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Tommi Jaakkola

Publications and source records attributed to Tommi Jaakkola.

At least 19 recordsLinked to original sources
arXiv2026

From Surfaces to Volumes: Registered Geometry for Protein Representation Learning

Existing protein geometry models typically represent molecular surfaces using local geometric features such as sampled points, normals, and curvature. While effective for capturing exposed molecular shape, these representations do not explicitly model the volumetric organization beneath the surface or provide a consistent coordinate system for residue-wise volumetric structure. We introduce Protein-TetSphere, a registered residue-wise volumetric representation for proteins. Each protein chain is tetrahedralized to obtain local volumetric regions associated with individual residues, which are then registered to a shared fixed-topology tetrahedral reference and represented in a common Laplacian basis. This registration establishes consistent volumetric coordinates across residues, enabling local three-dimensional deformation to be integrated with surface and chemical information in a multimodal protein representation. We evaluate Protein-TetSphere on ligand-binding pocket classification, protein--protein interface prediction, and de novo protein binder design. Across the three tasks, Protein-TetSphere improves ligand-binding pocket balanced accuracy from $0.795$ to $0.826$, Pinder-Pair/Site AUROC from $0.914/0.852$ to $0.932/0.866$, and binder-design success from $14.95\%$ to $19.90\%$ on the BoltzGen Challenge Set and from $27.62\%$ to $32.19\%$ at the ProtDBench backbone level. These results show that registered volumetric geometry provides complementary spatial information beyond molecular surfaces across protein recognition, interaction, and design.

cs.AI↗
arXiv2026

Online Reasoning Calibration: Test-Time Training Enables Generalizable Conformal LLM Reasoning

While test-time scaling has enabled large language models to solve highly difficult tasks, state-of-the-art results come at exorbitant compute costs. These inefficiencies can be attributed to the miscalibration of post-trained language models, and the lack of calibration in popular sampling techniques. Here, we present Online Reasoning Calibration (ORCA), a framework for calibrating the sampling process that draws upon conformal prediction and test-time training. Specifically, we introduce a meta-learning procedure that updates the calibration module for each input. This allows us to provide valid confidence estimates under distributional shift, e.g. in thought patterns that occur across different stages of reasoning, or in prompt distributions between model development and deployment. ORCA not only provides theoretical guarantees on conformal risks, but also empirically shows higher efficiency and generalization across different reasoning tasks. At risk level $δ=0.1$, ORCA improves Qwen2.5-32B efficiency on in-distribution tasks with savings up to 47.5% with supervised labels and 40.7% with self-consistency labels. Under zero-shot out-of-domain settings, it improves MATH-500 savings from 24.8% of the static calibration baseline to 67.0% while maintaining a low empirical error rate, and the same trend holds across model families and downstream benchmarks. Our code is publicly available at https://github.com/wzekai99/ORCA.

cs.LG↗
arXiv2026

Turbulence teaches equivariance to neural networks

We show that the rotational nature of turbulence affects how neural networks learn mappings between quantities governed by the Navier-Stokes equations. We train super-resolution models at different wall-normal locations in a turbulent channel flow, where anisotropy varies naturally, and test their generalization to new coordinate frames, new anisotropy regimes, and a higher Reynolds number. Our findings inform both the design of equivariant machine learning models for turbulence and our understanding of how turbulence shapes what those models learn. First, mappings that better respect the rotational symmetries of the Navier-Stokes equations generalize better to new flows. Coordinate-frame generalization is therefore a key part of the broader generalization problem, since turbulent flows contain a wide range of local orientations. Second, turbulence itself partially teaches equivariance to learned mappings, an effect we call implicit data augmentation. The effect strengthens with dataset size and with isotropy, since a more isotropic dataset samples more orientations under which the Navier-Stokes equations are covariant. Implicit augmentation is also scale-dependent, with smaller scales exhibiting lower equivariance error. This scale-dependency is consistent with Kolmogorov's hypothesis of local isotropy. Third, enforcing equivariance as an architectural inductive bias is the limit of these effects: an exactly equivariant network outperforms unconstrained CNNs on all generalization tests, with roughly an order of magnitude fewer parameters. We expect these effects to apply broadly to learned mappings between tensorial flow quantities, making them relevant to most machine learning applications in turbulence.

