In the big data era, spatial-network data has become increasingly important and popular in many real-world objects, ranging from micro-scale (e.g., molecule structures), to middle-scale (e.g., biological neural networks), to macro-scale (e.g., mobility networks). Spatial networks consist of nodes and edges that are embedded in a geometric space. Although, it is critical to model and understand the generative process of spatial networks, this task remains largely under-explored due to the significant difficulty in automatically modeling and distinguishing the dependency and relevance among various spatial and network semantic factors. In addition, containing both spatial and network information makes the modeling of spatial networks bear large time and memory cost, especially for large graphs. To address the aforementioned challenges, we first propose a novel objective for joint spatial-network disentangled representation learning from the perspective of information bottleneck as well as a novel progressive optimization algorithm to optimize the intractable objective. Based on this, a Spatial-Network Disentangled Variational Autoencoder (SND-VAE) is proposed to discover the independent and dependent latent factors of spatial and networks. To reduce the time complexity, an efficient version SND-VAE-light is proposed, which is based on a novel Efficient Spatial-Network Message Passing Neural Network (ES-MPNN). Qualitative and quantitative experiments on both synthetic and real-world datasets with various scales of graph size demonstrate the superiority of the proposed model over the state-of-the-arts by up to 66.9% for graph generation and 37.3% for interpretability. In addition, the ES-MPNN is also proved to reduce the time complexity of the encoder in the generative model from cubic to linear growth (The implementation of this work can be found at https://github.com/xguo7/SND-VAE ).

Addressing real-world optimization problems becomes particularly challenging when analytic objective functions or constraints are unavailable. While numerous studies have addressed the issue of unknown objectives, limited research has focused on scenarios where feasibility constraints are not given explicitly. Overlooking these constraints can lead to spurious solutions that are unrealistic in practice. To deal with such unknown constraints, we propose to perform optimization within the data manifold using diffusion models. To constrain the optimization process to the data manifold, we reformulate the original optimization problem as a sampling problem from the product of the Boltzmann distribution defined by the objective function and the data distribution learned by the diffusion model. Depending on the differentiability of the objective function, we propose two different sampling methods. For differentiable objectives, we propose a two-stage framework that begins with a guided diffusion process for warm-up, followed by a Langevin dynamics stage for further correction. For non-differentiable objectives, we propose an iterative importance sampling strategy using the diffusion model as the proposal distribution. Comprehensive experiments on a synthetic dataset, six real-world black-box optimization datasets, and a multi-objective molecule optimization dataset show that our method achieves better or comparable performance with previous state-of-the-art baselines.

Molecular discovery, when formulated as an optimization problem, presents significant computational challenges because optimization objectives can be non-differentiable. Evolutionary Algorithms (EAs), often used to optimize black-box objectives in molecular discovery, traverse chemical space by performing random mutations and crossovers, leading to a large number of expensive objective evaluations. In this work, we ameliorate this shortcoming by incorporating chemistry-aware Large Language Models (LLMs) into EAs. Namely, we redesign crossover and mutation operations in EAs using LLMs trained on large corpora of chemical information. We perform extensive empirical studies on both commercial and open-source models on multiple tasks involving property optimization, molecular rediscovery, and structure-based drug design, demonstrating that the joint usage of LLMs with EAs yields superior performance over all baseline models across single- and multi-objective settings. We demonstrate that our algorithm improves both the quality of the final solution and convergence speed, thereby reducing the number of required objective evaluations.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT’s capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

Retrosynthesis, the process of breaking down a target molecule into simpler precursors through a series of valid reactions, stands at the core of organic chemistry and drug development. Although recent machine learning (ML) research has advanced single-step retrosynthetic modeling and subsequent route searches, these solutions remain restricted by the extensive combinatorial space of possible pathways. Concurrently, large language models (LLMs) have exhibited remarkable chemical knowledge, hinting at their potential to tackle complex decision-making tasks in chemistry. In this work, we explore whether LLMs can successfully navigate the highly constrained, multi-step retrosynthesis planning problem. We introduce an efficient scheme for encoding reaction pathways and present a new route-level search strategy, moving beyond the conventional step-by-step reactant prediction. Through comprehensive evaluations, we show that our LLM-augmented approach excels at retrosynthesis planning and extends naturally to the broader challenge of synthesizable molecular design.

