Madeleine Udell

Joseph Stitt, Pratik Rathore, Madeleine Udell et al.

Full waveform inversion (FWI) is the gold standard for subsurface imaging, with applications from carbon sequestration to energy and mineral exploration to earthquake hazard assessment. Machine learning approaches to FWI need field-scale, geologically diverse, and physically realistic training data, but existing resources such as Marmousi, SEAM, and OpenFWI fall short on spatial extent, temporal extent, geological diversity, and physical realism. We address these limitations with SubsurfaceGen, a GPU-accelerated generator for 3D velocity models and seismic data. Along with SubsurfaceGen, we release a paired dataset of 4,276 2D velocity slices, 5 s wavefields, and 8 s shot gathers drawn from 42 realistic, field-scale 3D velocity models, each spanning 10 km x 10 km laterally and 6.19 km deep at 10 m resolution. The dataset spans six geological settings -- four built with SubsurfaceGen and two drawn from prior sources -- relevant for carbon sequestration and hydrocarbon exploration. We use this dataset to evaluate neural operators on wavefield prediction and encoder-decoders on end-to-end velocity inversion, holding out one geological setting for out-of-distribution testing. These experiments surface failure modes at field-scale and demonstrate how SubsurfaceGen and the associated dataset can impact ML-based FWI.

Sarah J. Zhang, Samuel Florin, Ariel N. Lee et al.

We curate a comprehensive dataset of 4,550 questions and solutions from problem sets, midterm exams, and final exams across all MIT Mathematics and Electrical Engineering and Computer Science (EECS) courses required for obtaining a degree. We evaluate the ability of large language models to fulfill the graduation requirements for any MIT major in Mathematics and EECS. Our results demonstrate that GPT-3.5 successfully solves a third of the entire MIT curriculum, while GPT-4, with prompt engineering, achieves a perfect solve rate on a test set excluding questions based on images. We fine-tune an open-source large language model on this dataset. We employ GPT-4 to automatically grade model responses, providing a detailed performance breakdown by course, question, and answer type. By embedding questions in a low-dimensional space, we explore the relationships between questions, topics, and classes and discover which questions and classes are required for solving other questions and classes through few-shot learning. Our analysis offers valuable insights into course prerequisites and curriculum design, highlighting language models' potential for learning and improving Mathematics and EECS education.

Chengrun Yang, Gabriel Bender, Hanxiao Liu et al. · deepmind

The best neural architecture for a given machine learning problem depends on many factors: not only the complexity and structure of the dataset, but also on resource constraints including latency, compute, energy consumption, etc. Neural architecture search (NAS) for tabular datasets is an important but under-explored problem. Previous NAS algorithms designed for image search spaces incorporate resource constraints directly into the reinforcement learning (RL) rewards. However, for NAS on tabular datasets, this protocol often discovers suboptimal architectures. This paper develops TabNAS, a new and more effective approach to handle resource constraints in tabular NAS using an RL controller motivated by the idea of rejection sampling. TabNAS immediately discards any architecture that violates the resource constraints without training or learning from that architecture. TabNAS uses a Monte-Carlo-based correction to the RL policy gradient update to account for this extra filtering step. Results on several tabular datasets demonstrate the superiority of TabNAS over previous reward-shaping methods: it finds better models that obey the constraints.

Joel A. Tropp, Alp Yurtsever, Madeleine Udell et al.

This paper argues that randomized linear sketching is a natural tool for on-the-fly compression of data matrices that arise from large-scale scientific simulations and data collection. The technical contribution consists in a new algorithm for constructing an accurate low-rank approximation of a matrix from streaming data. This method is accompanied by an a priori analysis that allows the user to set algorithm parameters with confidence and an a posteriori error estimator that allows the user to validate the quality of the reconstructed matrix. In comparison to previous techniques, the new method achieves smaller relative approximation errors and is less sensitive to parameter choices. As concrete applications, the paper outlines how the algorithm can be used to compress a Navier--Stokes simulation and a sea surface temperature dataset.

Ali AhmadiTeshnizi, Wenzhi Gao, Madeleine Udell

Optimization problems are pervasive across various sectors, from manufacturing and distribution to healthcare. However, most such problems are still solved heuristically by hand rather than optimally by state-of-the-art solvers, as the expertise required to formulate and solve these problems limits the widespread adoption of optimization tools and techniques. We introduce OptiMUS, a Large Language Model (LLM)-based agent designed to formulate and solve MILP problems from their natural language descriptions. OptiMUS is capable of developing mathematical models, writing and debugging solver code, developing tests, and checking the validity of generated solutions. To benchmark our agent, we present NLP4LP, a novel dataset of linear programming (LP) and mixed integer linear programming (MILP) problems. Our experiments demonstrate that OptiMUS solves nearly twice as many problems as a basic LLM prompting strategy. OptiMUS code and NLP4LP dataset are available at \href{https://github.com/teshnizi/OptiMUS}{https://github.com/teshnizi/OptiMUS}