physics.flu-dyn↗
arXiv2026

Few-step Cofolding with All-Atom Flow Maps

All-atom generative modeling of 3D biomolecular complexes has emerged as the dominant paradigm for predicting the structure of proteins and protein-ligand systems. Generating structures at the atomic level of fidelity, however, typically requires expensive iterative diffusion rollouts, making both conventional deployment and inference-time search techniques computationally costly. In this paper, we introduce the Denoiser Cofolding All-Atom Flowmap (DeCAF) framework for distilling state-of-the-art all-atom cofolding models into all-atom flow maps that produce high-quality samples in only a few inference steps. We build DeCAF on a denoiser-based formulation of flow maps with endpoint losses that naturally support SE(3) rigid alignment, which we show is critical for training accurate models. We further derive a simple change of variables that lets DeCAF operate in the σ-space noise schedule of EDM-style architectures, enabling direct distillation from pretrained cofolding diffusion models. Equipped with DeCAF's flowmap lookahead, we introduce a purpose-built inference-time framework that improves sampling through reward-guided search. Empirically, DeCAF-Boltz statistically improves over Boltz-1x in both accuracy (RMSD) and physical validity scores of protein-ligand poses at strict NFE budgets on the challenging Runs N' Poses, while also showing a more optimal Pareto frontier across all inference compute budgets on PoseBusters. Distilling the state-of-the-art Pearl cofolding model, DeCAF-Pearl outperforms diffusion-based cofolding models and matches its teacher on success rate while using 5x fewer NFEs. We release our code at https://github.com/genesistherapeutics/decaf.

cs.LG↗
arXiv2026

Divide-and-Denoise: A Game-Theoretic Method for Fairly Composing Diffusion Models

The abundance of pre-trained diffusion models provides an opportunity for composition. Combining several models, however, runs the risk of one model dominating or models disagreeing with each other. Here, we propose Divide-and-Denoise, a method for coordinating multiple pre-trained diffusion models during sampling. Much like managing a specialized workforce, our method creates a fair but efficient division of labor across models. Central to our method is the notion of an allocation which defines the responsibility of each model to every region of the noisy sample. At every timestep, we then denoise by (i) updating the allocation by solving a fair division game, where we divide the sample into regions that maximize total utility under fairness constraints, and (ii) aligning the models with this allocation, where we guide each model to denoise within its assigned region. This leads to a new composite denoising process that evolves in tandem with a division process. We evaluate Divide-and-Denoise on conditional image generation. Across several quality metrics, including the GenEval benchmark, our method outperforms baselines and resolves common failures including missing objects and mismatched attributes. Experiments show that Divide-and-Denoise utilizes each model's expertise without neglecting any other model.

cs.CV↗
arXiv2026

Diffusion Domain Expansion: Learning to Coordinate Pre-trained Diffusion Models

In this paper, we propose Diffusion Domain Expansion (DDE), a method that efficiently extends pre-trained diffusion models to generate larger objects and handle more complex conditioning beyond their original capabilities. Our method employs a compact trainable network designed to coordinate the denoised outputs of pre-trained diffusion models. We demonstrate that the coordinator can be universally simple while being capable of generalizing to domains larger than those observed during its training time. We evaluate DDE on long audio track generation and conditional image generation, demonstrating its applicability across domains. DDE outperforms other approaches to coordinated generation with diffusion models in qualitative and quantitative evaluations.

cs.LG↗
arXiv2026

Diamond Maps: Efficient Reward Alignment via Stochastic Flow Maps

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 afterthought, and redesign the model for adaptability. We propose "Diamond Maps", stochastic flow map models that enable efficient and accurate alignment to arbitrary rewards at inference time. Diamond Maps amortize many simulation steps into a single-step sampler, like flow maps, while preserving the stochasticity required for optimal reward alignment. This design makes search, Sequential Monte Carlo, and guidance scalable by enabling efficient and consistent estimation of the value function. Our experiments show that Diamond Maps can be learned efficiently via distillation from GLASS Flows, achieve stronger reward alignment performance, and scale better than existing methods. Our results point toward a practical route to generative models that can be rapidly adapted to arbitrary preferences and constraints at inference time.