Solving stochastic optimal control problems with quadratic control costs can be viewed as approximating a target path space measure, e.g. via gradient-based optimization. In practice, however, this optimization is challenging in particular if the target measure differs substantially from the prior. In this work, we therefore approach the problem by iteratively solving constrained problems incorporating trust regions that aim for approaching the target measure gradually in a systematic way. It turns out that this trust region based strategy can be understood as a geometric annealing from the prior to the target measure, where, however, the incorporated trust regions lead to a principled and educated way of choosing the time steps in the annealing path. We demonstrate in multiple optimal control applications that our novel method can improve performance significantly, including tasks in diffusion-based sampling and fine-tuning of diffusion models.

We present Free energy Estimators with Adaptive Transport (FEAT), a novel framework for free energy estimation---a critical challenge across scientific domains. FEAT leverages learned transports implemented via stochastic interpolants and provides consistent, minimum-variance estimators based on escorted Jarzynski equality and controlled Crooks theorem, alongside variational upper and lower bounds on free energy differences. Unifying equilibrium and non-equilibrium methods under a single theoretical framework, FEAT establishes a principled foundation for neural free energy calculations. Experimental validation on toy examples, molecular simulations, and quantum field theory demonstrates promising improvements over existing learning-based methods. Our PyTorch implementation is available at https://github.com/jiajunhe98/FEAT.

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D molecular graph or a single 3D structure, existing works often overlook the flexible nature of molecules, which continuously interconvert across conformations via chemical bond rotations and minor vibrational perturbations. To better account for molecular flexibility, some recent works formulate MRL as an ensemble learning problem, focusing on explicitly learning from a set of conformer structures. However, most of these studies have limited datasets, tasks, and models. In this work, we introduce the first MoleculAR Conformer Ensemble Learning (MARCEL) benchmark to thoroughly evaluate the potential of learning on con- former ensembles and suggest promising research directions. MARCEL includes four datasets covering diverse molecule- and reaction-level properties of chemically diverse molecules including organocatalysts and transition-metal catalysts, extending beyond the scope of common GNN benchmarks that are confined to drug-like molecules. In addition, we conduct a comprehensive empirical study, which benchmarks representative 1D, 2D, and 3D MRL models, along with two strategies that explicitly incorporate conformer ensembles into 3D models. Our findings reveal that direct learning from an accessible conformer space can improve performance on a variety of tasks and models.

Rare event sampling in dynamical systems is a fundamental problem arising in the natural sciences, which poses significant computational challenges due to an exponentially large space of trajectories. For settings where the dynamical system of interest follows a Brownian motion with known drift, the question of conditioning the process to reach a given endpoint or desired rare event is definitively answered by Doob's $h$-transform. However, the naive estimation of this transform is infeasible, as it requires simulating sufficiently many forward trajectories to estimate rare event probabilities. In this work, we propose a variational formulation of Doob's $h$-transform as an optimization problem over trajectories between a given initial point and the desired ending point. To solve this optimization, we propose a simulation-free training objective with a model parameterization that imposes the desired boundary conditions by design. Our approach significantly reduces the search space over trajectories and avoids expensive trajectory simulation and inefficient importance sampling estimators which are required in existing methods. We demonstrate the ability of our method to find feasible transition paths on real-world molecular simulation and protein folding tasks.