Iddo Drori, Sarah J. Zhang, Reece Shuttleworth et al. · harvard

A final exam in machine learning at a top institution such as MIT, Harvard, or Cornell typically takes faculty days to write, and students hours to solve. We demonstrate that large language models pass machine learning finals at a human level, on finals available online after the models were trained, and automatically generate new human-quality final exam questions in seconds. Previous work has developed program synthesis and few-shot learning methods to solve university-level problem set questions in mathematics and STEM courses. In this work, we develop and compare methods that solve final exams, which differ from problem sets in several ways: the questions are longer, have multiple parts, are more complicated, and span a broader set of topics. We curate a dataset and benchmark of questions from machine learning final exams available online and code for answering these questions and generating new questions. We show how to generate new questions from other questions and course notes. For reproducibility and future research on this final exam benchmark, we use automatic checkers for multiple-choice, numeric, and questions with expression answers. We perform ablation studies comparing zero-shot learning with few-shot learning and chain-of-thought prompting using GPT-3, OPT, Codex, and ChatGPT across machine learning topics and find that few-shot learning methods perform best. We highlight the transformative potential of language models to streamline the writing and solution of large-scale assessments, significantly reducing the workload from human days to mere machine seconds. Our results suggest that rather than banning large language models such as ChatGPT in class, instructors should teach students to harness them by asking students meta-questions about correctness, completeness, and originality of the responses generated, encouraging critical thinking in academic studies.

Brian Liu, Miaolan Xie, Haoyue Yang et al.

ControlBurn is a Python package to construct feature-sparse tree ensembles that support nonlinear feature selection and interpretable machine learning. The algorithms in this package first build large tree ensembles that prioritize basis functions with few features and then select a feature-sparse subset of these basis functions using a weighted lasso optimization criterion. The package includes visualizations to analyze the features selected by the ensemble and their impact on predictions. Hence ControlBurn offers the accuracy and flexibility of tree-ensemble models and the interpretability of sparse generalized additive models. ControlBurn is scalable and flexible: for example, it can use warm-start continuation to compute the regularization path (prediction error for any number of selected features) for a dataset with tens of thousands of samples and hundreds of features in seconds. For larger datasets, the runtime scales linearly in the number of samples and features (up to a log factor), and the package support acceleration using sketching. Moreover, the ControlBurn framework accommodates feature costs, feature groupings, and $\ell_0$-based regularizers. The package is user-friendly and open-source: its documentation and source code appear on https://pypi.org/project/ControlBurn/ and https://github.com/udellgroup/controlburn/.

Chun-Hao Chang, Jinsung Yoon, Sercan Arik et al.

Anomaly detection (AD) plays an important role in numerous applications. We focus on two understudied aspects of AD that are critical for integration into real-world applications. First, most AD methods cannot incorporate labeled data that are often available in practice in small quantities and can be crucial to achieve high AD accuracy. Second, most AD methods are not interpretable, a bottleneck that prevents stakeholders from understanding the reason behind the anomalies. In this paper, we propose a novel AD framework that adapts a white-box model class, Generalized Additive Models, to detect anomalies using a partial identification objective which naturally handles noisy or heterogeneous features. In addition, the proposed framework, DIAD, can incorporate a small amount of labeled data to further boost anomaly detection performances in semi-supervised settings. We demonstrate the superiority of our framework compared to previous work in both unsupervised and semi-supervised settings using diverse tabular datasets. For example, under 5 labeled anomalies DIAD improves from 86.2\% to 89.4\% AUC by learning AD from unlabeled data. We also present insightful interpretations that explain why DIAD deems certain samples as anomalies.

Shaghayegh Fazliani, Krissh Chawla, Jack Guo et al.

Rapid progress in aerodynamic shape optimization (ASO) has outpaced currently-available standardized evaluation frameworks. Fair comparison requires a unified benchmark spanning diverse shape classes, objective formulations, and matched-budget state-of-the-art baselines. We introduce ShapeBench, an open-source ASO benchmark with a unified API spanning 103 tasks across eight shape categories and multiple optimization regimes. Each ShapeBench task includes a validated surrogate for fast search; when feasible, a high-fidelity Computational Fluid Dynamics (CFD) pipeline for final verification is available, enabling systematic fidelity-gap analysis. ShapeBench provides a reproducible protocol with well-configured baselines to compare fairly using a consistent budget metric, allowing for comparison among both classical and LLM-driven methods, including general-purpose optimizers and a new domain-specialized evolutionary LLM baseline, ShapeEvolve. Results on ShapeBench demonstrate substantial variance in optimizer rankings across shape categories and problem formulations, with mean pairwise Spearman $ρ= 0.013$, so single-task conclusions do not reliably generalize across problem classes. The benchmark is also far from saturation; classical methods are rarely applicable across all shape categories and tasks, further highlighting the need for more general-purpose approaches.

Keith Tyser, Ben Segev, Gaston Longhitano et al.

Automatic reviewing helps handle a large volume of papers, provides early feedback and quality control, reduces bias, and allows the analysis of trends. We evaluate the alignment of automatic paper reviews with human reviews using an arena of human preferences by pairwise comparisons. Gathering human preference may be time-consuming; therefore, we also use an LLM to automatically evaluate reviews to increase sample efficiency while reducing bias. In addition to evaluating human and LLM preferences among LLM reviews, we fine-tune an LLM to predict human preferences, predicting which reviews humans will prefer in a head-to-head battle between LLMs. We artificially introduce errors into papers and analyze the LLM's responses to identify limitations, use adaptive review questions, meta prompting, role-playing, integrate visual and textual analysis, use venue-specific reviewing materials, and predict human preferences, improving upon the limitations of the traditional review processes. We make the reviews of publicly available arXiv and open-access Nature journal papers available online, along with a free service which helps authors review and revise their research papers and improve their quality. This work develops proof-of-concept LLM reviewing systems that quickly deliver consistent, high-quality reviews and evaluate their quality. We mitigate the risks of misuse, inflated review scores, overconfident ratings, and skewed score distributions by augmenting the LLM with multiple documents, including the review form, reviewer guide, code of ethics and conduct, area chair guidelines, and previous year statistics, by finding which errors and shortcomings of the paper may be detected by automated reviews, and evaluating pairwise reviewer preferences. This work identifies and addresses the limitations of using LLMs as reviewers and evaluators and enhances the quality of the reviewing process.

