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Although existing deep learning compressed-sensing-based Magnetic Resonance Imaging (CS-MRI) methods have achieved considerably impressive performance, explainability and generalizability continue to be challenging for such methods since…

Denoising-based generative models, particularly diffusion and flow matching algorithms, have achieved remarkable success. However, aligning their output distributions with complex downstream objectives, such as human preferences,…

Retrosynthesis is a major task for drug discovery. It is formulated as a graph-generating problem by many existing approaches. Specifically, these methods firstly identify the reaction center, and break target molecule accordingly to…

Retrieval-Augmented Generation (RAG) systems face significant performance gaps when applied to technical domains requiring precise information extraction from complex documents. Current evaluation methodologies relying on document-level…

The techniques of data-driven backmapping from coarse-grained (CG) to fine-grained (FG) representation often struggle with accuracy, unstable training, and physical realism, especially when applied to complex systems such as proteins. In…

Transformer-based models have recently shown success in representation learning on graph-structured data beyond natural language processing and computer vision. However, the success is limited to small-scale graphs due to the drawbacks of…

Synthesis planning seeks an efficient sequence of chemical reactions that produce a target molecule. Typically, a pretrained single-step (autoregressive) retrosynthesis model is repeatedly invoked to generate such a sequence. Classifier…

Supervised learning techniques have proven their efficacy in many applications with abundant data. However, applying these methods to medical imaging is challenging due to the scarcity of data, given the high acquisition costs and intricate…

Retrosynthesis prediction is one of the fundamental challenges in organic synthesis. The task is to predict the reactants given a core product. With the advancement of machine learning, computer-aided synthesis planning has gained…

How to produce expressive molecular representations is a fundamental challenge in AI-driven drug discovery. Graph neural network (GNN) has emerged as a powerful technique for modeling molecular data. However, previous supervised approaches…

In recent years, molecular graph representation learning (GRL) has drawn much more attention in molecular property prediction (MPP) problems. The existing graph methods have demonstrated that 3D geometric information is significant for…

Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees…

Gaussian Probability Path based Generative Models (GPPGMs) generate data by reversing a stochastic process that progressively corrupts samples with Gaussian noise. Despite state-of-the-art results in 3D molecular generation, their…

The downstream accuracy of self-supervised methods is tightly linked to the proxy task solved during training and the quality of the gradients extracted from it. Richer and more meaningful gradients updates are key to allow self-supervised…

Text-conditioned molecular generation aims to translate natural-language descriptions into chemical structures, enabling scientists to specify functional groups, scaffolds, and physicochemical constraints without handcrafted rules.…

Manipulating facial expressions is a challenging task due to fine-grained shape changes produced by facial muscles and the lack of input-output pairs for supervised learning. Unlike previous methods using Generative Adversarial Networks…

Diffusion-based Handwritten Text Generation (HTG) approaches achieve impressive results on frequent, in-vocabulary words observed at training time and on regular styles. However, they are prone to memorizing training samples and often…

In generative modeling, we often wish to produce samples that maximize a user-specified reward such as aesthetic quality or alignment with human preferences, a problem known as \textit{guidance}. Despite their widespread use, existing…

We have developed an end-to-end, retrosynthesis system, named ChemiRise, that can propose complete retrosynthesis routes for organic compounds rapidly and reliably. The system was trained on a processed patent database of over 3 million…

Retrieval-augmented code generation utilizes Large Language Models as the generator and significantly expands their code generation capabilities by providing relevant code, documentation, and more via the retriever. The current approach…