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Tommi Jaakkola

Publications and source records attributed to Tommi Jaakkola.

At least 73 records · Page 4Linked to original sources
arXiv2024

Improving Protein Optimization with Smoothed Fitness Landscapes

The ability to engineer novel proteins with higher fitness for a desired property would be revolutionary for biotechnology and medicine. Modeling the combinatorially large space of sequences is infeasible; prior methods often constrain optimization to a small mutational radius, but this drastically limits the design space. Instead of heuristics, we propose smoothing the fitness landscape to facilitate protein optimization. First, we formulate protein fitness as a graph signal then use Tikunov regularization to smooth the fitness landscape. We find optimizing in this smoothed landscape leads to improved performance across multiple methods in the GFP and AAV benchmarks. Second, we achieve state-of-the-art results utilizing discrete energy-based models and MCMC in the smoothed landscape. Our method, called Gibbs sampling with Graph-based Smoothing (GGS), demonstrates a unique ability to achieve 2.5 fold fitness improvement (with in-silico evaluation) over its training set. GGS demonstrates potential to optimize proteins in the limited data regime. Code: https://github.com/kirjner/GGS

q-bio.BM↗
arXiv2024

Deep Confident Steps to New Pockets: Strategies for Docking Generalization

Accurate blind docking has the potential to lead to new biological breakthroughs, but for this promise to be realized, docking methods must generalize well across the proteome. Existing benchmarks, however, fail to rigorously assess generalizability. Therefore, we develop DockGen, a new benchmark based on the ligand-binding domains of proteins, and we show that existing machine learning-based docking models have very weak generalization abilities. We carefully analyze the scaling laws of ML-based docking and show that, by scaling data and model size, as well as integrating synthetic data strategies, we are able to significantly increase the generalization capacity and set new state-of-the-art performance across benchmarks. Further, we propose Confidence Bootstrapping, a new training paradigm that solely relies on the interaction between diffusion and confidence models and exploits the multi-resolution generation process of diffusion models. We demonstrate that Confidence Bootstrapping significantly improves the ability of ML-based docking methods to dock to unseen protein classes, edging closer to accurate and generalizable blind docking methods.

q-bio.BM↗
arXiv2023

Fast non-autoregressive inverse folding with discrete diffusion

Generating protein sequences that fold into a intended 3D structure is a fundamental step in de novo protein design. De facto methods utilize autoregressive generation, but this eschews higher order interactions that could be exploited to improve inference speed. We describe a non-autoregressive alternative that performs inference using a constant number of calls resulting in a 23 times speed up without a loss in performance on the CATH benchmark. Conditioned on the 3D structure, we fine-tune ProteinMPNN to perform discrete diffusion with a purity prior over the index sampling order. Our approach gives the flexibility in trading off inference speed and accuracy by modulating the diffusion speed. Code: https://github.com/johnyang101/pmpnndiff

q-bio.BM↗
arXiv2023

Risk-Controlling Model Selection via Guided Bayesian Optimization

Adjustable hyperparameters of machine learning models typically impact various key trade-offs such as accuracy, fairness, robustness, or inference cost. Our goal in this paper is to find a configuration that adheres to user-specified limits on certain risks while being useful with respect to other conflicting metrics. We solve this by combining Bayesian Optimization (BO) with rigorous risk-controlling procedures, where our core idea is to steer BO towards an efficient testing strategy. Our BO method identifies a set of Pareto optimal configurations residing in a designated region of interest. The resulting candidates are statistically verified and the best-performing configuration is selected with guaranteed risk levels. We demonstrate the effectiveness of our approach on a range of tasks with multiple desiderata, including low error rates, equitable predictions, handling spurious correlations, managing rate and distortion in generative models, and reducing computational costs.

cs.LG↗
arXiv2023

Removing Biases from Molecular Representations via Information Maximization

High-throughput drug screening -- using cell imaging or gene expression measurements as readouts of drug effect -- is a critical tool in biotechnology to assess and understand the relationship between the chemical structure and biological activity of a drug. Since large-scale screens have to be divided into multiple experiments, a key difficulty is dealing with batch effects, which can introduce systematic errors and non-biological associations in the data. We propose InfoCORE, an Information maximization approach for COnfounder REmoval, to effectively deal with batch effects and obtain refined molecular representations. InfoCORE establishes a variational lower bound on the conditional mutual information of the latent representations given a batch identifier. It adaptively reweighs samples to equalize their implied batch distribution. Extensive experiments on drug screening data reveal InfoCORE's superior performance in a multitude of tasks including molecular property prediction and molecule-phenotype retrieval. Additionally, we show results for how InfoCORE offers a versatile framework and resolves general distribution shifts and issues of data fairness by minimizing correlation with spurious features or removing sensitive attributes. The code is available at https://github.com/uhlerlab/InfoCORE.