Aligning large language models (LLMs) with human objectives is crucial for real-world applications. However, fine-tuning LLMs for alignment often suffers from unstable training and requires substantial computing resources. Test-time alignment techniques, such as prompting and guided decoding, do not modify the underlying model, and their performance remains dependent on the original model's capabilities. To address these challenges, we propose aligning LLMs through representation editing. The core of our method is to view a pre-trained autoregressive LLM as a discrete-time stochastic dynamical system. To achieve alignment for specific objectives, we introduce external control signals into the state space of this language dynamical system. We train a value function directly on the hidden states according to the Bellman equation, enabling gradient-based optimization to obtain the optimal control signals at test time. Our experiments demonstrate that our method outperforms existing test-time alignment techniques while requiring significantly fewer resources compared to fine-tuning methods. Our code is available at [https://github.com/Lingkai-Kong/RE-Control](https://github.com/Lingkai-Kong/RE-Control).

Recent progress of deep generative models in the vision and language domain has stimulated significant interest in more structured data generation such as molecules. However, beyond generating new random molecules, efficient exploration and a comprehensive understanding of the vast chemical space are of great importance to molecular science and applications in drug design and materials discovery. In this paper, we propose a new framework, ChemFlow, to traverse chemical space through navigating the latent space learned by molecule generative models through flows. We introduce a dynamical system perspective that formulates the problem as learning a vector field that transports the mass of the molecular distribution to the region with desired molecular properties or structure diversity. Under this framework, we unify previous approaches on molecule latent space traversal and optimization and propose alternative competing methods incorporating different physical priors. We validate the efficacy of ChemFlow on molecule manipulation and single- and multi-objective molecule optimization tasks under both supervised and unsupervised molecular discovery settings. Codes and demos are publicly available on GitHub at [https://github.com/garywei944/ChemFlow](https://github.com/garywei944/ChemFlow).

The top-$k$ classification accuracy is a crucial metric in machine learning and is often used to evaluate the performance of deep neural networks. These networks are typically trained using the cross-entropy loss, which optimizes for top-$1$ classification and is considered optimal in the case of infinite data. However, in real-world scenarios, data is often noisy and limited, leading to the need for more robust losses. In this paper, we propose using the Weighted Sampling Without Replacement (WSWR) method as a learning objective for top-$k$ loss. While traditional methods for evaluating WSWR-based top-$k$ loss are computationally impractical, we show a novel connection between WSWR and Reinforcement Learning (RL) and apply well-established RL algorithms to estimate gradients. We compared our method with recently proposed top-$k$ losses in various regimes of noise and data size for the prevalent use case of $k = 5$. Our experimental results reveal that our method consistently outperforms all other methods on the top-$k$ metric for noisy datasets, has more robustness on extreme testing scenarios, and achieves competitive results on training with limited data.

Denoising diffusion (score-based) generative models have become a popular choice for modeling complex data. Recently, a deep connection between forward-backward stochastic differential equations (SDEs) and diffusion-based models has been established, leading to the development of new SDE variants such as sub-VP and critically-damped Langevin. Despite the empirical success of some hand-crafted forward SDEs, many potentially promising forward SDEs remain unexplored. In this work, we propose a general framework for parameterizing diffusion models, particularly the spatial part of forward SDEs, by leveraging the symplectic and Riemannian geometry of the data manifold. We introduce a systematic formalism with theoretical guarantees and connect it with previous diffusion models. Finally, we demonstrate the theoretical advantages of our method from a variational optimization perspective. We present numerical experiments on synthetic datasets, MNIST and CIFAR10 to validate the effectiveness of our framework.

Deep learning has achieved remarkable success in learning representations for molecules, which is crucial for various biochemical applications, ranging from property prediction to drug design. However, training Deep Neural Networks (DNNs) from scratch often requires abundant labeled molecules, which are expensive to acquire in the real world. To alleviate this issue, tremendous efforts have been devoted to Chemical Pre-trained Models (CPMs), where DNNs are pre-trained using large-scale unlabeled molecular databases and then fine-tuned over specific downstream tasks. Despite the prosperity, there lacks a systematic review of this fast-growing field. In this paper, we present the first survey that summarizes the current progress of CPMs. We first highlight the limitations of training molecular representation models from scratch to motivate CPM studies. Next, we systematically review recent advances on this topic from several key perspectives, including molecular descriptors, encoder architectures, pre-training strategies, and applications. We also highlight the challenges and promising avenues for future research, providing a useful resource for both machine learning and scientific communities.