cs.LG↗
arXiv2026

Zatom-1: Towards a Multimodal Foundation Model for 3D Molecules and Materials

General-purpose 3D modeling in chemistry encompasses molecules and materials, requiring both generative and predictive capabilities. However, most existing AI approaches are optimized for a single domain (molecules or materials) and a single task (generation or prediction), which limits representation sharing and transfer. We introduce Zatom-1, a cross-domain, general-purpose model architecture that unifies generative and predictive learning of 3D molecules and materials. Zatom-1 is a deliberately simplified Transformer trained with a multimodal flow matching objective that jointly models discrete atom types and continuous 3D geometries. This approach supports scalable pretraining with predictable gains as model capacity increases, while enabling fast and stable sampling. We use cross-domain generative pretraining as a universal initialization for downstream multi-task prediction of properties, energies, and forces. Empirically, Zatom-1 outperforms or competes with specialized baselines on both multi-task generative and predictive benchmarks in data-controlled settings, while improving generative inference speed by more than an order of magnitude. Our experiments demonstrate positive predictive transfer between data domains from joint generative pretraining: modeling materials during generative pretraining improves molecular property prediction accuracy. Open-source code and model weights are freely available at https://github.com/Zatom-AI/zatom.

cs.LG↗
arXiv2026

Coevolutionary Continuous Discrete Diffusion: Make Your Diffusion Language Model a Latent Reasoner

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 chain-of-thoughts, continuous diffusion models typically underperform their discrete counterparts. In this paper, we argue that diffusion language models do not necessarily need to be in the discrete space. In particular, we prove that continuous diffusion models have stronger expressivity than discrete diffusions and looped transformers. We attribute the contradiction between the theoretical expressiveness and empirical performance to their practical trainability: while continuous diffusion provides intermediate supervision that looped transformers lack, they introduce additional difficulty decoding tokens into the discrete token space from the continuous representation space. We therefore propose Coevolutionary Continuous Discrete Diffusion (CCDD), which defines a joint multimodal diffusion process on the union of a continuous representation space and a discrete token space, leveraging a single model to simultaneously denoise in the joint space. By combining two modalities, CCDD is expressive with rich semantics in the latent space, as well as good trainability and sample quality with the help of explicit discrete tokens. We also propose effective architectures and advanced training/sampling techniques for CCDD, which reveals strong empirical performance in extensive language modeling experiments on real-world tasks.

cs.AI↗
arXiv2026

SPG: Sandwiched Policy Gradient for Masked Diffusion Language Models

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 intractable log-likelihood precludes the direct application of standard policy gradient methods. While prior work uses surrogates like the evidence lower bound (ELBO), these one-sided approximations can introduce significant policy gradient bias. To address this, we propose the Sandwiched Policy Gradient (SPG) that leverages both an upper and a lower bound of the true log-likelihood. Experiments show that SPG significantly outperforms baselines based on ELBO or one-step estimation. Specifically, SPG improves the accuracy over state-of-the-art RL methods for dLLMs by 3.6% in GSM8K, 2.6% in MATH500, 18.4% in Countdown and 27.0% in Sudoku.

cs.CL↗
arXiv2026

How Well Do Agentic Skills Work in the Wild: Benchmarking LLM Skill Usage in Realistic Settings

