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Tommi Jaakkola

Publications and source records attributed to Tommi Jaakkola.

At least 91 records · Page 5Linked to original sources
arXiv2023

GenPhys: From Physical Processes to Generative Models

Since diffusion models (DM) and the more recent Poisson flow generative models (PFGM) are inspired by physical processes, it is reasonable to ask: Can physical processes offer additional new generative models? We show that the answer is yes. We introduce a general family, Generative Models from Physical Processes (GenPhys), where we translate partial differential equations (PDEs) describing physical processes to generative models. We show that generative models can be constructed from s-generative PDEs (s for smooth). GenPhys subsume the two existing generative models (DM and PFGM) and even give rise to new families of generative models, e.g., "Yukawa Generative Models" inspired from weak interactions. On the other hand, some physical processes by default do not belong to the GenPhys family, e.g., the wave equation and the Schrödinger equation, but could be made into the GenPhys family with some modifications. Our goal with GenPhys is to explore and expand the design space of generative models.

cs.LG↗
arXiv2023

Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem

Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes. But a general solution to this motif-scaffolding problem remains open. Current machine-learning techniques for scaffold design are either limited to unrealistically small scaffolds (up to length 20) or struggle to produce multiple diverse scaffolds. We propose to learn a distribution over diverse and longer protein backbone structures via an E(3)-equivariant graph neural network. We develop SMCDiff to efficiently sample scaffolds from this distribution conditioned on a given motif; our algorithm is the first to theoretically guarantee conditional samples from a diffusion model in the large-compute limit. We evaluate our designed backbones by how well they align with AlphaFold2-predicted structures. We show that our method can (1) sample scaffolds up to 80 residues and (2) achieve structurally diverse scaffolds for a fixed motif.

q-bio.BM↗
arXiv2023

Torsional Diffusion for Molecular Conformer Generation

Molecular conformer generation is a fundamental task in computational chemistry. Several machine learning approaches have been developed, but none have outperformed state-of-the-art cheminformatics methods. We propose torsional diffusion, a novel diffusion framework that operates on the space of torsion angles via a diffusion process on the hypertorus and an extrinsic-to-intrinsic score model. On a standard benchmark of drug-like molecules, torsional diffusion generates superior conformer ensembles compared to machine learning and cheminformatics methods in terms of both RMSD and chemical properties, and is orders of magnitude faster than previous diffusion-based models. Moreover, our model provides exact likelihoods, which we employ to build the first generalizable Boltzmann generator. Code is available at https://github.com/gcorso/torsional-diffusion.

physics.chem-ph↗
arXiv2023

Subspace Diffusion Generative Models

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 onto subspaces as the data distribution evolves toward noise. When applied to state-of-the-art models, our framework simultaneously improves sample quality -- reaching an FID of 2.17 on unconditional CIFAR-10 -- and reduces the computational cost of inference for the same number of denoising steps. Our framework is fully compatible with continuous-time diffusion and retains its flexible capabilities, including exact log-likelihoods and controllable generation. Code is available at https://github.com/bjing2016/subspace-diffusion.

cs.LG↗
arXiv2023

Stable Target Field for Reduced Variance Score Estimation in Diffusion Models

Diffusion models generate samples by reversing a fixed forward diffusion process. Despite already providing impressive empirical results, these diffusion models algorithms can be further improved by reducing the variance of the training targets in their denoising score-matching objective. We argue that the source of such variance lies in the handling of intermediate noise-variance scales, where multiple modes in the data affect the direction of reverse paths. We propose to remedy the problem by incorporating a reference batch which we use to calculate weighted conditional scores as more stable training targets. We show that the procedure indeed helps in the challenging intermediate regime by reducing (the trace of) the covariance of training targets. The new stable targets can be seen as trading bias for reduced variance, where the bias vanishes with increasing reference batch size. Empirically, we show that the new objective improves the image quality, stability, and training speed of various popular diffusion models across datasets with both general ODE and SDE solvers. When used in combination with EDM, our method yields a current SOTA FID of 1.90 with 35 network evaluations on the unconditional CIFAR-10 generation task. The code is available at https://github.com/Newbeeer/stf

