73 accepted papers
Diffusion language models, especially masked discrete diffusion models, have achieved great success recently. While there are some theoretical and primary empirical results showing the advantages of latent reasoning with looped transformers or continuous CoT, continuous diffusion models typically un…
Flow and diffusion models produce high-quality samples, but adapting them to user preferences or constraints post-training remains costly and brittle, a challenge commonly called reward alignment. We argue that efficient reward alignment should be a property of the generative model itself, not an af…
With the widespread availability of pre-trained diffusion models, there are many options for which models to use and how to use them together. Making these decisions depends highly on both the user's goals and the expertise of each model. Taking this into account, we propose coordinating models as o…
State-of-the-art flow models achieve remarkable quality but require slow, iterative sampling. To accelerate this, flow maps can be distilled from pre-trained teachers, a procedure that conventionally requires sampling from an external dataset. We argue that this data-dependency introduces a fundamen
The performance of flow matching and diffusion models can be greatly improved at inference time using reward adaptation algorithms, yet efficiency remains a major limitation. While several algorithms were proposed, we demonstrate that a common bottleneck is the *sampling* method these algorithms rel…
Diffusion large language models (dLLMs) are emerging as an efficient alternative to autoregressive models due to their ability to decode multiple tokens in parallel. However, aligning dLLMs with human preferences or task-specific rewards via reinforcement learning (RL) is challenging because their i…
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 gener…
Diffusion models have emerged as a successful approach for molecular docking, but they often cannot model protein flexibility or generate nonphysical poses. We argue that both these challenges can be tackled by framing the problem as a transport between distributions. Still, existing paradigms lack…
The goal of protein design typically involves increasing fitness (extrapolating) beyond what is seen during training (e.g., towards higher stability, stronger binding affinity, etc.). State-of-the-art methods assume that one can safely steer proteins towards such extrapolated regions by learning fro…
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 P…
Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences (i.e., discrete diffusion models) across domains such as natural language and biological sequence generation. For example, in the protein inverse folding task, where the goal is to generate a…
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 gen…
Identifying variables responsible for changes to a biological system enables applications in drug target discovery and cell engineering. Given a pair of observational and interventional datasets, the goal is to isolate the subset of observed variables that were the targets of the intervention. Dire…
We propose *LEAPS*, an algorithm to sample from discrete distributions known up to normalization by learning a rate matrix of a continuous-time Markov chain (CTMC). LEAPS can be seen as a continuous-time formulation of annealed importance sampling and sequential Monte Carlo methods, extended so that…
Diffusion models can be improved with additional guidance towards more effective representations of input. Indeed, prior empirical work has already shown that aligning internal representations of the diffusion model with those of pre-trained models improves generation quality. In this paper, we pres…
In this paper we introduce Hierarchical Diffusion Language Models (HDLM) -- a novel family of discrete diffusion models for language modeling. HDLM builds on a hierarchical vocabulary where low-level tokens with detailed semantics are surjectively mapped to high-level tokens with coarse-grained mean…
We develop ProtComposer to generate protein structures conditioned on spatial protein layouts that are specified via a set of 3D ellipsoids capturing substructure shapes and semantics. At inference time, we condition on ellipsoids that are hand-constructed, extracted from existing proteins, or from…
Generative models have made significant impacts across various domains, largely due to their ability to scale during training by increasing data, computational resources, and model size, a phenomenon characterized by the scaling laws. Recent research has begun to explore inference-time scaling behav…
We introduce a novel approach for discovering effective degrees of freedom (DOF) in molecular dynamics simulations by mapping the DOF to approximate symmetries of the energy landscape. Unlike most existing methods, we do not require trajectory data but instead rely on knowledge of the forcefield (en…
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 a…
Reasoning large language models achieve impressive test-time scaling by thinking for longer, but this performance gain comes at significant compute cost. Directly limiting test-time budget hurts overall performance, but not all problems are equally difficult. We propose thought calibration to decide
In density functional theory, charge density is the core attribute of atomic systems from which all chemical properties can be derived. Machine learning methods are promising in significantly accelerating charge density prediction, yet existing approaches either lack accuracy or scalability. We prop…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly accurate single-state predictors such as AlphaFold and ESMFol…
Despite diffusion models' superior capabilities in modeling complex distributions there are still non-trivial distributional discrepancies between generated and ground-truth images which has resulted in several notable problems in image generation including missing object errors in text-to-image gen…
Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that naive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To…
Diffusion models (DMs) have revolutionized generative learning. They utilize a diffusion process to encode data into a simple Gaussian distribution. However, encoding a complex, potentially multimodal data distribution into a single *continuous* Gaussian distribution arguably represents an unnecessa…
