MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce \ours, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol), outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.

Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks

Advanced generative model (e.g., diffusion model) derived from simplified continuity assumptions of data distribution, though showing promising progress, has been difficult to apply directly to geometry generation applications due to the multi-modality and noise-sensitive nature of molecule geometry. This work introduces Geometric Bayesian Flow Networks (GeoBFN), which naturally fits molecule geometry by modeling diverse modalities in the differentiable parameter space of distributions. GeoBFN maintains the SE-(3) invariant density modeling property by incorporating equivariant inter-dependency modeling on parameters of distributions and unifying the probabilistic modeling of different modalities. Through optimized training and sampling techniques, we demonstrate that GeoBFN achieves state-of-the-art performance on multiple 3D molecule generation benchmarks in terms of generation quality (90.87% molecule stability in QM9 and 85.6% atom stability in GEOM-DRUG. GeoBFN can also conduct sampling with any number of steps to reach an optimal trade-off between efficiency and quality (e.g., 20-times speedup without sacrificing performance).

Equivariant Flow Matching with Hybrid Probability Transport

The generation of 3D molecules requires simultaneously deciding the categorical features~(atom types) and continuous features~(atom coordinates). Deep generative models, especially Diffusion Models (DMs), have demonstrated effectiveness in generating feature-rich geometries. However, existing DMs typically suffer from unstable probability dynamics with inefficient sampling speed. In this paper, we introduce geometric flow matching, which enjoys the advantages of both equivariant modeling and stabilized probability dynamics. More specifically, we propose a hybrid probability path where the coordinates probability path is regularized by an equivariant optimal transport, and the information between different modalities is aligned. Experimentally, the proposed method could consistently achieve better performance on multiple molecule generation benchmarks with 4.75$\times$ speed up of sampling on average.

RetroDiff: Retrosynthesis as Multi-stage Distribution Interpolation

Retrosynthesis poses a fundamental challenge in biopharmaceuticals, aiming to aid chemists in finding appropriate reactant molecules and synthetic pathways given determined product molecules. With the reactant and product represented as 2D graphs, retrosynthesis constitutes a conditional graph-to-graph generative task. Inspired by the recent advancements in discrete diffusion models for graph generation, we introduce Retrosynthesis Diffusion (RetroDiff), a novel diffusion-based method designed to address this problem. However, integrating a diffusion-based graph-to-graph framework while retaining essential chemical reaction template information presents a notable challenge. Our key innovation is to develop a multi-stage diffusion process. In this method, we decompose the retrosynthesis procedure to first sample external groups from the dummy distribution given products and then generate the external bonds to connect the products and generated groups. Interestingly, such a generation process is exactly the reverse of the widely adapted semi-template retrosynthesis procedure, i.e. from reaction center identification to synthon completion, which significantly reduces the error accumulation. Experimental results on the benchmark have demonstrated the superiority of our method over all other semi-template methods.

Camouflaged Object Detection with Feature Grafting and Distractor Aware

The task of Camouflaged Object Detection (COD) aims to accurately segment camouflaged objects that integrated into the environment, which is more challenging than ordinary detection as the texture between the target and background is visually indistinguishable. In this paper, we proposed a novel Feature Grafting and Distractor Aware network (FDNet) to handle the COD task. Specifically, we use CNN and Transformer to encode multi-scale images in parallel. In order to better explore the advantages of the two encoders, we design a cross-attention-based Feature Grafting Module to graft features extracted from Transformer branch into CNN branch, after which the features are aggregated in the Feature Fusion Module. A Distractor Aware Module is designed to explicitly model the two possible distractors in the COD task to refine the coarse camouflage map. We also proposed the largest artificial camouflaged object dataset which contains 2000 images with annotations, named ACOD2K. We conducted extensive experiments on four widely used benchmark datasets and the ACOD2K dataset. The results show that our method significantly outperforms other state-of-the-art methods. The code and the ACOD2K will be available at https://github.com/syxvision/FDNet.

Towards High-Performance Exploratory Data Analysis (EDA) Via Stable Equilibrium Point

Exploratory data analysis (EDA) is a vital procedure for data science projects. In this work, we introduce a stable equilibrium point (SEP) - based framework for improving the efficiency and solution quality of EDA. By exploiting the SEPs to be the representative points, our approach aims to generate high-quality clustering and data visualization for large-scale data sets. A very unique property of the proposed method is that the SEPs will directly encode the clustering properties of data sets. Compared with prior state-of-the-art clustering and data visualization methods, the proposed methods allow substantially improving computing efficiency and solution quality for large-scale data analysis tasks.

Accelerate Support Vector Clustering via Spectrum-Preserving Data Compression

Support vector clustering is an important clustering method. However, it suffers from a scalability issue due to its computational expensive cluster assignment step. In this paper we accelertate the support vector clustering via spectrum-preserving data compression. Specifically, we first compress the original data set into a small amount of spectrally representative aggregated data points. Then, we perform standard support vector clustering on the compressed data set. Finally, we map the clustering results of the compressed data set back to discover the clusters in the original data set. Our extensive experimental results on real-world data set demonstrate dramatically speedups over standard support vector clustering without sacrificing clustering quality.

Accelerate Support Vector Clustering via Spectrum-Preserving Data Compression?

Support vector clustering is an important clustering method. However, it suffers from a scalability issue due to its computational expensive cluster assignment step. In this paper we accelertate the support vector clustering via spectrum-preserving data compression. Specifically, we first compress the original data set into a small amount of spectrally representative aggregated data points. Then, we perform standard support vector clustering on the compressed data set. Finally, we map the clustering results of the compressed data set back to discover the clusters in the original data set. Our extensive experimental results on real-world data set demonstrate dramatically speedups over standard support vector clustering without sacrificing clustering quality.

Follow Your Path: a Progressive Method for Knowledge Distillation

Deep neural networks often have a huge number of parameters, which posts challenges in deployment in application scenarios with limited memory and computation capacity. Knowledge distillation is one approach to derive compact models from bigger ones. However, it has been observed that a converged heavy teacher model is strongly constrained for learning a compact student network and could make the optimization subject to poor local optima. In this paper, we propose ProKT, a new model-agnostic method by projecting the supervision signals of a teacher model into the student's parameter space. Such projection is implemented by decomposing the training objective into local intermediate targets with an approximate mirror descent technique. The proposed method could be less sensitive with the quirks during optimization which could result in a better local optimum. Experiments on both image and text datasets show that our proposed ProKT consistently achieves superior performance compared to other existing knowledge distillation methods.

Do You Have the Right Scissors? Tailoring Pre-trained Language Models via Monte-Carlo Methods

It has been a common approach to pre-train a language model on a large corpus and fine-tune it on task-specific data. In practice, we observe that fine-tuning a pre-trained model on a small dataset may lead to over- and/or under-estimation problem. In this paper, we propose MC-Tailor, a novel method to alleviate the above issue in text generation tasks by truncating and transferring the probability mass from over-estimated regions to under-estimated ones. Experiments on a variety of text generation datasets show that MC-Tailor consistently and significantly outperforms the fine-tuning approach. Our code is available at this url.