Agent skills, which are reusable, domain-specific knowledge artifacts, have become a popular mechanism for extending LLM-based agents, yet formally benchmarking skill usage performance remains scarce. Existing skill benchmarking efforts focus on overly idealized conditions, where LLMs are directly provided with hand-crafted, narrowly-tailored task-specific skills for each task, whereas in many realistic settings, the LLM agent may have to search for and select relevant skills on its own, and even the closest matching skills may not be well-tailored for the task. In this paper, we conduct the first comprehensive study of skill utility under progressively challenging realistic settings, where agents must retrieve skills from a large collection of 34k real-world skills and may not have access to any hand-curated skills. Our findings reveal that the benefits of skills are fragile: performance gains degrade consistently as settings become more realistic, with pass rates approaching no-skill baselines in the most challenging scenarios. To narrow this gap, we study skill refinement strategies, including query-specific and query-agnostic approaches, and we show that query-specific refinement substantially recovers lost performance when the initial skills are of reasonable relevance and quality. We further demonstrate the generality of retrieval and refinement on Terminal-Bench 2.0, where they improve the pass rate of Claude Opus 4.6 from 57.7% to 65.5%. Our results, consistent across multiple models, highlight both the promise and the current limitations of skills for LLM-based agents. Our code is available at https://github.com/UCSB-NLP-Chang/Skill-Usage.

cs.CL↗
arXiv2026

Rethinking Diffusion Models with Symmetries through Canonicalization with Applications to Molecular Graph Generation

Many generative tasks in chemistry and science involve distributions invariant to group symmetries (e.g., permutation and rotation). A common strategy enforces invariance and equivariance through architectural constraints such as equivariant denoisers and invariant priors. In this paper, we challenge this tradition through the alternative canonicalization perspective: first map each sample to an orbit representative with a canonical pose or order, train an unconstrained (non-equivariant) diffusion or flow model on the canonical slice, and finally recover the invariant distribution by sampling a random symmetry transform at generation time. Building on a formal quotient-space perspective, our work provides a comprehensive theory of canonical diffusion by proving: (i) the correctness, universality and superior expressivity of canonical generative models over invariant targets; (ii) canonicalization accelerates training by removing diffusion score complexity induced by group mixtures and reducing conditional variance in flow matching. We then show that aligned priors and optimal transport act complementarily with canonicalization and further improves training efficiency. We instantiate the framework for molecular graph generation under $S_n \times SE(3)$ symmetries. By leveraging geometric spectra-based canonicalization and mild positional encodings, canonical diffusion significantly outperforms equivariant baselines in 3D molecule generation tasks, with similar or even less computation. Moreover, with a novel architecture Canon, CanonFlow achieves state-of-the-art performance on the challenging GEOM-DRUG dataset, and the advantage remains large in few-step generation.

cs.LG↗
arXiv2026

GLASS Flows: Transition Sampling for Alignment of Flow and Diffusion Models

The performance of flow matching and diffusion models can be greatly improved at inference time using reward alignment algorithms, yet efficiency remains a major limitation. While several algorithms were proposed, we demonstrate that a common bottleneck is the sampling method these algorithms rely on: many algorithms require to sample Markov transitions via SDE sampling, which is significantly less efficient and often less performant than ODE sampling. To remove this bottleneck, we introduce GLASS Flows, a new sampling paradigm that simulates a "flow matching model within a flow matching model" to sample Markov transitions. As we show in this work, this "inner" flow matching model can be retrieved from a pre-trained model without any re-training, combining the efficiency of ODEs with the stochastic evolution of SDEs. On large-scale text-to-image models, we show that GLASS Flows eliminate the trade-off between stochastic evolution and efficiency. Combined with Feynman-Kac Steering, GLASS Flows improve state-of-the-art performance in text-to-image generation, making it a simple, drop-in solution for inference-time scaling of flow and diffusion models.

cs.LG↗
arXiv2026

FragmentFlow: Scalable Transition State Generation for Large Molecules

Transition states (TSs) are central to understanding and quantitatively predicting chemical reactivity and reaction mechanisms. Although traditional TS generation methods are computationally expensive, recent generative modeling approaches have enabled chemically meaningful TS prediction for relatively small molecules. However, these methods fail to generalize to practically relevant reaction substrates because of distribution shifts induced by increasing molecular sizes. Furthermore, TS geometries for larger molecules are not available at scale, making it infeasible to train generative models from scratch on such molecules. To address these challenges, we introduce FragmentFlow: a divide-and-conquer approach that trains a generative model to predict TS geometries for the reactive core atoms, which define the reaction mechanism. The full TS structure is then reconstructed by re-attaching substituent fragments to the predicted core. By operating on reactive cores, whose size and composition remain relatively invariant across molecular contexts, FragmentFlow mitigates distribution shifts in generative modeling. Evaluated on a new curated dataset of reactions involving reactants with up to 33 heavy atoms, FragmentFlow correctly identifies 90% of TSs while requiring 30% fewer saddle-point optimization steps than classical initialization schemes. These results point toward scalable TS generation for high-throughput reactivity studies.