cs.LG↗
arXiv2023

Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models

In light of the widespread success of generative models, a significant amount of research has gone into speeding up their sampling time. However, generative models are often sampled multiple times to obtain a diverse set incurring a cost that is orthogonal to sampling time. We tackle the question of how to improve diversity and sample efficiency by moving beyond the common assumption of independent samples. We propose particle guidance, an extension of diffusion-based generative sampling where a joint-particle time-evolving potential enforces diversity. We analyze theoretically the joint distribution that particle guidance generates, how to learn a potential that achieves optimal diversity, and the connections with methods in other disciplines. Empirically, we test the framework both in the setting of conditional image generation, where we are able to increase diversity without affecting quality, and molecular conformer generation, where we reduce the state-of-the-art median error by 13% on average.

cs.LG↗
arXiv2023

Restart Sampling for Improving Generative Processes

Generative processes that involve solving differential equations, such as diffusion models, frequently necessitate balancing speed and quality. ODE-based samplers are fast but plateau in performance while SDE-based samplers deliver higher sample quality at the cost of increased sampling time. We attribute this difference to sampling errors: ODE-samplers involve smaller discretization errors while stochasticity in SDE contracts accumulated errors. Based on these findings, we propose a novel sampling algorithm called Restart in order to better balance discretization errors and contraction. The sampling method alternates between adding substantial noise in additional forward steps and strictly following a backward ODE. Empirically, Restart sampler surpasses previous SDE and ODE samplers in both speed and accuracy. Restart not only outperforms the previous best SDE results, but also accelerates the sampling speed by 10-fold / 2-fold on CIFAR-10 / ImageNet $64 \times 64$. In addition, it attains significantly better sample quality than ODE samplers within comparable sampling times. Moreover, Restart better balances text-image alignment/visual quality versus diversity than previous samplers in the large-scale text-to-image Stable Diffusion model pre-trained on LAION $512 \times 512$. Code is available at https://github.com/Newbeeer/diffusion_restart_sampling

cs.LG↗
arXiv2023

Learning Interatomic Potentials at Multiple Scales

The need to use a short time step is a key limit on the speed of molecular dynamics (MD) simulations. Simulations governed by classical potentials are often accelerated by using a multiple-time-step (MTS) integrator that evaluates certain potential energy terms that vary more slowly than others less frequently. This approach is enabled by the simple but limiting analytic forms of classical potentials. Machine learning interatomic potentials (MLIPs), in particular recent equivariant neural networks, are much more broadly applicable than classical potentials and can faithfully reproduce the expensive but accurate reference electronic structure calculations used to train them. They still, however, require the use of a single short time step, as they lack the inherent term-by-term scale separation of classical potentials. This work introduces a method to learn a scale separation in complex interatomic interactions by co-training two MLIPs. Initially, a small and efficient model is trained to reproduce short-time-scale interactions. Subsequently, a large and expressive model is trained jointly to capture the remaining interactions not captured by the small model. When running MD, the MTS integrator then evaluates the smaller model for every time step and the larger model less frequently, accelerating simulation. Compared to a conventionally trained MLIP, our approach can achieve a significant speedup (~3x in our experiments) without a loss of accuracy on the potential energy or simulation-derived quantities.

physics.chem-ph↗
arXiv2023

MOFDiff: Coarse-grained Diffusion for Metal-Organic Framework Design

Metal-organic frameworks (MOFs) are of immense interest in applications such as gas storage and carbon capture due to their exceptional porosity and tunable chemistry. Their modular nature has enabled the use of template-based methods to generate hypothetical MOFs by combining molecular building blocks in accordance with known network topologies. However, the ability of these methods to identify top-performing MOFs is often hindered by the limited diversity of the resulting chemical space. In this work, we propose MOFDiff: a coarse-grained (CG) diffusion model that generates CG MOF structures through a denoising diffusion process over the coordinates and identities of the building blocks. The all-atom MOF structure is then determined through a novel assembly algorithm. Equivariant graph neural networks are used for the diffusion model to respect the permutational and roto-translational symmetries. We comprehensively evaluate our model's capability to generate valid and novel MOF structures and its effectiveness in designing outstanding MOF materials for carbon capture applications with molecular simulations.