Mike Van Ness, Tomas M. Bosschieter, Roberto Halpin-Gregorio et al.

Missing data is common in applied data science, particularly for tabular data sets found in healthcare, social sciences, and natural sciences. Most supervised learning methods only work on complete data, thus requiring preprocessing such as missing value imputation to work on incomplete data sets. However, imputation alone does not encode useful information about the missing values themselves. For data sets with informative missing patterns, the Missing Indicator Method (MIM), which adds indicator variables to indicate the missing pattern, can be used in conjunction with imputation to improve model performance. While commonly used in data science, MIM is surprisingly understudied from an empirical and especially theoretical perspective. In this paper, we show empirically and theoretically that MIM improves performance for informative missing values, and we prove that MIM does not hurt linear models asymptotically for uninformative missing values. Additionally, we find that for high-dimensional data sets with many uninformative indicators, MIM can induce model overfitting and thus test performance. To address this issue, we introduce Selective MIM (SMIM), a novel MIM extension that adds missing indicators only for features that have informative missing patterns. We show empirically that SMIM performs at least as well as MIM in general, and improves MIM for high-dimensional data. Lastly, to demonstrate the utility of MIM on real-world data science tasks, we demonstrate the effectiveness of MIM and SMIM on clinical tasks generated from the MIMIC-III database of electronic health records.

Zachary Frangella, Pratik Rathore, Shipu Zhao et al.

SketchySGD improves upon existing stochastic gradient methods in machine learning by using randomized low-rank approximations to the subsampled Hessian and by introducing an automated stepsize that works well across a wide range of convex machine learning problems. We show theoretically that SketchySGD with a fixed stepsize converges linearly to a small ball around the optimum. Further, in the ill-conditioned setting we show SketchySGD converges at a faster rate than SGD for least-squares problems. We validate this improvement empirically with ridge regression experiments on real data. Numerical experiments on both ridge and logistic regression problems with dense and sparse data, show that SketchySGD equipped with its default hyperparameters can achieve comparable or better results than popular stochastic gradient methods, even when they have been tuned to yield their best performance. In particular, SketchySGD is able to solve an ill-conditioned logistic regression problem with a data matrix that takes more than $840$GB RAM to store, while its competitors, even when tuned, are unable to make any progress. SketchySGD's ability to work out-of-the box with its default hyperparameters and excel on ill-conditioned problems is an advantage over other stochastic gradient methods, most of which require careful hyperparameter tuning (especially of the learning rate) to obtain good performance and degrade in the presence of ill-conditioning.

Ali AhmadiTeshnizi, Wenzhi Gao, Herman Brunborg et al.

Optimization problems are pervasive in sectors from manufacturing and distribution to healthcare. However, most such problems are still solved heuristically by hand rather than optimally by state-of-the-art solvers because the expertise required to formulate and solve these problems limits the widespread adoption of optimization tools and techniques. We introduce a Large Language Model (LLM)-based system designed to formulate and solve (mixed integer) linear programming problems from their natural language descriptions. Our system is capable of developing mathematical models, writing and debugging solver code, evaluating the generated solutions, and improving efficiency and correctness of its model and code based on these evaluations. OptiMUS-0.3 utilizes a modular structure to process problems, allowing it to handle problems with long descriptions and complex data without long prompts. Experiments demonstrate that OptiMUS-0.3 outperforms existing state-of-the-art methods on easy datasets by more than 22% and on hard datasets (including a new dataset, NLP4LP, released with this paper that features long and complex problems) by more than 24%.

Zachary Frangella, Pratik Rathore, Shipu Zhao et al.

This paper introduces PROMISE ($\textbf{Pr}$econditioned Stochastic $\textbf{O}$ptimization $\textbf{M}$ethods by $\textbf{I}$ncorporating $\textbf{S}$calable Curvature $\textbf{E}$stimates), a suite of sketching-based preconditioned stochastic gradient algorithms for solving large-scale convex optimization problems arising in machine learning. PROMISE includes preconditioned versions of SVRG, SAGA, and Katyusha; each algorithm comes with a strong theoretical analysis and effective default hyperparameter values. In contrast, traditional stochastic gradient methods require careful hyperparameter tuning to succeed, and degrade in the presence of ill-conditioning, a ubiquitous phenomenon in machine learning. Empirically, we verify the superiority of the proposed algorithms by showing that, using default hyperparameter values, they outperform or match popular tuned stochastic gradient optimizers on a test bed of $51$ ridge and logistic regression problems assembled from benchmark machine learning repositories. On the theoretical side, this paper introduces the notion of quadratic regularity in order to establish linear convergence of all proposed methods even when the preconditioner is updated infrequently. The speed of linear convergence is determined by the quadratic regularity ratio, which often provides a tighter bound on the convergence rate compared to the condition number, both in theory and in practice, and explains the fast global linear convergence of the proposed methods.

Pratik Rathore, Zachary Frangella, Jiaming Yang et al.