physics.chem-ph↗
arXiv2025

Flow Map Distillation Without Data

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 fundamental risk of Teacher-Data Mismatch, as a static dataset may provide an incomplete or even misaligned representation of the teacher's full generative capabilities. This leads us to question whether this reliance on data is truly necessary for successful flow map distillation. In this work, we explore a data-free alternative that samples only from the prior distribution, a distribution the teacher is guaranteed to follow by construction, thereby circumventing the mismatch risk entirely. To demonstrate the practical viability of this philosophy, we introduce a principled framework that learns to predict the teacher's sampling path while actively correcting for its own compounding errors to ensure high fidelity. Our approach surpasses all data-based counterparts and establishes a new state-of-the-art by a significant margin. Specifically, distilling from SiT-XL/2+REPA, our method reaches an impressive FID of 1.45 on ImageNet 256x256, and 1.49 on ImageNet 512x512, both with only 1 sampling step. We hope our work establishes a more robust paradigm for accelerating generative models and motivates the broader adoption of flow map distillation without data.

cs.LG↗
arXiv2025

HarnessLLM: Automatic Testing Harness Generation via Reinforcement Learning

Existing LLM-based automatic test generation methods mainly produce input and expected output pairs to categorize the intended behavior of correct programs. Although straightforward, these methods have limited diversity in generated tests and cannot provide enough debugging information. We propose HarnessLLM, a two-stage training pipeline that enables LLMs to write harness code for testing. Particularly, LLMs generate code that synthesizes inputs and validates the observed outputs, allowing complex test cases and flexible output validation such as invariant checking. To achieve this, we train LLMs with SFT followed by RLVR with a customized reward design. Experiments show that HarnessLLM outperforms input-output-based testing in bug finding and testing strategy diversity. HarnessLLM further benefits the code generation performance through test-time scaling with our generated test cases as inference-phase validation. Our code is available at https://github.com/UCSB-NLP-Chang/HarnessLLM.git.

cs.SE↗
arXiv2025

Learning Diffusion Models with Flexible Representation Guidance

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 present a systematic framework for incorporating representation guidance into diffusion models. We provide alternative decompositions of denoising models along with their associated training criteria, where the decompositions determine when and how the auxiliary representations are incorporated. Guided by our theoretical insights, we introduce two new strategies for enhancing representation alignment in diffusion models. First, we pair examples with target representations either derived from themselves or arisen from different synthetic modalities, and subsequently learn a joint model over the multimodal pairs. Second, we design an optimal training curriculum that balances representation learning and data generation. Our experiments across image, protein sequence, and molecule generation tasks demonstrate superior performance as well as accelerated training. In particular, on the class-conditional ImageNet $256\times 256$ benchmark, our guidance results in $23.3$ times faster training than the original SiT-XL as well as four times speedup over the state-of-the-art method REPA. The code is available at https://github.com/ChenyuWang-Monica/REED.

cs.LG↗
arXiv2025

Next Semantic Scale Prediction via Hierarchical Diffusion Language Models

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 meanings. In the forward process, each token is independently perturbed to its higher-level ancestor with more abstract semantics according to the scheduler, while in the reverse process the model progressively predicts the next, more detailed semantics. Taken together, HDLM provides a general time-varying next semantic scale prediction process for language modeling. We derive closed-form expressions for the diffusion Evidence Lower Bound (ELBO), and show that HDLM can be implemented in a flexible manner while including the existing MDLM as a special case. We also propose practical training techniques based on the insights. Extensive text generation experiments validate the effectiveness of HDLM, which demonstrates consistently lower validation and generative perplexity than baselines.

cs.CL↗