Molecular Representation Learning (MRL) has emerged as a powerful tool for drug and materials discovery in a variety of tasks such as virtual screening and inverse design. While there has been a surge of interest in advancing model-centric techniques, the influence of both data quantity and quality on molecular representations is not yet clearly understood within this field. In this paper, we delve into the neural scaling behaviors of MRL from a data-centric viewpoint, examining four key dimensions: (1) data modalities, (2) dataset splitting, (3) the role of pre-training, and (4) model capacity.Our empirical studies confirm a consistent power-law relationship between data volume and MRL performance across these dimensions. Additionally, through detailed analysis, we identify potential avenues for improving learning efficiency.To challenge these scaling laws, we adapt seven popular data pruning strategies to molecular data and benchmark their performance. Our findings underline the importance of data-centric MRL and highlight possible directions for future research.

Self-supervised training methods for transformers have demonstrated remarkable performance across various domains. Previous transformer-based models, such as masked autoencoders (MAE), typically utilize a single normalization layer for both the [CLS] symbol and the tokens. We propose in this paper a simple modification that employs separate normalization layers for the tokens and the [CLS] symbol to better capture their distinct characteristics and enhance downstream task performance. Our method aims to alleviate the potential negative effects of using the same normalization statistics for both token types, which may not be optimally aligned with their individual roles. We empirically show that by utilizing a separate normalization layer, the [CLS] embeddings can better encode the global contextual information and are distributed more uniformly in its anisotropic space. When replacing the conventional normalization layer with the two separate layers, we observe an average 2.7% performance improvement over the image, natural language, and graph domains.

Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks (GNNs), a comprehensive evaluation of the expressiveness of these network architectures through a local-to-global analysis lacks today. In this paper, we propose a local hierarchy of 3D isomorphism to evaluate the expressive power of equivariant GNNs and investigate the process of representing global geometric information from local patches. Our work leads to two crucial modules for designing expressive and efficient geometric GNNs; namely local substructure encoding (\textbf{LSE}) and frame transition encoding (\textbf{FTE}). To demonstrate the applicability of our theory, we propose LEFTNet which effectively implements these modules and achieves state-of-the-art performance on both scalar-valued and vector-valued molecular property prediction tasks. We further point out future design space for 3D equivariant graph neural networks. Our codes are available at \url{https://github.com/yuanqidu/LeftNet}.

We introduce M$^2$Hub, a toolkit for advancing machine learning in materials discovery. Machine learning has achieved remarkable progress in modeling molecular structures, especially biomolecules for drug discovery. However, the development of machine learning approaches for modeling materials structures lag behind, which is partly due to the lack of an integrated platform that enables access to diverse tasks for materials discovery. To bridge this gap, M$^2$Hub will enable easy access to materials discovery tasks, datasets, machine learning methods, evaluations, and benchmark results that cover the entire workflow. Specifically, the first release of M$^2$Hub focuses on three key stages in materials discovery: virtual screening, inverse design, and molecular simulation, including 9 datasets that covers 6 types of materials with 56 tasks across 8 types of material properties. We further provide 2 synthetic datasets for the purpose of generative tasks on materials. In addition to random data splits, we also provide 3 additional data partitions to reflect the real-world materials discovery scenarios. State-of-the-art machine learning methods (including those are suitable for materials structures but never compared in the literature) are benchmarked on representative tasks. Our codes and library are publicly available at \url{https://github.com/yuanqidu/M2Hub}.

