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Chris Maddison

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10 papers

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NeurIPS Conference 2025 Conference Paper

A Geometric Analysis of PCA

Ayoub El Hanchi
Murat Erdogdu
Chris Maddison

What property of the data distribution determines the excess risk of principal component analysis? In this paper, we provide a precise answer to this question. We establish a central limit theorem for the error of the principal subspace estimated by PCA, and derive the asymptotic distribution of its excess risk under the reconstruction loss. We obtain a non-asymptotic upper bound on the excess risk of PCA that recovers, in the large sample limit, our asymptotic characterization. Underlying our contributions is the following result: we prove that the negative block Rayleigh quotient, defined on the Grassmannian, is generalized self-concordant along geodesics emanating from its minimizer of maximum rotation less than $\pi/4$.

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NeurIPS Conference 2025 Conference Paper

BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model

Adibvafa Fallahpour
Andrew Magnuson
Purav Gupta
Shihao Ma
Jack Naimer
Arnav Shah
Haonan Duan
Omar Ibrahim

Unlocking deep and interpretable biological reasoning from complex genomic data remains a major AI challenge limiting scientific progress. While current DNA foundation models excel at representing sequences, they struggle with multi-step reasoning and lack transparent, biologically meaningful explanations. BioReason addresses this by tightly integrating a DNA foundation model with a large language model (LLM), enabling the LLM to directly interpret and reason over genomic information. Through supervised fine-tuning and reinforcement learning, BioReason learns to produce logical, biologically coherent deductions. It achieves major performance gains, boosting KEGG-based disease pathway prediction accuracy from 86% to 98% and improving variant effect prediction by an average of 15% over strong baselines. BioReason can reason over unseen biological entities and explain its decisions step by step, offering a transformative framework for interpretable, mechanistic AI in biology. All data, code, and checkpoints are available at https: //github. com/bowang-lab/BioReason.

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NeurIPS Conference 2025 Conference Paper

Measuring Scientific Capabilities of Language Models with a Systems Biology Dry Lab

Haonan Duan
Stephen Lu
Caitlin F Harrigan
Nishkrit Desai
Jiarui Lu
Michał Koziarski
Leonardo Cotta
Chris Maddison

Designing experiments and result interpretations are core scientific competencies, particularly in biology, where researchers perturb complex systems to uncover the underlying systems. Recent efforts to evaluate the scientific capabilities of large language models (LLMs) fail to test these competencies because wet-lab experimentation is prohibitively expensive: in expertise, time and equipment. We introduce SciGym, a first-in-class benchmark that assesses LLMs' iterative experiment design and analysis abilities in open-ended scientific discovery tasks. SciGym overcomes the challenge of wet-lab costs by running a dry lab of biological systems. These models, encoded in Systems Biology Markup Language, are efficient for generating simulated data, making them ideal testbeds for experimentation on realistically complex systems. We evaluated six frontier LLMs on 137 small systems, and released a total of 350 systems at https: //huggingface. co/datasets/h4duan/scigym-sbml. Our evaluation shows that while more capable models demonstrated superior performance, all models' performance declined significantly as system complexity increased, suggesting substantial room for improvement in the scientific capabilities of LLM agents.

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AAAI Conference 2021 Conference Paper

Learning Branching Heuristics for Propositional Model Counting

Pashootan Vaezipoor
Gil Lederman
Yuhuai Wu
Chris Maddison
Roger B Grosse
Sanjit A. Seshia
Fahiem Bacchus

Propositional model counting, or #SAT, is the problem of computing the number of satisfying assignments of a Boolean formula. Many problems from different application areas, including many discrete probabilistic inference problems, can be translated into model counting problems to be solved by #SAT solvers. Exact #SAT solvers, however, are often not scalable to industrial size instances. In this paper, we present Neuro#, an approach for learning branching heuristics to improve the performance of exact #SAT solvers on instances from a given family of problems. We experimentally show that our method reduces the step count on similarly distributed held-out instances and generalizes to much larger instances from the same problem family. It is able to achieve these results on a number of different problem families having very different structures. In addition to step count improvements, Neuro# can also achieve orders of magnitude wall-clock speedups over the vanilla solver on larger instances in some problem families, despite the runtime overhead of querying the model.

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NeurIPS Conference 2019 Conference Paper

Continuous Hierarchical Representations with Poincaré Variational Auto-Encoders

Emile Mathieu
Charline Le Lan
Chris Maddison
Ryota Tomioka
Yee Whye Teh

The Variational Auto-Encoder (VAE) is a popular method for learning a generative model and embeddings of the data. Many real datasets are hierarchically structured. However, traditional VAEs map data in a Euclidean latent space which cannot efficiently embed tree-like structures. Hyperbolic spaces with negative curvature can. We therefore endow VAEs with a Poincaré ball model of hyperbolic geometry as a latent space and rigorously derive the necessary methods to work with two main Gaussian generalisations on that space. We empirically show better generalisation to unseen data than the Euclidean counterpart, and can qualitatively and quantitatively better recover hierarchical structures.

