An Information Criterion for Controlled Disentanglement of Multimodal Data

Multimodal representation learning seeks to relate and decompose information inherent in multiple modalities. By disentangling modality-specific information from information that is shared across modalities, we can improve interpretability and robustness and enable downstream tasks such as the generation of counterfactual outcomes. Separating the two types of information is challenging since they are often deeply entangled in many real-world applications. We propose Disentangled Self-Supervised Learning (DisentangledSSL), a novel self-supervised approach for learning disentangled representations. We present a comprehensive analysis of the optimality of each disentangled representation, particularly focusing on the scenario not covered in prior work where the so-called Minimum Necessary Information (MNI) point is not attainable. We demonstrate that DisentangledSSL successfully learns shared and modality-specific features on multiple synthetic and real-world datasets and consistently outperforms baselines on various downstream tasks, including prediction tasks for vision-language data, as well as molecule-phenotype retrieval tasks for biological data.

Hamiltonian Score Matching and Generative Flows

Classical Hamiltonian mechanics has been widely used in machine learning in the form of Hamiltonian Monte Carlo for applications with predetermined force fields. In this work, we explore the potential of deliberately designing force fields for Hamiltonian ODEs, introducing Hamiltonian velocity predictors (HVPs) as a tool for score matching and generative models. We present two innovations constructed with HVPs: Hamiltonian Score Matching (HSM), which estimates score functions by augmenting data via Hamiltonian trajectories, and Hamiltonian Generative Flows (HGFs), a novel generative model that encompasses diffusion models and flow matching as HGFs with zero force fields. We showcase the extended design space of force fields by introducing Oscillation HGFs, a generative model inspired by harmonic oscillators. Our experiments validate our theoretical insights about HSM as a novel score matching metric and demonstrate that HGFs rival leading generative modeling techniques.

A Cosmic-Scale Benchmark for Symmetry-Preserving Data Processing

Efficiently processing structured point cloud data while preserving multiscale information is a key challenge across domains, from graphics to atomistic modeling. Using a curated dataset of simulated galaxy positions and properties, represented as point clouds, we benchmark the ability of graph neural networks to simultaneously capture local clustering environments and long-range correlations. Given the homogeneous and isotropic nature of the Universe, the data exhibits a high degree of symmetry. We therefore focus on evaluating the performance of Euclidean symmetry-preserving ($E(3)$-equivariant) graph neural networks, showing that they can outperform non-equivariant counterparts and domain-specific information extraction techniques in downstream performance as well as simulation-efficiency. However, we find that current architectures fail to capture information from long-range correlations as effectively as domain-specific baselines, motivating future work on architectures better suited for extracting long-range information.

Generator Matching: Generative modeling with arbitrary Markov processes

We introduce generator matching, a modality-agnostic framework for generative modeling using arbitrary Markov processes. Generators characterize the infinitesimal evolution of a Markov process, which we leverage for generative modeling in a similar vein to flow matching: we construct conditional generators which generate single data points, then learn to approximate the marginal generator which generates the full data distribution. We show that generator matching unifies various generative modeling methods, including diffusion models, flow matching and discrete diffusion models. Furthermore, it provides the foundation to expand the design space to new and unexplored Markov processes such as jump processes. Finally, generator matching enables the construction of superpositions of Markov generative processes and enables the construction of multimodal models in a rigorous manner. We empirically validate our method on protein and image structure generation, showing that superposition with a jump process improves image generation.

Fictitious Synthetic Data Can Improve LLM Factuality via Prerequisite Learning

Recent studies have identified one aggravating factor of LLM hallucinations as the knowledge inconsistency between pre-training and fine-tuning, where unfamiliar fine-tuning data mislead the LLM to fabricate plausible but wrong outputs. In this paper, we propose a novel fine-tuning strategy called Prereq-Tune to address this knowledge inconsistency and reduce hallucinations. Fundamentally, Prereq-Tune disentangles the learning of skills and knowledge, so the model learns only the task skills without being impacted by the knowledge inconsistency. To achieve this, Prereq-Tune introduces an additional prerequisite learning stage to learn the necessary knowledge for SFT, allowing subsequent SFT to focus only on task skills. Prereq-Tune can also be combined with fictitious synthetic data to enhance the grounding of LLM outputs to their internal knowledge. Experiments show that Prereq-Tune outperforms existing baselines in improving LLM's factuality across short QA and long-form generation tasks. It also opens new possibilities for knowledge-controlled generation in LLMs. Our code is available at https://github.com/UCSB-NLP-Chang/Prereq_tune.git.