We introduce GAUCHE, an open-source library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to molecular representations, however, necessitates kernels defined over structured inputs such as graphs, strings and bit vectors. By providing such kernels in a modular, robust and easy-to-use framework, we seek to enable expert chemists and materials scientists to make use of state-of-the-art black-box optimization techniques. Motivated by scenarios frequently encountered in practice, we showcase applications for GAUCHE in molecular discovery, chemical reaction optimisation and protein design. The codebase is made available at https://github.com/leojklarner/gauche.

We consider the problem of sampling transition paths between two given metastable states of a molecular system, eg. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy barriers separating the states, these transition paths are unlikely to be sampled with standard Molecular Dynamics (MD) simulation. Traditional methods to augment MD with a bias potential to increase the probability of the transition rely on a dimensionality reduction step based on Collective Variables (CVs). Unfortunately, selecting appropriate CVs requires chemical intuition and traditional methods are therefore not always applicable to larger systems. Additionally, when incorrect CVs are used, the bias potential might not be minimal and bias the system along dimensions irrelevant to the transition. Showing a formal relation between the problem of sampling molecular transition paths, the Schrodinger bridge problem and stochastic optimal control with neural network policies, we propose a machine learning method for sampling said transitions. Unlike previous non-machine learning approaches our method, named PIPS, does not depend on CVs. We show that our method successful generates low energy transitions for Alanine Dipeptide as well as the larger Polyproline and Chignolin proteins.

Restoring and inpainting the visual memories that are present, but often impaired, in old photos remains an intriguing but unsolved research topic. Decades-old photos often suffer from severe and commingled degradation such as cracks, defocus, and color-fading, which are difficult to treat individually and harder to repair when they interact. Deep learning presents a plausible avenue, but the lack of large-scale datasets of old photos makes addressing this restoration task very challenging. Here we present a novel reference-based end-to-end learning framework that is able to both repair and colorize old, degraded pictures. Our proposed framework consists of three modules: a restoration sub-network that conducts restoration from degradations, a similarity network that performs color histogram matching and color transfer, and a colorization subnet that learns to predict the chroma elements of images conditioned on chromatic reference signals. The overall system makes uses of color histogram priors from reference images, which greatly reduces the need for large-scale training data. We have also created a first-of-a-kind public dataset of real old photos that are paired with ground truth "pristine" photos that have been manually restored by PhotoShop experts. We conducted extensive experiments on this dataset and synthetic datasets, and found that our method significantly outperforms previous state-of-the-art models using both qualitative comparisons and quantitative measurements. The code is available at https://github.com/DerrickXuNu/Pik-Fix.

Spatiotemporal graph represents a crucial data structure where the nodes and edges are embedded in a geometric space and their attribute values can evolve dynamically over time. Nowadays, spatiotemporal graph data is becoming increasingly popular and important, ranging from microscale (e.g. protein folding), to middle-scale (e.g. dynamic functional connectivity), to macro-scale (e.g. human mobility network). Although disentangling and understanding the correlations among spatial, temporal, and graph aspects have been a long-standing key topic in network science, they typically rely on network processes hypothesized by human knowledge. They usually fit well towards the properties that the predefined principles are tailored for, but usually cannot do well for the others, especially for many key domains where the human has yet very limited knowledge such as protein folding and biological neuronal networks. In this paper, we aim at pushing forward the modeling and understanding of spatiotemporal graphs via new disentangled deep generative models. Specifically, a new Bayesian model is proposed that factorizes spatiotemporal graphs into spatial, temporal, and graph factors as well as the factors that explain the interplay among them. A variational objective function and new mutual information thresholding algorithms driven by information bottleneck theory have been proposed to maximize the disentanglement among the factors with theoretical guarantees. Qualitative and quantitative experiments on both synthetic and real-world datasets demonstrate the superiority of the proposed model over the state-of-the-arts by up to 69.2% for graph generation and 41.5% for interpretability.