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NeurIPS Conference 2019 Conference Paper

Hamiltonian descent for composite objectives

Brendan O'Donoghue
Chris Maddison

In optimization the duality gap between the primal and the dual problems is a measure of the suboptimality of any primal-dual point. In classical mechanics the equations of motion of a system can be derived from the Hamiltonian function, which is a quantity that describes the total energy of the system. In this paper we consider a convex optimization problem consisting of the sum of two convex functions, sometimes referred to as a composite objective, and we identify the duality gap to be the `energy' of the system. In the Hamiltonian formalism the energy is conserved, so we add a contractive term to the standard equations of motion so that this energy decreases linearly (ie, geometrically) with time. This yields a continuous-time ordinary differential equation (ODE) in the primal and dual variables which converges to zero duality gap, ie, optimality. This ODE has several useful properties: it induces a natural operator splitting; at convergence it yields both the primal and dual solutions; and it is invariant to affine transformation despite only using first order information. We provide several discretizations of this ODE, some of which are new algorithms and others correspond to known techniques, such as the alternating direction method of multipliers (ADMM). We conclude with some numerical examples that show the promise of our approach. We give an example where our technique can solve a convex quadratic minimization problem orders of magnitude faster than several commonly-used gradient methods, including conjugate gradient, when the conditioning of the problem is poor. Our framework provides new insights into previously known algorithms in the literature as well as providing a technique to generate new primal-dual algorithms.

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NeurIPS Conference 2017 Conference Paper

Filtering Variational Objectives

Chris Maddison
John Lawson
George Tucker
Nicolas Heess
Mohammad Norouzi
Andriy Mnih
Arnaud Doucet
Yee Teh

When used as a surrogate objective for maximum likelihood estimation in latent variable models, the evidence lower bound (ELBO) produces state-of-the-art results. Inspired by this, we consider the extension of the ELBO to a family of lower bounds defined by a particle filter's estimator of the marginal likelihood, the filtering variational objectives (FIVOs). FIVOs take the same arguments as the ELBO, but can exploit a model's sequential structure to form tighter bounds. We present results that relate the tightness of FIVO's bound to the variance of the particle filter's estimator by considering the generic case of bounds defined as log-transformed likelihood estimators. Experimentally, we show that training with FIVO results in substantial improvements over training the same model architecture with the ELBO on sequential data.

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NeurIPS Conference 2017 Conference Paper

REBAR: Low-variance, unbiased gradient estimates for discrete latent variable models

George Tucker
Andriy Mnih
Chris Maddison
John Lawson
Jascha Sohl-Dickstein

Learning in models with discrete latent variables is challenging due to high variance gradient estimators. Generally, approaches have relied on control variates to reduce the variance of the REINFORCE estimator. Recent work \citep{jang2016categorical, maddison2016concrete} has taken a different approach, introducing a continuous relaxation of discrete variables to produce low-variance, but biased, gradient estimates. In this work, we combine the two approaches through a novel control variate that produces low-variance, \emph{unbiased} gradient estimates. Then, we introduce a modification to the continuous relaxation and show that the tightness of the relaxation can be adapted online, removing it as a hyperparameter. We show state-of-the-art variance reduction on several benchmark generative modeling tasks, generally leading to faster convergence to a better final log-likelihood.

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NeurIPS Conference 2014 Conference Paper

A* Sampling

Chris Maddison
Daniel Tarlow
Tom Minka

The problem of drawing samples from a discrete distribution can be converted into a discrete optimization problem. In this work, we show how sampling from a continuous distribution can be converted into an optimization problem over continuous space. Central to the method is a stochastic process recently described in mathematical statistics that we call the Gumbel process. We present a new construction of the Gumbel process and A* sampling, a practical generic sampling algorithm that searches for the maximum of a Gumbel process using A* search. We analyze the correctness and convergence time of A* sampling and demonstrate empirically that it makes more efficient use of bound and likelihood evaluations than the most closely related adaptive rejection sampling-based algorithms.

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NeurIPS Conference 2013 Conference Paper

Annealing between distributions by averaging moments

Roger Grosse
Chris Maddison
Russ Salakhutdinov

Many powerful Monte Carlo techniques for estimating partition functions, such as annealed importance sampling (AIS), are based on sampling from a sequence of intermediate distributions which interpolate between a tractable initial distribution and an intractable target distribution. The near-universal practice is to use geometric averages of the initial and target distributions, but alternative paths can perform substantially better. We present a novel sequence of intermediate distributions for exponential families: averaging the moments of the initial and target distributions. We derive an asymptotically optimal piecewise linear schedule for the moments path and show that it performs at least as well as geometric averages with a linear schedule. Moment averaging performs well empirically at estimating partition functions of restricted Boltzmann machines (RBMs), which form the building blocks of many deep learning models, including Deep Belief Networks and Deep Boltzmann Machines.

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