cs.LG↗
arXiv2023

DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime compared to traditional search-based methods but have yet to offer substantial improvements in accuracy. We instead frame molecular docking as a generative modeling problem and develop DiffDock, a diffusion generative model over the non-Euclidean manifold of ligand poses. To do so, we map this manifold to the product space of the degrees of freedom (translational, rotational, and torsional) involved in docking and develop an efficient diffusion process on this space. Empirically, DiffDock obtains a 38% top-1 success rate (RMSD<2A) on PDBBind, significantly outperforming the previous state-of-the-art of traditional docking (23%) and deep learning (20%) methods. Moreover, while previous methods are not able to dock on computationally folded structures (maximum accuracy 10.4%), DiffDock maintains significantly higher precision (21.7%). Finally, DiffDock has fast inference times and provides confidence estimates with high selective accuracy.

q-bio.BM↗
arXiv2023

PFGM++: Unlocking the Potential of Physics-Inspired Generative Models

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for $N$ dimensional data by embedding paths in $N{+}D$ dimensional space while still controlling the progression with a simple scalar norm of the $D$ additional variables. The new models reduce to PFGM when $D{=}1$ and to diffusion models when $D{\to}\infty$. The flexibility of choosing $D$ allows us to trade off robustness against rigidity as increasing $D$ results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of $D$, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models ($D{\to} \infty$) to any finite $D$ values. Our experiments show that models with finite $D$ can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ $64{\times}64$ datasets, with FID scores of $1.91/2.43$ when $D{=}2048/128$. In class-conditional setting, $D{=}2048$ yields current state-of-the-art FID of $1.74$ on CIFAR-10. In addition, we demonstrate that models with smaller $D$ exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp

cs.LG↗
arXiv2022

Poisson Flow Generative Models

We propose a new "Poisson flow" generative model (PFGM) that maps a uniform distribution on a high-dimensional hemisphere into any data distribution. We interpret the data points as electrical charges on the $z=0$ hyperplane in a space augmented with an additional dimension $z$, generating a high-dimensional electric field (the gradient of the solution to Poisson equation). We prove that if these charges flow upward along electric field lines, their initial distribution in the $z=0$ plane transforms into a distribution on the hemisphere of radius $r$ that becomes uniform in the $r \to\infty$ limit. To learn the bijective transformation, we estimate the normalized field in the augmented space. For sampling, we devise a backward ODE that is anchored by the physically meaningful additional dimension: the samples hit the unaugmented data manifold when the $z$ reaches zero. Experimentally, PFGM achieves current state-of-the-art performance among the normalizing flow models on CIFAR-10, with an Inception score of $9.68$ and a FID score of $2.35$. It also performs on par with the state-of-the-art SDE approaches while offering $10\times $ to $20 \times$ acceleration on image generation tasks. Additionally, PFGM appears more tolerant of estimation errors on a weaker network architecture and robust to the step size in the Euler method. The code is available at https://github.com/Newbeeer/poisson_flow .

cs.LG↗
arXiv2022

Efficiently Controlling Multiple Risks with Pareto Testing

Machine learning applications frequently come with multiple diverse objectives and constraints that can change over time. Accordingly, trained models can be tuned with sets of hyper-parameters that affect their predictive behavior (e.g., their run-time efficiency versus error rate). As the number of constraints and hyper-parameter dimensions grow, naively selected settings may lead to sub-optimal and/or unreliable results. We develop an efficient method for calibrating models such that their predictions provably satisfy multiple explicit and simultaneous statistical guarantees (e.g., upper-bounded error rates), while also optimizing any number of additional, unconstrained objectives (e.g., total run-time cost). Building on recent results in distribution-free, finite-sample risk control for general losses, we propose Pareto Testing: a two-stage process which combines multi-objective optimization with multiple hypothesis testing. The optimization stage constructs a set of promising combinations on the Pareto frontier. We then apply statistical testing to this frontier only to identify configurations that have (i) high utility with respect to our objectives, and (ii) guaranteed risk levels with respect to our constraints, with specifiable high probability. We demonstrate the effectiveness of our approach to reliably accelerate the execution of large-scale Transformer models in natural language processing (NLP) applications. In particular, we show how Pareto Testing can be used to dynamically configure multiple inter-dependent model attributes -- including the number of layers computed before exiting, number of attention heads pruned, or number of text tokens considered -- to simultaneously control and optimize various accuracy and cost metrics.

