Generative Modeling
Visualization comparing Optimal Transport (straight paths) vs Diffusion (curved paths) for Flow Matching

Flow Matching for Generative Modeling: Scalable CNFs

Introduces Flow Matching, a scalable method for training CNFs by regressing vector fields of conditional probability paths. It generalizes diffusion and enables Optimal Transport paths for straighter, more efficient sampling.

Machine Learning
Comparison of Residual Network vs ODE Network architectures showing discrete layers versus continuous transformations

Neural ODEs: Continuous-Depth Deep Learning Models

This paper replaces discrete network layers with continuous ordinary differential equations (ODEs), allowing for adaptive computation depth and constant memory cost during training via the adjoint sensitivity method. It introduces Continuous Normalizing Flows and latent ODEs for time-series.

Generative Modeling
Visualization showing linear interpolation, learned ODE trajectories, and the reflow straightening process for rectified flow

Rectified Flow: Learning to Generate and Transfer Data

Introduces ‘Rectified Flow,’ a method to transport distributions via ODEs with straight paths. Uses a ‘reflow’ procedure to iteratively straighten trajectories, enabling high-quality 1-step generation with optional lightweight distillation.

Generative Modeling
Denoising Score Matching Intuition - Vectors point from corrupted samples back to clean data, approximating the score

Score Matching and Denoising Autoencoders: A Connection

This paper provides a rigorous probabilistic foundation for Denoising Autoencoders by proving they are mathematically equivalent to Score Matching on a kernel-smoothed data distribution. It derives a specific energy function for DAEs and justifies the use of tied weights.

Generative Modeling
Forward and Reverse SDE trajectories showing the diffusion process from data to noise and back

Score-Based Generative Modeling with SDEs (Song 2021)

This paper unifies previous score-based methods (SMLD and DDPM) under a continuous-time SDE framework. It introduces Predictor-Corrector samplers for improved generation and Probability Flow ODEs for near-exact likelihood computation, setting new records on CIFAR-10.

Computational Biology
DynamicFlow illustration showing the transformation from apo pocket to holo pocket with ligand molecule generation

DynamicFlow: Integrating Protein Dynamics into Drug Design

This paper introduces DynamicFlow, a full-atom stochastic flow matching model that simultaneously generates ligand molecules and transforms protein pockets from apo to holo states. It also contributes a new dataset of MD-simulated apo-holo pairs derived from MISATO.

Optical Chemical Structure Recognition

Online Handwritten Chemical Formula Structure Analysis

A three-level grammatical framework (formula, molecule, text) for parsing online handwritten chemical formulas, generating semantic graphs that capture both connectivity and layout using context-free grammars and HMMs.

Optical Chemical Structure Recognition

SVM-HMM Online Classifier for Chemical Symbols

This paper proposes a double-stage architecture using SVM for rough classification and HMM for fine recognition. It features a novel Point Sequence Reordering (PSR) algorithm that significantly improves accuracy on organic ring structures.

Optical Chemical Structure Recognition
Unified framework converts handwritten chemical expressions to structured graph representations

Unified Framework for Handwritten Chemical Expressions

Proposes a unified statistical framework for recognizing both inorganic and organic handwritten chemical expressions. Introduces the Chemical Expression Structure Graph (CESG) and uses a weighted direction graph search for structural analysis, achieving 83.1% top-5 accuracy on a large proprietary dataset.

Optical Chemical Structure Recognition
Diagram of the chemoCR pipeline converting a bitmap chemical structure into a connection table

Chemical Structure Reconstruction with chemoCR (2011)

Describes chemoCR, a system that converts bitmap chemical diagrams into connection tables using a pipeline of texture-based vectorization, OCR, and a rule-based expert system, achieving 65.6% perfect recall on the TREC 2011 task.

Optical Chemical Structure Recognition
Diagram of the ChemInk sketch recognition system converting freehand chemical drawings into structured molecular data

ChemInk: Real-Time Recognition for Chemical Drawings

ChemInk introduces a sketch recognition system for chemical diagrams that combines multi-level visual features via a joint Conditional Random Field (CRF), achieving 97.4% accuracy and outperforming CAD tools in user speed.

Optical Chemical Structure Recognition
Diagram of the CLiDE Pro system for segmenting document images and reconstructing chemical connection tables

CLiDE Pro: Optical Chemical Structure Recognition Tool

This paper introduces CLiDE Pro, an advanced OCSR system that segments document images and reconstructs chemical connection tables. It features novel handling for crossing bonds and generic structures, validating performance on a publicly released benchmark of 454 scanned images.