Kernel ridge regression (KRR) is a fundamental computational tool, appearing in problems that range from computational chemistry to health analytics, with a particular interest due to its starring role in Gaussian process regression. However, full KRR solvers are challenging to scale to large datasets: both direct (i.e., Cholesky decomposition) and iterative methods (i.e., PCG) incur prohibitive computational and storage costs. The standard approach to scale KRR to large datasets chooses a set of inducing points and solves an approximate version of the problem, inducing points KRR. However, the resulting solution tends to have worse predictive performance than the full KRR solution. In this work, we introduce a new solver, ASkotch, for full KRR that provides better solutions faster than state-of-the-art solvers for full and inducing points KRR. ASkotch is a scalable, accelerated, iterative method for full KRR that provably obtains linear convergence. Under appropriate conditions, we show that ASkotch obtains condition-number-free linear convergence. This convergence analysis rests on the theory of ridge leverage scores and determinantal point processes. ASkotch outperforms state-of-the-art KRR solvers on a testbed of 23 large-scale KRR regression and classification tasks derived from a wide range of application domains, demonstrating the superiority of full KRR over inducing points KRR. Our work opens up the possibility of as-yet-unimagined applications of full KRR across a number of disciplines.

Mike Van Ness, Tomas Bosschieter, Natasha Din et al.

Survival analysis, or time-to-event analysis, is an important and widespread problem in healthcare research. Medical research has traditionally relied on Cox models for survival analysis, due to their simplicity and interpretability. Cox models assume a log-linear hazard function as well as proportional hazards over time, and can perform poorly when these assumptions fail. Newer survival models based on machine learning avoid these assumptions and offer improved accuracy, yet sometimes at the expense of model interpretability, which is vital for clinical use. We propose a novel survival analysis pipeline that is both interpretable and competitive with state-of-the-art survival models. Specifically, we use an improved version of survival stacking to transform a survival analysis problem to a classification problem, ControlBurn to perform feature selection, and Explainable Boosting Machines to generate interpretable predictions. To evaluate our pipeline, we predict risk of heart failure using a large-scale EHR database. Our pipeline achieves state-of-the-art performance and provides interesting and novel insights about risk factors for heart failure.

Wenzhi Gao, Chang He, Madeleine Udell

This paper introduces a new problem-dependent regret measure for online convex optimization with smooth losses. The notion, which we call the $G^\star$ regret, depends on the cumulative squared gradient norm evaluated at the decision in hindsight $\sum_{t=1}^T \|\nabla \ell(x^\star)\|^2$. We show that the $G^\star$ regret strictly refines the existing $L^\star$ (small loss) regret, and that it can be arbitrarily sharper when the losses have vanishing curvature around the hindsight decision. We establish upper and lower bounds on the $G^\star$ regret and extend our results to dynamic regret and bandit settings. As a byproduct, we refine the existing convergence analysis of stochastic optimization algorithms in the interpolation regime. Some experiments validate our theoretical findings.

Ya-Chi Chu, Alkiviades Boukas, Madeleine Udell

Neural networks are increasingly used as surrogate solvers and control policies, but unconstrained predictions can violate physical, operational, or safety requirements. We propose SnareNet, a feasibility-controlled architecture for learning mappings whose outputs must satisfy input-dependent nonlinear constraints. SnareNet appends a differentiable repair layer that navigates in the constraint map's range space, steering iterates toward feasibility and producing a repaired output that satisfies constraints to a user-specified tolerance. To stabilize end-to-end training, we introduce adaptive relaxation, which designs a relaxed feasible set that snares the neural network at initialization and shrinks it into the feasible set, enabling early exploration and strict feasibility later in training. On optimization-learning and trajectory planning benchmarks, SnareNet consistently attains improved objective quality while satisfying constraints more reliably than prior work.

Pratik Rathore, Weimu Lei, Zachary Frangella et al.

This paper explores challenges in training Physics-Informed Neural Networks (PINNs), emphasizing the role of the loss landscape in the training process. We examine difficulties in minimizing the PINN loss function, particularly due to ill-conditioning caused by differential operators in the residual term. We compare gradient-based optimizers Adam, L-BFGS, and their combination Adam+L-BFGS, showing the superiority of Adam+L-BFGS, and introduce a novel second-order optimizer, NysNewton-CG (NNCG), which significantly improves PINN performance. Theoretically, our work elucidates the connection between ill-conditioned differential operators and ill-conditioning in the PINN loss and shows the benefits of combining first- and second-order optimization methods. Our work presents valuable insights and more powerful optimization strategies for training PINNs, which could improve the utility of PINNs for solving difficult partial differential equations.

Shaghayegh Fazliani, Madeleine Udell

Current LLM-driven approaches using test-time computing to generate PDE solvers execute a large number of solver samples to identify high-accuracy solvers. These paradigms are especially costly for complex PDEs requiring substantial computational resources for numerical evaluation. We introduce PDE-SHARP, a framework to reduce computational costs by replacing expensive scientific computation by cheaper LLM inference that achieves superior solver accuracy with 60-75% fewer computational evaluations. PDE-SHARP employs three stages: (1) Analysis: mathematical chain-of-thought analysis including PDE classification, solution type detection, and stability analysis; (2) Genesis: solver generation based on mathematical insights from the previous stage; and (3) Synthesis: collaborative selection-hybridization tournaments in which LLM judges iteratively refine implementations through flexible performance feedback. To generate high-quality solvers, PDE-SHARP requires fewer than 13 solver evaluations on average compared to 30+ for baseline methods, improving accuracy uniformly across tested PDEs by $4\times$ on average, and demonstrates robust performance across LLM architectures, from general-purpose to specialized reasoning models.