physics.chem-ph↗
arXiv2023

Fast protein backbone generation with SE(3) flow matching

We present FrameFlow, a method for fast protein backbone generation using SE(3) flow matching. Specifically, we adapt FrameDiff, a state-of-the-art diffusion model, to the flow-matching generative modeling paradigm. We show how flow matching can be applied on SE(3) and propose modifications during training to effectively learn the vector field. Compared to FrameDiff, FrameFlow requires five times fewer sampling timesteps while achieving two fold better designability. The ability to generate high quality protein samples at a fraction of the cost of previous methods paves the way towards more efficient generative models in de novo protein design.

q-bio.QM↗
arXiv2023

Compositional Sculpting of Iterative Generative Processes

High training costs of generative models and the need to fine-tune them for specific tasks have created a strong interest in model reuse and composition. A key challenge in composing iterative generative processes, such as GFlowNets and diffusion models, is that to realize the desired target distribution, all steps of the generative process need to be coordinated, and satisfy delicate balance conditions. In this work, we propose Compositional Sculpting: a general approach for defining compositions of iterative generative processes. We then introduce a method for sampling from these compositions built on classifier guidance. We showcase ways to accomplish compositional sculpting in both GFlowNets and diffusion models. We highlight two binary operations $\unicode{x2014}$ the harmonic mean ($p_1 \otimes p_2$) and the contrast ($p_1 \unicode{x25D1}\,p_2$) between pairs, and the generalization of these operations to multiple component distributions. We offer empirical results on image and molecular generation tasks.

cs.LG↗
arXiv2023

Compositional Foundation Models for Hierarchical Planning

To make effective decisions in novel environments with long-horizon goals, it is crucial to engage in hierarchical reasoning across spatial and temporal scales. This entails planning abstract subgoal sequences, visually reasoning about the underlying plans, and executing actions in accordance with the devised plan through visual-motor control. We propose Compositional Foundation Models for Hierarchical Planning (HiP), a foundation model which leverages multiple expert foundation model trained on language, vision and action data individually jointly together to solve long-horizon tasks. We use a large language model to construct symbolic plans that are grounded in the environment through a large video diffusion model. Generated video plans are then grounded to visual-motor control, through an inverse dynamics model that infers actions from generated videos. To enable effective reasoning within this hierarchy, we enforce consistency between the models via iterative refinement. We illustrate the efficacy and adaptability of our approach in three different long-horizon table-top manipulation tasks.

cs.LG↗
arXiv2023

Simulate Time-integrated Coarse-grained Molecular Dynamics with Multi-Scale Graph Networks

Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for many real-world applications due to slow inference for large systems and small time steps (femtosecond-level). We aim to address these challenges by learning a multi-scale graph neural network that directly simulates coarse-grained MD with a very large time step (nanosecond-level) and a novel refinement module based on diffusion models to mitigate simulation instability. The effectiveness of our method is demonstrated in two complex systems: single-chain coarse-grained polymers and multi-component Li-ion polymer electrolytes. For evaluation, we simulate trajectories much longer than the training trajectories for systems with different chemical compositions that the model is not trained on. Structural and dynamical properties can be accurately recovered at several orders of magnitude higher speed than classical force fields by getting out of the femtosecond regime.

cs.LG↗
arXiv2023

Forces are not Enough: Benchmark and Critical Evaluation for Machine Learning Force Fields with Molecular Simulations

Molecular dynamics (MD) simulation techniques are widely used for various natural science applications. Increasingly, machine learning (ML) force field (FF) models begin to replace ab-initio simulations by predicting forces directly from atomic structures. Despite significant progress in this area, such techniques are primarily benchmarked by their force/energy prediction errors, even though the practical use case would be to produce realistic MD trajectories. We aim to fill this gap by introducing a novel benchmark suite for learned MD simulation. We curate representative MD systems, including water, organic molecules, a peptide, and materials, and design evaluation metrics corresponding to the scientific objectives of respective systems. We benchmark a collection of state-of-the-art (SOTA) ML FF models and illustrate, in particular, how the commonly benchmarked force accuracy is not well aligned with relevant simulation metrics. We demonstrate when and how selected SOTA methods fail, along with offering directions for further improvement. Specifically, we identify stability as a key metric for ML models to improve. Our benchmark suite comes with a comprehensive open-source codebase for training and simulation with ML FFs to facilitate future work.

physics.comp-ph↗
arXiv2023

Is Conditional Generative Modeling all you need for Decision-Making?