cs.LG↗
arXiv2022

Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement

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, predicting 3D paratope-epitope complex (docking) is the key to finding the best paratope. In this paper, we propose a new model called Hierarchical Equivariant Refinement Network (HERN) for paratope docking and design. During docking, HERN employs a hierarchical message passing network to predict atomic forces and use them to refine a binding complex in an iterative, equivariant manner. During generation, its autoregressive decoder progressively docks generated paratopes and builds a geometric representation of the binding interface to guide the next residue choice. Our results show that HERN significantly outperforms prior state-of-the-art on paratope docking and design benchmarks.

q-bio.BM↗
arXiv2022

EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction

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 heavy candidate sampling coupled with scoring, ranking, and fine-tuning steps. We challenge this paradigm with EquiBind, an SE(3)-equivariant geometric deep learning model performing direct-shot prediction of both i) the receptor binding location (blind docking) and ii) the ligand's bound pose and orientation. EquiBind achieves significant speed-ups and better quality compared to traditional and recent baselines. Further, we show extra improvements when coupling it with existing fine-tuning techniques at the cost of increased running time. Finally, we propose a novel and fast fine-tuning model that adjusts torsion angles of a ligand's rotatable bonds based on closed-form global minima of the von Mises angular distance to a given input atomic point cloud, avoiding previous expensive differential evolution strategies for energy minimization.

q-bio.BM↗
arXiv2022

Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking

Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering. We tackle rigid body protein-protein docking, i.e., computationally predicting the 3D structure of a protein-protein complex from the individual unbound structures, assuming no conformational change within the proteins happens during binding. We design a novel pairwise-independent SE(3)-equivariant graph matching network to predict the rotation and translation to place one of the proteins at the right docked position relative to the second protein. We mathematically guarantee a basic principle: the predicted complex is always identical regardless of the initial locations and orientations of the two structures. Our model, named EquiDock, approximates the binding pockets and predicts the docking poses using keypoint matching and alignment, achieved through optimal transport and a differentiable Kabsch algorithm. Empirically, we achieve significant running time improvements and often outperform existing docking software despite not relying on heavy candidate sampling, structure refinement, or templates.

cs.AI↗
arXiv2022

Crystal Diffusion Variational Autoencoder for Periodic Material Generation

Generating the periodic structure of stable materials is a long-standing challenge for the material design community. This task is difficult because stable materials only exist in a low-dimensional subspace of all possible periodic arrangements of atoms: 1) the coordinates must lie in the local energy minimum defined by quantum mechanics, and 2) global stability also requires the structure to follow the complex, yet specific bonding preferences between different atom types. Existing methods fail to incorporate these factors and often lack proper invariances. We propose a Crystal Diffusion Variational Autoencoder (CDVAE) that captures the physical inductive bias of material stability. By learning from the data distribution of stable materials, the decoder generates materials in a diffusion process that moves atomic coordinates towards a lower energy state and updates atom types to satisfy bonding preferences between neighbors. Our model also explicitly encodes interactions across periodic boundaries and respects permutation, translation, rotation, and periodic invariances. We significantly outperform past methods in three tasks: 1) reconstructing the input structure, 2) generating valid, diverse, and realistic materials, and 3) generating materials that optimize a specific property. We also provide several standard datasets and evaluation metrics for the broader machine learning community.