Ali AhmadiTeshnizi, Wenzhi Gao, Madeleine Udell

Optimization problems are pervasive in sectors from manufacturing and distribution to healthcare. However, most such problems are still solved heuristically by hand rather than optimally by state-of-the-art solvers because the expertise required to formulate and solve these problems limits the widespread adoption of optimization tools and techniques. This paper introduces OptiMUS, a Large Language Model (LLM)-based agent designed to formulate and solve (mixed integer) linear programming problems from their natural language descriptions. OptiMUS can develop mathematical models, write and debug solver code, evaluate the generated solutions, and improve its model and code based on these evaluations. OptiMUS utilizes a modular structure to process problems, allowing it to handle problems with long descriptions and complex data without long prompts. Experiments demonstrate that OptiMUS outperforms existing state-of-the-art methods on easy datasets by more than $20\%$ and on hard datasets (including a new dataset, NLP4LP, released with this paper that features long and complex problems) by more than $30\%$.

Wenzhi Gao, Ya-Chi Chu, Yinyu Ye et al.

We introduce a framework to accelerate the convergence of gradient-based methods with online learning. The framework learns to scale the gradient at each iteration through an online learning algorithm and provably accelerates gradient-based methods asymptotically. In contrast with previous literature, where convergence is established based on worst-case analysis, our framework provides a strong convergence guarantee with respect to the optimal scaling matrix for the iteration trajectory. For smooth strongly convex optimization, our results provide an $O(κ^\star \log(1/\varepsilon)$) complexity result, where $κ^\star$ is the condition number achievable by the optimal preconditioner, improving on the previous $O(\sqrt{n}κ^\star \log(1/\varepsilon))$ result. In particular, a variant of our method achieves superlinear convergence on convex quadratics. For smooth convex optimization, we show for the first time that the widely-used hypergradient descent heuristic improves on the convergence of gradient descent.

Connor Lawless, Yingxi Li, Anders Wikum et al.

Mixed integer linear programming (MILP) solvers expose hundreds of parameters that have an outsized impact on performance but are difficult to configure for all but expert users. Existing machine learning (ML) approaches require training on thousands of related instances, generalize poorly and can be difficult to integrate into existing solver workflows. We propose a large language model (LLM)-based framework that configures cutting plane separators using problem descriptions and solver-specific separator summaries. To reduce variance in LLM outputs, we introduce an ensembling strategy that clusters and aggregates candidate configurations into a small portfolio of high-performing configurations. Our method requires no custom solver interface, generates configurations in seconds via simple API calls, and requires solving only a small number of instances. Extensive experiments on standard synthetic and real-world MILPs show our approach matches or outperforms state-of-the-art configuration methods with a fraction of the data and computation.

Ya-Chi Chu, Wenzhi Gao, Yinyu Ye et al.

This paper investigates the convergence properties of the hypergradient descent method (HDM), a 25-year-old heuristic originally proposed for adaptive stepsize selection in stochastic first-order methods. We provide the first rigorous convergence analysis of HDM using the online learning framework of [Gao24] and apply this analysis to develop new state-of-the-art adaptive gradient methods with empirical and theoretical support. Notably, HDM automatically identifies the optimal stepsize for the local optimization landscape and achieves local superlinear convergence. Our analysis explains the instability of HDM reported in the literature and proposes efficient strategies to address it. We also develop two HDM variants with heavy-ball and Nesterov momentum. Experiments on deterministic convex problems show HDM with heavy-ball momentum (HDM-HB) exhibits robust performance and significantly outperforms other adaptive first-order methods. Moreover, HDM-HB often matches the performance of L-BFGS, an efficient and practical quasi-Newton method, using less memory and cheaper iterations.

Shaghayegh Fazliani, Zachary Frangella, Madeleine Udell

Physics-Informed Neural Networks (PINNs) seek to solve partial differential equations (PDEs) with deep learning. Mainstream approaches that deploy fully-connected multi-layer deep learning architectures require prolonged training to achieve even moderate accuracy, while recent work on feature engineering allows higher accuracy and faster convergence. This paper introduces SAFE-NET, a Single-layered Adaptive Feature Engineering NETwork that achieves orders-of-magnitude lower errors with far fewer parameters than baseline feature engineering methods. SAFE-NET returns to basic ideas in machine learning, using Fourier features, a simplified single hidden layer network architecture, and an effective optimizer that improves the conditioning of the PINN optimization problem. Numerical results show that SAFE-NET converges faster and typically outperforms deeper networks and more complex architectures. It consistently uses fewer parameters -- on average, 65% fewer than the competing feature engineering methods -- while achieving comparable accuracy in less than 30% of the training epochs. Moreover, each SAFE-NET epoch is 95% faster than those of competing feature engineering approaches. These findings challenge the prevailing belief that modern PINNs effectively learn features in these scientific applications and highlight the efficiency gains possible through feature engineering.

Wenzhi Gao, Ya-Chi Chu, Yinyu Ye et al.

This paper establishes the theoretical foundations of the online scaled gradient methods (OSGM), a framework that utilizes online learning to adapt stepsizes and provably accelerate first-order methods. OSGM quantifies the effectiveness of a stepsize by a feedback function motivated from a convergence measure and uses the feedback to adjust the stepsize through an online learning algorithm. Consequently, instantiations of OSGM achieve convergence rates that are asymptotically no worse than the optimal stepsize. OSGM yields desirable convergence guarantees on smooth convex problems, including 1) trajectory-dependent global convergence on smooth convex objectives; 2) an improved complexity result on smooth strongly convex problems, and 3) local superlinear convergence. Notably, OSGM constitutes a new family of first-order methods with non-asymptotic superlinear convergence, joining the celebrated quasi-Newton methods. Finally, OSGM explains the empirical success of the popular hypergradient-descent heuristic in optimization for machine learning.