Designing molecules with desired biological properties remains an outstanding challenge both in the wet and dry laboratories. Meeting this challenge promises great translational impacts across drug discovery, material sciences, biotechnology, and more. Recent momentum in deep learning promises to advance our computational capabilities on molecule generation. In particular, deep graph generative models which treat molecule design as a graph generation problem are allowing us to directly learn from existing databases of small molecules and generate novel, valid molecules. Currently, these models have many shortcomings, including poor controllability of desired molecular properties, especially in practical application where the training data is usually small, noisy, and incomplete. This paper focuses on equipping graph variational autoencoders with the ability to control for desired properties and its practical application in a practical application which is the generation of Quaternary Ammonium Compounds (QAC). Several controllable graph generation mechanisms are investigated for their effectiveness. A general framework is then proposed to extend these mechanisms by our newly proposed objective function to handle the challenges in practical applications where the property value annotations are usually censored and not fully available in all training samples. The experimental evaluation considers an experimentally-characterized dataset of antimicrobial small molecules with wet-lab characterized activity against antibiotic-resistant bacteria. Extensive experiments demonstrate the superiority of the proposed models and control of desired properties.

Group equivariance (e.g. SE(3) equivariance) is a critical physical symmetry in science, from classical and quantum physics to computational biology. It enables robust and accurate prediction under arbitrary reference transformations. In light of this, great efforts have been put on encoding this symmetry into deep neural networks, which has been shown to improve the generalization performance and data efficiency for downstream tasks. Constructing an equivariant neural network generally brings high computational costs to ensure expressiveness. Therefore, how to better trade-off the expressiveness and computational efficiency plays a core role in the design of the equivariant deep learning models. In this paper, we propose a framework to construct SE(3) equivariant graph neural networks that can approximate the geometric quantities efficiently. Inspired by differential geometry and physics, we introduce equivariant local complete frames to graph neural networks, such that tensor information at given orders can be projected onto the frames. The local frame is constructed to form an orthonormal basis that avoids direction degeneration and ensure completeness. Since the frames are built only by cross product operations, our method is computationally efficient. We evaluate our method on two tasks: Newton mechanics modeling and equilibrium molecule conformation generation. Extensive experimental results demonstrate that our model achieves the best or competitive performance in two types of datasets.

Geometric deep learning has broad applications in biology, a domain where relational structure in data is often intrinsic to modelling the underlying phenomena. Currently, efforts in both geometric deep learning and, more broadly, deep learning applied to biomolecular tasks have been hampered by a scarcity of appropriate datasets accessible to domain specialists and machine learning researchers alike. To address this, we introduce Graphein as a turn-key tool for transforming raw data from widely-used bioinformatics databases into machine learning-ready datasets in a high-throughput and flexible manner. Graphein is a Python library for constructing graph and surface-mesh representations of biomolecular structures, such as proteins, nucleic acids and small molecules, and biological interaction networks for computational analysis and machine learning. Graphein provides utilities for data retrieval from widely-used bioinformatics databases for structural data, including the Protein Data Bank, the AlphaFold Structure Database, chemical data from ZINC and ChEMBL, and for biomolecular interaction networks from STRINGdb, BioGrid, TRRUST and RegNetwork. The library interfaces with popular geometric deep learning libraries: DGL, Jraph, PyTorch Geometric and PyTorch3D though remains framework agnostic as it is built on top of the PyData ecosystem to enable inter-operability with scientific computing tools and libraries. Graphein is designed to be highly flexible, allowing the user to specify each step of the data preparation, scalable to facilitate working with large protein complexes and interaction graphs, and contains useful pre-processing tools for preparing experimental files. Graphein facilitates network-based, graph-theoretic and topological analyses of structural and interaction datasets in a high-throughput manner. We envision that Graphein will facilitate developments in computational biology, graph representation learning and drug discovery. Availability and implementation: Graphein is written in Python. Source code, example usage and tutorials, datasets, and documentation are made freely available under the MIT License at the following URL: https://anonymous.4open.science/r/graphein-3472/README.md