Combining discrete and continuous data is an important capability for generative models. We present Discrete Flow Models (DFMs), a new flow-based model of discrete data that provides the missing link in enabling flow-based generative models to be applied to multimodal continuous and discrete data pr…
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 mu…
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 paper, we explore the potential of deliberately designing force fields for Hamiltonian systems, introducing Hamiltonian velocity p…
A significant amount of protein function requires binding small molecules, including enzymatic catalysis. As such, designing binding pockets for small molecules has several impactful applications ranging from drug synthesis to energy storage. Towards this goal, we first develop HarmonicFlow, an impr…
At the core of self-supervised learning for vision is the idea of learning invariant or equivariant representations with respect to a set of data transformations. This approach, however, introduces strong inductive biases, which can render the representations fragile in downstream tasks that do not…
We propose a novel approach to molecular simulations using neural network reparametrization, which offers a flexible alternative to traditional coarse-graining methods. Unlike conventional techniques that strictly reduce degrees of freedom, the complexity of the system can be adjusted in our model,…
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 un…
Computational antibody design seeks to automatically create an antibody that binds to an antigen. The binding affinity is governed by the 3D binding interface where antibody residues (paratope) closely interact with antigen residues (epitope). Thus, the key question of antibody design is how to pred…
We develop a new approach to multi-label conformal prediction in which we aim to output a precise set of promising prediction candidates with a bounded number of incorrect answers. Standard conformal prediction provides the ability to adapt to model uncertainty by constructing a calibrated candidate…
Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on…
"Score-based models generate samples by mapping noise to data (and vice versa) via a high-dimensional diffusion process. We question whether it is necessary to run this entire process at high dimensionality and incur all the inconveniences thereof. Instead, we restrict the diffusion via projections…
We develop a novel approach for confidently accelerating inference in the large and expensive multilayer Transformers that are now ubiquitous in natural language processing (NLP). Amortized or approximate computational methods increase efficiency, but can come with unpredictable performance costs. I…
We develop a novel approach to conformal prediction when the target task has limited data available for training. Conformal prediction identifies a small set of promising output candidates in place of a single prediction, with guarantees that the set contains the correct answer with high probability…
While the advent of Graph Neural Networks (GNNs) has greatly improved node and graph representation learning in many applications, the neighborhood aggregation scheme exposes additional vulnerabilities to adversaries seeking to extract node-level information about sensitive attributes. In this paper…
Current model-based reinforcement learning methods struggle when operating from complex visual scenes due to their inability to prioritize task-relevant features. To mitigate this problem, we propose learning Task Informed Abstractions (TIA) that explicitly separates reward-correlated visual feature…
In this paper, we aim to synthesize cell microscopy images under different molecular interventions, motivated by practical applications to drug development. Building on the recent success of graph neural networks for learning molecular embeddings and flow-based models for image generation, we propos…
Generative autoencoders offer a promising approach for controllable text generation by leveraging their learned sentence representations. However, current models struggle to maintain coherent latent spaces required to perform meaningful text manipulations via latent vector operations. Specifically,…
We address two fundamental questions about graph neural networks (GNNs). First, we prove that several important graph properties, e.g., shortest/longest cycle, diameter, or certain motifs, cannot be computed by GNNs that rely entirely on local information. Such GNNs include the standard message pass…
Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to smaller molecules. Indeed, as we demonstrate, their performance…
Generative models in molecular design tend to be richly parameterized, data-hungry neural models, as they must create complex structured objects as outputs. Estimating such models from data may be challenging due to the lack of sufficient training data. In this paper, we propose a surprisingly effec…
Selective rationalization improves neural network interpretability by identifying a small subset of input features {—} the rationale {—} that best explains or supports the prediction. A typical rationalization criterion, i.e. maximum mutual information (MMI), finds the rationale that maximizes the p…
Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes increasingly challenging when there are many property constraints.…
We extend structured prediction to deliberative outcomes. Specifically, we learn parameterized games that can map any inputs to equilibria as the outcomes. Standard structured prediction models rely heavily on global scoring functions and are therefore unable to model individual player preferences o…
Learning home appliance usage is important for understanding people's activities and optimizing energy consumption. The problem is modeled as an event detection task, where the objective is to learn when a user turns an appliance on, and which appliance it is (microwave, hair dryer, etc.). Ideally,…
This paper focuses on the problem of unsupervised alignment of hierarchical data such as ontologies or lexical databases. This problem arises across areas, from natural language processing to bioinformatics, and is typically solved by appeal to outside knowledge bases and label-textual similarity. I…