Mike Van Ness, Madeleine Udell

Survival analysis is widely used as a technique to model time-to-event data when some data is censored, particularly in healthcare for predicting future patient risk. In such settings, survival models must be both accurate and interpretable so that users (such as doctors) can trust the model and understand model predictions. While most literature focuses on discrimination, interpretability is equally as important. A successful interpretable model should be able to describe how changing each feature impacts the outcome, and should only use a small number of features. In this paper, we present DyS (pronounced ``dice''), a new survival analysis model that achieves both strong discrimination and interpretability. DyS is a feature-sparse Generalized Additive Model, combining feature selection and interpretable prediction into one model. While DyS works well for all survival analysis problems, it is particularly useful for large (in $n$ and $p$) survival datasets such as those commonly found in observational healthcare studies. Empirical studies show that DyS competes with other state-of-the-art machine learning models for survival analysis, while being highly interpretable.

Pratik Rathore, Zachary Frangella, Sachin Garg et al.

Gaussian processes (GPs) play an essential role in biostatistics, scientific machine learning, and Bayesian optimization for their ability to provide probabilistic predictions and model uncertainty. However, GP inference struggles to scale to large datasets (which are common in modern applications), since it requires the solution of a linear system whose size scales quadratically with the number of samples in the dataset. We propose an approximate, distributed, accelerated sketch-and-project algorithm ($\texttt{ADASAP}$) for solving these linear systems, which improves scalability. We use the theory of determinantal point processes to show that the posterior mean induced by sketch-and-project rapidly converges to the true posterior mean. In particular, this yields the first efficient, condition number-free algorithm for estimating the posterior mean along the top spectral basis functions, showing that our approach is principled for GP inference. $\texttt{ADASAP}$ outperforms state-of-the-art solvers based on conjugate gradient and coordinate descent across several benchmark datasets and a large-scale Bayesian optimization task. Moreover, $\texttt{ADASAP}$ scales to a dataset with $> 3 \cdot 10^8$ samples, a feat which has not been accomplished in the literature.

Mike Van Ness, Billy Block, Madeleine Udell

Survival analysis is a classic problem in statistics with important applications in healthcare. Most machine learning models for survival analysis are black-box models, limiting their use in healthcare settings where interpretability is paramount. More recently, glass-box machine learning models have been introduced for survival analysis, with both strong predictive performance and interpretability. Still, several gaps remain, as no prior glass-box survival model can produce calibrated shape functions with enough flexibility to capture the complex patterns often found in real data. To fill this gap, we introduce a new glass-box machine learning model for survival analysis called DNAMite. DNAMite uses feature discretization and kernel smoothing in its embedding module, making it possible to learn shape functions with a flexible balance of smoothness and jaggedness. Further, DNAMite produces calibrated shape functions that can be directly interpreted as contributions to the cumulative incidence function. Our experiments show that DNAMite generates shape functions closer to true shape functions on synthetic data, while making predictions with comparable predictive performance and better calibration than previous glass-box and black-box models.

Connor Lawless, Tsui-Wei Weng, Berk Ustun et al.

Machine learning models can assign fixed predictions that preclude individuals from changing their outcome. Existing approaches to audit fixed predictions do so on a pointwise basis, which requires access to an existing dataset of individuals and may fail to anticipate fixed predictions in out-of-sample data. This work presents a new paradigm to identify fixed predictions by finding confined regions of the feature space in which all individuals receive fixed predictions. This paradigm enables the certification of recourse for out-of-sample data, works in settings without representative datasets, and provides interpretable descriptions of individuals with fixed predictions. We develop a fast method to discover confined regions for linear classifiers using mixed-integer quadratically constrained programming. We conduct a comprehensive empirical study of confined regions across diverse applications. Our results highlight that existing pointwise verification methods fail to anticipate future individuals with fixed predictions, while our method both identifies them and provides an interpretable description.

Jingruo Sun, Zachary Frangella, Madeleine Udell

Regularized empirical risk minimization (rERM) has become important in data-intensive fields such as genomics and advertising, with stochastic gradient methods typically used to solve the largest problems. However, ill-conditioned objectives and non-smooth regularizers undermine the performance of traditional stochastic gradient methods, leading to slow convergence and significant computational costs. To address these challenges, we propose the $\texttt{SAPPHIRE}$ ($\textbf{S}$ketching-based $\textbf{A}$pproximations for $\textbf{P}$roximal $\textbf{P}$reconditioning and $\textbf{H}$essian $\textbf{I}$nexactness with Variance-$\textbf{RE}$educed Gradients) algorithm, which integrates sketch-based preconditioning to tackle ill-conditioning and uses a scaled proximal mapping to minimize the non-smooth regularizer. This stochastic variance-reduced algorithm achieves condition-number-free linear convergence to the optimum, delivering an efficient and scalable solution for ill-conditioned composite large-scale convex machine learning problems. Extensive experiments on lasso and logistic regression demonstrate that $\texttt{SAPPHIRE}$ often converges $20$ times faster than other common choices such as $\texttt{Catalyst}$, $\texttt{SAGA}$, and $\texttt{SVRG}$. This advantage persists even when the objective is non-convex or the preconditioner is infrequently updated, highlighting its robust and practical effectiveness.

Ya-Chi Chu, Wenzhi Gao, Yinyu Ye et al.