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

Think While You Generate: Discrete Diffusion with Planned Denoising

Discrete diffusion has achieved state-of-the-art performance, outperforming or approaching autoregressive models on standard benchmarks. In this work, we introduce Discrete Diffusion with Planned Denoising (DDPD), a novel framework that separates the generation process into two models: a planner and a denoiser. At inference time, the planner selects which positions to denoise next by identifying the most corrupted positions in need of denoising, including both initially corrupted and those requiring additional refinement. This plan-and-denoise approach enables more efficient reconstruction during generation by iteratively identifying and denoising corruptions in the optimal order. DDPD outperforms traditional denoiser-only mask diffusion methods, achieving superior results on language modeling benchmarks such as text8, OpenWebText, and token-based generation on ImageNet $256 \times 256$. Notably, in language modeling, DDPD significantly reduces the performance gap between diffusion-based and autoregressive methods in terms of generative perplexity. Code is available at https://github.com/liusulin/DDPD.

Predicting perturbation targets with causal differential networks

Rationally identifying variables responsible for changes to a biological system can enable myriad applications in disease understanding and cell engineering. From a causality perspective, we are given two datasets generated by the same causal model, one observational (control) and one interventional (perturbed). The goal is to isolate the subset of measured variables (e.g. genes) that were the targets of the intervention, i.e. those whose conditional independencies have changed. Knowing the causal graph would limit the search space, allowing us to efficiently pinpoint these variables. However, current algorithms that infer causal graphs in the presence of unknown intervention targets scale poorly to the hundreds or thousands of variables in biological data, as they must jointly search the combinatorial spaces of graphs and consistent intervention targets. In this work, we propose a causality-inspired approach for predicting perturbation targets that decouples the two search steps. First, we use an amortized causal discovery model to separately infer causal graphs from the observational and interventional datasets. Then, we learn to map these paired graphs to the sets of variables that were intervened upon, in a supervised learning framework. This approach consistently outperforms baselines for perturbation modeling on seven single-cell transcriptomics datasets, each with thousands of measured variables. We also demonstrate significant improvements over six causal discovery algorithms in predicting intervention targets across a variety of tractable, synthetic datasets.

Generative Modeling of Molecular Dynamics Trajectories

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible multi-task surrogate models of MD from data. By conditioning on appropriately chosen frames of the trajectory, we show such generative models can be adapted to diverse tasks such as forward simulation, transition path sampling, and trajectory upsampling. By alternatively conditioning on part of the molecular system and inpainting the rest, we also demonstrate the first steps towards dynamics-conditioned molecular design. We validate the full set of these capabilities on tetrapeptide simulations and show that our model can produce reasonable ensembles of protein monomers. Altogether, our work illustrates how generative modeling can unlock value from MD data towards diverse downstream tasks that are not straightforward to address with existing methods or even MD itself. Code is available at https://github.com/bjing2016/mdgen.

Revisiting Who's Harry Potter: Towards Targeted Unlearning from a Causal Intervention Perspective

This paper investigates Who's Harry Potter (WHP), a pioneering yet insufficiently understood method for LLM unlearning. We explore it in two steps. First, we introduce a new task of LLM targeted unlearning, where given an unlearning target (e.g., a person) and some unlearning documents, we aim to unlearn only the information about the target, rather than everything in the unlearning documents. We further argue that a successful unlearning should satisfy criteria such as not outputting gibberish, not fabricating facts about the unlearning target, and not releasing factual information under jailbreak attacks. Second, we construct a causal intervention framework for targeted unlearning, where the knowledge of the unlearning target is modeled as a confounder between LLM input and output, and the unlearning process as a deconfounding process. This framework justifies and extends WHP, deriving a simple unlearning algorithm that includes WHP as a special case. Experiments on existing and new datasets show that our approach, without explicitly optimizing for the aforementioned criteria, achieves competitive performance in all of them. Our code is available at https://github.com/UCSB-NLP-Chang/causal_unlearn.git.