Related papers: Hierarchy-Guided Topology Latent Flow for Molecula…

Exploring molecular energy landscapes and identifying ground-state conformations are central challenges in computational chemistry. However, generating diverse low-energy conformers from molecular graphs remains expensive with traditional…

Molecular graphs generally contain subgraphs (known as groups) that are identifiable and significant in composition, functionality, geometry, etc. Flat latent representations (node embeddings or graph embeddings) fail to represent, and…

A key challenge in automated chemical compound space explorations is ensuring veracity in minimum energy geometries---to preserve intended bonding connectivities. We discuss an iterative high-throughput workflow for connectivity preserving…

Molecular structure elucidation is a fundamental step in understanding chemical phenomena, with applications in identifying molecules in natural products, lab syntheses, forensic samples, and the interstellar medium. We consider the task of…

Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…

Graph-structured data jointly contain discrete topology and continuous geometry, which poses fundamental challenges for generative modeling due to heterogeneous distributions, incompatible noise dynamics, and the need for equivariant…

A generative model capable of sampling realistic molecules with desired properties could accelerate chemical discovery across a wide range of applications. Toward this goal, significant effort has focused on developing models that jointly…

Large language models perform well in short text generation but still struggle with long text generation, particularly under complex constraints. Such tasks involve multiple tightly coupled objectives, including global structural…

Transformer language models generate text autoregressively, making inference latency proportional to the number of tokens generated. Speculative decoding reduces this latency without sacrificing output quality, by leveraging a small draft…

Many generative applications, such as synthesis-based 3D molecular design, involve constructing compositional objects with continuous features. Here, we introduce Compositional Generative Flows (CGFlow), a novel framework that extends flow…

We propose a robust and efficient framework to generate global trajectories for ground robots in complex 3D environments. The proposed method takes point cloud as input and efficiently constructs a multi-level map using triangular patches…

Accurate characterization of the equilibrium distributions of complex molecular systems and their dependence on environmental factors such as temperature is essential for understanding thermodynamic properties and transition mechanisms.…

We introduce nested diffusion models, an efficient and powerful hierarchical generative framework that substantially enhances the generation quality of diffusion models, particularly for images of complex scenes. Our approach employs a…

3D Scene Graph (3DSG) generation plays a pivotal role in spatial understanding and affordance perception. To mitigate generalization issues from data scarcity, joint-embedding and generative proxy tasks are proposed to pre-train 3DSG…

Privacy and regulatory constraints make data generation vital to advancing machine learning without relying on real-world datasets. A leading approach for tabular data generation is the Forest Flow (FF) method, which combines Flow Matching…

Developing bioactive molecules remains a central, time- and cost-heavy challenge in drug discovery, particularly for novel targets lacking structural or functional data. Pharmacophore modeling presents an alternative for capturing the key…

The efficacy of segmentation algorithms is frequently compromised by topological errors like overlapping regions, disrupted connections, and voids. To tackle this problem, we introduce a novel loss function, namely Topology-Aware Focal Loss…

In Table-to-Text (T2T) generation, existing approaches predominantly focus on providing objective descriptions of tabular data. However, generating text that incorporates subjectivity, where subjectivity refers to interpretations beyond raw…

Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled…

Topological techniques are powerful tools for characterizing the complexity of many dynamical systems, including the commonly studied area-preserving maps of the plane. However, the extension of many topological techniques to higher…