Selection of input features such as relevant pieces of text has become a common technique of highlighting how complex neural predictors operate. The selection can be optimized post-hoc for trained models or incorporated directly into the method itself (self-explaining). However, an overall selection…
Reparameterization of variational auto-encoders with continuous random variables is an effective method for reducing the variance of their gradient estimates. In the discrete case, one can perform reparametrization using the Gumbel-Max trick, but the resulting objective relies on an $\arg \max$ oper…
We provide a new approach to training neural models to exhibit transparency in a well-defined, functional manner. Our approach naturally operates over structured data and tailors the predictor, functionally, towards a chosen family of (local) witnesses. The estimation problem is setup as a co-operat…
Engineered proteins offer the potential to solve many problems in biomedicine, energy, and materials science, but creating designs that succeed is difficult in practice. A significant aspect of this challenge is the complex coupling between protein sequence and 3D structure, with the task of finding…
We view molecule optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be optimized in different ways, there are multiple viable translations f…
We propose a new approach to graph compression by appeal to optimal transport. The transport problem is seeded with prior information about node importance, attributes, and edges in the graph. The transport formulation can be setup for either directed or undirected graphs, and its dual characterizat…
Strong theoretical guarantees of robustness can be given for ensembles of classifiers generated by input randomization. Specifically, an $\ell_2$ bounded adversary cannot alter the ensemble prediction generated by an additive isotropic Gaussian noise, where the radius for the adversary depends on bo…
We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating li…
Optimal Transport has recently gained interest in machine learning for applications ranging from domain adaptation to sentence similarities or deep learning. Yet, its ability to capture frequently occurring structure beyond the "ground metric" is limited. In this work, we develop a nonlinear general…
Most recent work on interpretability of complex machine learning models has focused on estimating a-posteriori explanations for previously trained models around specific predictions. Self-explaining models where interpretability plays a key role already during learning have received much less attent…
The design of neural architectures for structured objects is typically guided by experimental insights rather than a formal process. In this work, we appeal to kernels over combinatorial structures, such as sequences and graphs, to derive appropriate neural operations. We introduce a class of deep r…
Our goal is to identify beneficial interventions from observational data. We consider interventions that are narrowly focused (impacting few covariates) and may be tailored to each individual or globally enacted over a population. For applications where harmful intervention is drastically worse th…
Aggregative games provide a rich abstraction to model strategic multi-agent interactions. We focus on learning local aggregative games, where the payoff of each player is a function of its own action and the aggregate behavior of its neighbors in a connected digraph. We show the existence of a pure…
The prediction of organic reaction outcomes is a fundamental problem in computational chemistry. Since a reaction may involve hundreds of atoms, fully exploring the space of possible transformations is intractable. The current solution utilizes reaction templates to limit the space, but it suffers f…
We present a model that, after learning on observations of (sequence, outcome) pairs, can be efficiently used to revise a new sequence in order to improve its associated outcome. Our framework requires neither example improvements, nor additional evaluation of outcomes for proposed revisions. To avo…
This paper focuses on style transfer on the basis of non-parallel text. This is an instance of a broad family of problems including machine translation, decipherment, and sentiment modification. The key challenge is to separate the content from other aspects such as style. We assume a shared latent…
We present a hierarchical Bayesian framework for clustering with cluster-specific feature selection. We derive a simplified model, CRAFT, by analyzing the asymptotic behavior of the log posterior formulations in a nonparametric MAP-based clustering setting in this framework. CRAFT handles assorted d…
We estimate stochastic processes that govern the dynamics of evolving populations such as cell differentiation. The problem is challenging since longitudinal trajectory measurements of individuals in a population are rarely available due to experimental cost and/or privacy. We show that cross-sectio…
Many real phenomena, including behaviors, involve strategic interactions that can be learned from data. We focus on learning tree structured potential games where equilibria are represented by local maxima of an underlying potential function. We cast the learning problem within a max margin setting…
Large unweighted directed graphs are commonly used to capture relations between entities. A fundamental problem in the analysis of such networks is to properly define the similarity or dissimilarity between any two vertices. Despite the significance of this problem, statistical characterization of t…
We analyze directed, unweighted graphs obtained from x_i∈\RR^d by connecting vertex i to j iff |x_i - x_j| < ε(x_i). Examples of such graphs include k-nearest neighbor graphs, where ε(x_i) varies from point to point, and, arguably, many real world graphs such as co-purchasing graphs. We ask whether…
We introduce principal differences analysis for analyzing differences between high-dimensional distributions. The method operates by finding the projection that maximizes the Wasserstein divergence between the resulting univariate populations. Relying on the Cramer-Wold device, it requires no assump…