Part I of this work [Gao25] establishes online scaled gradient methods (OSGM), a framework that utilizes online convex optimization to adapt stepsizes in gradient methods. This paper focuses on the practical aspects of OSGM. We leverage the OSGM framework to design new adaptive first-order methods and provide insights into their empirical behavior. The resulting method, OSGM-Best, matches the performance of quasi-Newton variants while requiring less memory and cheaper iterations. We also extend OSGM to nonconvex optimization and outline directions that connect OSGM to existing branches of optimization theory and practice.

Mike Van Ness, Madeleine Udell

Additive models offer accurate and interpretable predictions for tabular data, a critical tool for statistical modeling. Recent advances in Neural Additive Models (NAMs) allow these models to handle complex machine learning tasks, including feature selection and survival analysis, on large-scale data. This paper introduces dnamite, a Python package that implements NAMs for these advanced applications. dnamite provides a scikit-learn style interface to train regression, classification, and survival analysis NAMs, with built-in support for feature selection. We describe the methodology underlying dnamite, its design principles, and its implementation. Through an application to the MIMIC III clinical dataset, we demonstrate the utility of dnamite in a real-world setting where feature selection and survival analysis are both important. The package is publicly available via pip and documented at dnamite.readthedocs.io.

Iddo Drori, Gaston Longhitano, Mao Mao et al.

Reasoning LLMs such as OpenAI o1, o3 and DeepSeek R1 have made significant progress in mathematics and coding, yet find challenging advanced tasks such as International Mathematical Olympiad (IMO) combinatorics problems, Abstraction and Reasoning Corpus (ARC) puzzles, and Humanity's Last Exam (HLE) questions. We use a diverse inference approach that combines multiple models and methods at test time. We find that verifying mathematics and code problems, and rejection sampling on other problems is simple and effective. We automatically verify correctness of solutions to IMO problems by Lean, and ARC puzzles by code, and find that best-of-N effectively answers HLE questions. Our approach increases answer accuracy on IMO combinatorics problems from 33.3% to 77.8%, accuracy on HLE questions from 8% to 37%, and solves 80% of ARC puzzles that 948 humans could not and 26.5% of ARC puzzles that o3 high compute does not. Test-time simulations, reinforcement learning, and meta-learning with inference feedback improve generalization by adapting agent graph representations and varying prompts, code, and datasets. Our approach is reliable, robust, and scalable, and in the spirit of reproducible research, we will make it publicly available upon publication.

Vishnu Suresh Lokhande, Kihyuk Sohn, Jinsung Yoon et al.

Learning invariant representations is an important requirement when training machine learning models that are driven by spurious correlations in the datasets. These spurious correlations, between input samples and the target labels, wrongly direct the neural network predictions resulting in poor performance on certain groups, especially the minority groups. Robust training against these spurious correlations requires the knowledge of group membership for every sample. Such a requirement is impractical in situations where the data labeling efforts for minority or rare groups are significantly laborious or where the individuals comprising the dataset choose to conceal sensitive information. On the other hand, the presence of such data collection efforts results in datasets that contain partially labeled group information. Recent works have tackled the fully unsupervised scenario where no labels for groups are available. Thus, we aim to fill the missing gap in the literature by tackling a more realistic setting that can leverage partially available sensitive or group information during training. First, we construct a constraint set and derive a high probability bound for the group assignment to belong to the set. Second, we propose an algorithm that optimizes for the worst-off group assignments from the constraint set. Through experiments on image and tabular datasets, we show improvements in the minority group's performance while preserving overall aggregate accuracy across groups.

William T. Stephenson, Zachary Frangella, Madeleine Udell et al.

Models like LASSO and ridge regression are extensively used in practice due to their interpretability, ease of use, and strong theoretical guarantees. Cross-validation (CV) is widely used for hyperparameter tuning in these models, but do practical optimization methods minimize the true out-of-sample loss? A recent line of research promises to show that the optimum of the CV loss matches the optimum of the out-of-sample loss (possibly after simple corrections). It remains to show how tractable it is to minimize the CV loss. In the present paper, we show that, in the case of ridge regression, the CV loss may fail to be quasiconvex and thus may have multiple local optima. We can guarantee that the CV loss is quasiconvex in at least one case: when the spectrum of the covariate matrix is nearly flat and the noise in the observed responses is not too high. More generally, we show that quasiconvexity status is independent of many properties of the observed data (response norm, covariate-matrix right singular vectors and singular-value scaling) and has a complex dependence on the few that remain. We empirically confirm our theory using simulated experiments.

Brian Liu, Miaolan Xie, Madeleine Udell

Tree ensembles distribute feature importance evenly amongst groups of correlated features. The average feature ranking of the correlated group is suppressed, which reduces interpretability and complicates feature selection. In this paper we present ControlBurn, a feature selection algorithm that uses a weighted LASSO-based feature selection method to prune unnecessary features from tree ensembles, just as low-intensity fire reduces overgrown vegetation. Like the linear LASSO, ControlBurn assigns all the feature importance of a correlated group of features to a single feature. Moreover, the algorithm is efficient and only requires a single training iteration to run, unlike iterative wrapper-based feature selection methods. We show that ControlBurn performs substantially better than feature selection methods with comparable computational costs on datasets with correlated features.

Nikhil Singh, Brandon Kates, Jeff Mentch et al.