Recent improvements in conditional generative modeling have made it possible to generate high-quality images from language descriptions alone. We investigate whether these methods can directly address the problem of sequential decision-making. We view decision-making not through the lens of reinforcement learning (RL), but rather through conditional generative modeling. To our surprise, we find that our formulation leads to policies that can outperform existing offline RL approaches across standard benchmarks. By modeling a policy as a return-conditional diffusion model, we illustrate how we may circumvent the need for dynamic programming and subsequently eliminate many of the complexities that come with traditional offline RL. We further demonstrate the advantages of modeling policies as conditional diffusion models by considering two other conditioning variables: constraints and skills. Conditioning on a single constraint or skill during training leads to behaviors at test-time that can satisfy several constraints together or demonstrate a composition of skills. Our results illustrate that conditional generative modeling is a powerful tool for decision-making.

cs.LG↗
arXiv2023

SE(3) diffusion model with application to protein backbone generation

The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry. In this line of work, a diffusion model over rigid bodies in 3D (referred to as frames) has shown success in generating novel, functional protein backbones that have not been observed in nature. However, there exists no principled methodological framework for diffusion on SE(3), the space of orientation preserving rigid motions in R3, that operates on frames and confers the group invariance. We address these shortcomings by developing theoretical foundations of SE(3) invariant diffusion models on multiple frames followed by a novel framework, FrameDiff, for learning the SE(3) equivariant score over multiple frames. We apply FrameDiff on monomer backbone generation and find it can generate designable monomers up to 500 amino acids without relying on a pretrained protein structure prediction network that has been integral to previous methods. We find our samples are capable of generalizing beyond any known protein structure.

cs.LG↗
arXiv2023

Towards Coherent Image Inpainting Using Denoising Diffusion Implicit Models

Image inpainting refers to the task of generating a complete, natural image based on a partially revealed reference image. Recently, many research interests have been focused on addressing this problem using fixed diffusion models. These approaches typically directly replace the revealed region of the intermediate or final generated images with that of the reference image or its variants. However, since the unrevealed regions are not directly modified to match the context, it results in incoherence between revealed and unrevealed regions. To address the incoherence problem, a small number of methods introduce a rigorous Bayesian framework, but they tend to introduce mismatches between the generated and the reference images due to the approximation errors in computing the posterior distributions. In this paper, we propose COPAINT, which can coherently inpaint the whole image without introducing mismatches. COPAINT also uses the Bayesian framework to jointly modify both revealed and unrevealed regions, but approximates the posterior distribution in a way that allows the errors to gradually drop to zero throughout the denoising steps, thus strongly penalizing any mismatches with the reference image. Our experiments verify that COPAINT can outperform the existing diffusion-based methods under both objective and subjective metrics. The codes are available at https://github.com/UCSB-NLP-Chang/CoPaint/.

cs.CV↗
arXiv2023

EigenFold: Generative Protein Structure Prediction with Diffusion Models

Protein structure prediction has reached revolutionary levels of accuracy on single structures, yet distributional modeling paradigms are needed to capture the conformational ensembles and flexibility that underlie biological function. Towards this goal, we develop EigenFold, a diffusion generative modeling framework for sampling a distribution of structures from a given protein sequence. We define a diffusion process that models the structure as a system of harmonic oscillators and which naturally induces a cascading-resolution generative process along the eigenmodes of the system. On recent CAMEO targets, EigenFold achieves a median TMScore of 0.84, while providing a more comprehensive picture of model uncertainty via the ensemble of sampled structures relative to existing methods. We then assess EigenFold's ability to model and predict conformational heterogeneity for fold-switching proteins and ligand-induced conformational change. Code is available at https://github.com/bjing2016/EigenFold.

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