Co-speech gesture is crucial for human-machine interaction and digital entertainment. While previous works mostly map speech audio to human skeletons (e.g., 2D keypoints), directly generating speakers' gestures in the image domain remains unsolved. In this work, we formally define and study this challenging problem of audio-driven co-speech gesture video generation, i.e., using a unified framework to generate speaker image sequence driven by speech audio. Our key insight is that the co-speech gestures can be decomposed into common motion patterns and subtle rhythmic dynamics. To this end, we propose a novel framework, Audio-driveN Gesture vIdeo gEneration (ANGIE), to effectively capture the reusable co-speech gesture patterns as well as fine-grained rhythmic movements. To achieve high-fidelity image sequence generation, we leverage an unsupervised motion representation instead of a structural human body prior (e.g., 2D skeletons). Specifically, 1) we propose a vector quantized motion extractor (VQ-Motion Extractor) to summarize common co-speech gesture patterns from implicit motion representation to codebooks. 2) Moreover, a co-speech gesture GPT with motion refinement (Co-Speech GPT) is devised to complement the subtle prosodic motion details. Extensive experiments demonstrate that our framework renders realistic and vivid co-speech gesture video. Demo video and more resources can be found in: https://alvinliu0.github.io/projects/ANGIE

Developing deep generative models has been an emerging field due to the ability to model and generate complex data for various purposes, such as image synthesis and molecular design. However, the advance of deep generative models is limited by the challenges to generate objects that possess multiple desired properties because: 1) the existence of complex correlation among real-world properties is common but hard to identify; 2) controlling individual property enforces an implicit partially control of its correlated properties, which is difficult to model; 3) controlling multiple properties under variour manners simultaneously is hard and underexplored. We address these challenges by proposing a novel deep generative framework that recovers semantics and correlation of properties through disentangled latent vectors. The correlation is handled via an explainable mask pooling layer, and properties are precisely retained by the generated objects via the mutual dependence between latent vectors and properties. Our generative model preserves properties of interest while handles correlation and conflicts of properties under a multi-objective optimization framework. The experiments demonstrate our model's superior performance in generating objects with desired properties.

Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design as graph generation problems which provide new opportunities toward the breakthrough of this long-lasting problem. Existing models, however, have many shortcomings, including poor interpretability and controllability toward desired molecular properties. This paper focuses on new methodologies for molecule generation with interpretable and controllable deep generative models, by proposing new monotonically-regularized graph variational autoencoders. The proposed models learn to represent the molecules with latent variables and then learn the correspondence between them and molecule properties parameterized by polynomial functions. To further improve the intepretability and controllability of molecule generation towards desired properties, we derive new objectives which further enforce monotonicity of the relation between some latent variables and target molecule properties such as toxicity and clogP. Extensive experimental evaluation demonstrates the superiority of the proposed framework on accuracy, novelty, disentanglement, and control towards desired molecular properties. The code is anonymized at https://anonymous.4open.science/r/MDVAE-FD2C.

