decoding of a graph as is framed as a sequential deconstruction and construction process, respectively, enabling the the learning of a latent space. Experiments on a cycle dataset show promise, but highlight the need for a relaxation of the distribution over node permutations.

Bowen Jing, William Yin

Multi-agent reinforcement learning has shown promise on a variety of cooperative tasks as a consequence of recent developments in differentiable inter-agent communication. However, most architectures are limited to pools of homogeneous agents, limiting their applicability. Here we propose a modular framework for learning complex tasks in which a traditional monolithic agent is framed as a collection of cooperating heterogeneous agents. We apply this approach to model sensorimotor coordination in the neocortex as a multi-agent reinforcement learning problem. Our results demonstrate proof-of-concept of the proposed architecture and open new avenues for learning complex tasks and for understanding functional localization in the brain and future intelligent systems.