cs.LG↗
arXiv2022

Conformal Prediction Sets with Limited False Positives

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 set in place of a single prediction, with guarantees that the set contains the correct answer with high probability. In order to obey this coverage property, however, conformal sets can become inundated with noisy candidates -- which can render them unhelpful in practice. This is particularly relevant to practical applications where there is a limited budget, and the cost (monetary or otherwise) associated with false positives is non-negligible. We propose to trade coverage for a notion of precision by enforcing that the presence of incorrect candidates in the predicted conformal sets (i.e., the total number of false positives) is bounded according to a user-specified tolerance. Subject to this constraint, our algorithm then optimizes for a generalized notion of set coverage (i.e., the true positive rate) that allows for any number of true answers for a given query (including zero). We demonstrate the effectiveness of this approach across a number of classification tasks in natural language processing, computer vision, and computational chemistry.

cs.LG↗
arXiv2022

Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design

Antibodies are versatile proteins that bind to pathogens like viruses and stimulate the adaptive immune system. The specificity of antibody binding is determined by complementarity-determining regions (CDRs) at the tips of these Y-shaped proteins. In this paper, we propose a generative model to automatically design the CDRs of antibodies with enhanced binding specificity or neutralization capabilities. Previous generative approaches formulate protein design as a structure-conditioned sequence generation task, assuming the desired 3D structure is given a priori. In contrast, we propose to co-design the sequence and 3D structure of CDRs as graphs. Our model unravels a sequence autoregressively while iteratively refining its predicted global structure. The inferred structure in turn guides subsequent residue choices. For efficiency, we model the conditional dependence between residues inside and outside of a CDR in a coarse-grained manner. Our method achieves superior log-likelihood on the test set and outperforms previous baselines in designing antibodies capable of neutralizing the SARS-CoV-2 virus.

q-bio.BM↗
arXiv2022

Controlling Directions Orthogonal to a Classifier

We propose to identify directions invariant to a given classifier so that these directions can be controlled in tasks such as style transfer. While orthogonal decomposition is directly identifiable when the given classifier is linear, we formally define a notion of orthogonality in the non-linear case. We also provide a surprisingly simple method for constructing the orthogonal classifier (a classifier utilizing directions other than those of the given classifier). Empirically, we present three use cases where controlling orthogonal variation is important: style transfer, domain adaptation, and fairness. The orthogonal classifier enables desired style transfer when domains vary in multiple aspects, improves domain adaptation with label shifts and mitigates the unfairness as a predictor. The code is available at http://github.com/Newbeeer/orthogonal_classifier

cs.LG↗
arXiv2021

Fragment-based Sequential Translation for Molecular Optimization

Searching for novel molecular compounds with desired properties is an important problem in drug discovery. Many existing frameworks generate molecules one atom at a time. We instead propose a flexible editing paradigm that generates molecules using learned molecular fragments--meaningful substructures of molecules. To do so, we train a variational autoencoder (VAE) to encode molecular fragments in a coherent latent space, which we then utilize as a vocabulary for editing molecules to explore the complex chemical property space. Equipped with the learned fragment vocabulary, we propose Fragment-based Sequential Translation (FaST), which learns a reinforcement learning (RL) policy to iteratively translate model-discovered molecules into increasingly novel molecules while satisfying desired properties. Empirical evaluation shows that FaST significantly improves over state-of-the-art methods on benchmark single/multi-objective molecular optimization tasks.

q-bio.BM↗
arXiv2021

Learning Representations that Support Robust Transfer of Predictors

Ensuring generalization to unseen environments remains a challenge. Domain shift can lead to substantially degraded performance unless shifts are well-exercised within the available training environments. We introduce a simple robust estimation criterion -- transfer risk -- that is specifically geared towards optimizing transfer to new environments. Effectively, the criterion amounts to finding a representation that minimizes the risk of applying any optimal predictor trained on one environment to another. The transfer risk essentially decomposes into two terms, a direct transfer term and a weighted gradient-matching term arising from the optimality of per-environment predictors. Although inspired by IRM, we show that transfer risk serves as a better out-of-distribution generalization criterion, both theoretically and empirically. We further demonstrate the impact of optimizing such transfer risk on two controlled settings, each representing a different pattern of environment shift, as well as on two real-world datasets. Experimentally, the approach outperforms baselines across various out-of-distribution generalization tasks. Code is available at \url{https://github.com/Newbeeer/TRM}.

cs.LG↗