MOTIVATION: Expanding our knowledge of small molecules beyond what is known in nature or designed in wet laboratories promises to significantly advance cheminformatics, drug discovery, biotechnology and material science. In silico molecular design remains challenging, primarily due to the complexity of the chemical space and the non-trivial relationship between chemical structures and biological properties. Deep generative models that learn directly from data are intriguing, but they have yet to demonstrate interpretability in the learned representation, so we can learn more about the relationship between the chemical and biological space. In this article, we advance research on disentangled representation learning for small molecule generation. We build on recent work by us and others on deep graph generative frameworks, which capture atomic interactions via a graph-based representation of a small molecule. The methodological novelty is how we leverage the concept of disentanglement in the graph variational autoencoder framework both to generate biologically relevant small molecules and to enhance model interpretability. RESULTS: Extensive qualitative and quantitative experimental evaluation in comparison with state-of-the-art models demonstrate the superiority of our disentanglement framework. We believe this work is an important step to address key challenges in small molecule generation with deep generative frameworks. AVAILABILITY AND IMPLEMENTATION: Training and generated data are made available at https://ieee-dataport.org/documents/dataset-disentangled-representation-learning-interpretable-molecule-generation. All code is made available at https://anonymous.4open.science/r/D-MolVAE-2799/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Representation learning via deep generative models is opening a new avenue for small molecule generation in silico. Linking chemical and biological space remains a key challenge. In this paper, we debut a graph-based variational autoencoder framework to address this challenge under the umbrella of disentangled representation learning. The framework permits several inductive biases that connect the learned latent factors to molecular properties. Evaluation on diverse benchmark datasets shows that the resulting models are powerful and open up an exciting line of research on controllable molecule generation in support of cheminformatics, drug discovery, and other application settings.

Spatial networks represent crucial data structures where the nodes and edges are embedded in a geometric space. Nowadays, spatial network data is becoming increasingly popular and important, ranging from microscale (e.g., protein structures), to middle-scale (e.g., biological neural networks), to macro-scale (e.g., mobility networks). Although, modeling and understanding the generative process of spatial networks are very important, they remain largely under-explored due to the significant challenges in automatically modeling and distinguishing the independency and correlation among various spatial and network factors. To address these challenges, we first propose a novel objective for joint spatial-network disentanglement from the perspective of information bottleneck as well as a novel optimization algorithm to optimize the intractable objective. Based on this, a spatial-network variational autoencoder (SND-VAE) with a new spatial-network message passing neural network (S-MPNN) is proposed to discover the independent and dependent latent factors of spatial and networks. Qualitative and quantitative experiments on both synthetic and real-world datasets demonstrate the superiority of the proposed model over the state-of-the-arts by up to 66.9% for graph generation and 37.3% for interpretability.

In today's digital world, rapid technological advancements continue to lessen the burden of tasks for individuals. Among these tasks is communication across perceived language barriers. Indeed, increased attention has been drawn to American Sign Language (ASL) recognition in recent years. Camera-based and motion detection-based methods have been researched extensively; however, there remains a divide in communication between ASL users and non-users. Therefore, this research team proposes the use of a novel wireless sensor (Frequency-Modulated Continuous-Wave Radar) to help bridge the gap in communication. In short, this device sends out signals that detect the user's body positioning in space. These signals then reflect off the body and back to the sensor, developing thousands of cloud points per second, indicating where the body is positioned in space. These cloud points can then be examined for movement over multiple consecutive time frames using a cell division algorithm, ultimately showing how the body moves through space as it completes a single gesture or sentence. At the end of the project, 95% accuracy was achieved in one-object prediction as well as 80% accuracy on cross-object prediction with 30% other objects' data introduced on 19 commonly used gestures. There are 30 samples for each gesture per person from three persons.

Over half a million people in the United States use American Sign Language (ASL) as their primary mode of communication. Automatic ASL recognition would enable Deaf and Hard of Hearing (DHH) users to interact with others who are not familiar with ASL as well as voice-controlled digital assistants (e.g., Alexa, Siri, etc.). While ASL recognition has been extensively studied, there is a little attention given to recognition of ASL non-manual body markers. The non-manual markers are typically expressed through head, torso and shoulder movements, and add essential meaning and context to the signed sentences. In this work, we present ExASL, a sentence-level ASL recognition system using millimeter-wave radars. ExASL can recognize manual markers (hand gestures) and non-manual markers (head and torso movements). It utilizes multi-distance clustering to recognize body parts and cluster mmWave point clouds. We then present a multi-view deep learning algorithm that can learn from clustered body part representation for an expressive sentence-level recognition. Our evaluation shows that ExASL can recognize ASL sentences with a word error rate of 0.79%, sentence error rate of 1.25%, and non-manual markers with an accuracy of 83.5%.