This work improves the quality of automated machine learning (AutoML) systems by using dataset and function descriptions while significantly decreasing computation time from minutes to milliseconds by using a zero-shot approach. Given a new dataset and a well-defined machine learning task, humans begin by reading a description of the dataset and documentation for the algorithms to be used. This work is the first to use these textual descriptions, which we call privileged information, for AutoML. We use a pre-trained Transformer model to process the privileged text and demonstrate that using this information improves AutoML performance. Thus, our approach leverages the progress of unsupervised representation learning in natural language processing to provide a significant boost to AutoML. We demonstrate that using only textual descriptions of the data and functions achieves reasonable classification performance, and adding textual descriptions to data meta-features improves classification across tabular datasets. To achieve zero-shot AutoML we train a graph neural network with these description embeddings and the data meta-features. Each node represents a training dataset, which we use to predict the best machine learning pipeline for a new test dataset in a zero-shot fashion. Our zero-shot approach rapidly predicts a high-quality pipeline for a supervised learning task and dataset. In contrast, most AutoML systems require tens or hundreds of pipeline evaluations. We show that zero-shot AutoML reduces running and prediction times from minutes to milliseconds, consistently across datasets. By speeding up AutoML by orders of magnitude this work demonstrates real-time AutoML.

Chengrun Yang, Ziyang Wu, Jerry Chee et al.

Low-precision arithmetic trains deep learning models using less energy, less memory and less time. However, we pay a price for the savings: lower precision may yield larger round-off error and hence larger prediction error. As applications proliferate, users must choose which precision to use to train a new model, and chip manufacturers must decide which precisions to manufacture. We view these precision choices as a hyperparameter tuning problem, and borrow ideas from meta-learning to learn the tradeoff between memory and error. In this paper, we introduce Pareto Estimation to Pick the Perfect Precision (PEPPP). We use matrix factorization to find non-dominated configurations (the Pareto frontier) with a limited number of network evaluations. For any given memory budget, the precision that minimizes error is a point on this frontier. Practitioners can use the frontier to trade memory for error and choose the best precision for their goals.

Yiming Sun, Yang Guo, Joel A. Tropp et al.

Random projections reduce the dimension of a set of vectors while preserving structural information, such as distances between vectors in the set. This paper proposes a novel use of row-product random matrices in random projection, where we call it Tensor Random Projection (TRP). It requires substantially less memory than existing dimension reduction maps. The TRP map is formed as the Khatri-Rao product of several smaller random projections, and is compatible with any base random projection including sparse maps, which enable dimension reduction with very low query cost and no floating point operations. We also develop a reduced variance extension. We provide a theoretical analysis of the bias and variance of the TRP, and a non-asymptotic error analysis for a TRP composed of two smaller maps. Experiments on both synthetic and MNIST data show that our method performs as well as conventional methods with substantially less storage.

Chengrun Yang, Lijun Ding, Ziyang Wu et al.

Tensors are widely used to represent multiway arrays of data. The recovery of missing entries in a tensor has been extensively studied, generally under the assumption that entries are missing completely at random (MCAR). However, in most practical settings, observations are missing not at random (MNAR): the probability that a given entry is observed (also called the propensity) may depend on other entries in the tensor or even on the value of the missing entry. In this paper, we study the problem of completing a partially observed tensor with MNAR observations, without prior information about the propensities. To complete the tensor, we assume that both the original tensor and the tensor of propensities have low multilinear rank. The algorithm first estimates the propensities using a convex relaxation and then predicts missing values using a higher-order SVD approach, reweighting the observed tensor by the inverse propensities. We provide finite-sample error bounds on the resulting complete tensor. Numerical experiments demonstrate the effectiveness of our approach.

Jicong Fan, Lijun Ding, Chengrun Yang et al.

The nuclear norm and Schatten-$p$ quasi-norm are popular rank proxies in low-rank matrix recovery. However, computing the nuclear norm or Schatten-$p$ quasi-norm of a tensor is hard in both theory and practice, hindering their application to low-rank tensor completion (LRTC) and tensor robust principal component analysis (TRPCA). In this paper, we propose a new class of tensor rank regularizers based on the Euclidean norms of the CP component vectors of a tensor and show that these regularizers are monotonic transformations of tensor Schatten-$p$ quasi-norm. This connection enables us to minimize the Schatten-$p$ quasi-norm in LRTC and TRPCA implicitly via the component vectors. The method scales to big tensors and provides an arbitrarily sharper rank proxy for low-rank tensor recovery compared to the nuclear norm. On the other hand, we study the generalization abilities of LRTC with the Schatten-$p$ quasi-norm regularizer and LRTC with the proposed regularizers. The theorems show that a relatively sharper regularizer leads to a tighter error bound, which is consistent with our numerical results. Particularly, we prove that for LRTC with Schatten-$p$ quasi-norm regularizer on $d$-order tensors, $p=1/d$ is always better than any $p>1/d$ in terms of the generalization ability. We also provide a recovery error bound to verify the usefulness of small $p$ in the Schatten-$p$ quasi-norm for TRPCA. Numerical results on synthetic data and real data demonstrate the effectiveness of the regularization methods and theorems.

Brian Liu, Madeleine Udell

Model interpretations are often used in practice to extract real world insights from machine learning models. These interpretations have a wide range of applications; they can be presented as business recommendations or used to evaluate model bias. It is vital for a data scientist to choose trustworthy interpretations to drive real world impact. Doing so requires an understanding of how the accuracy of a model impacts the quality of standard interpretation tools. In this paper, we will explore how a model's predictive accuracy affects interpretation quality. We propose two metrics to quantify the quality of an interpretation and design an experiment to test how these metrics vary with model accuracy. We find that for datasets that can be modeled accurately by a variety of methods, simpler methods yield higher quality interpretations. We also identify which interpretation method works the best for lower levels of model accuracy.

Yuxuan Zhao, Eric Landgrebe, Eliot Shekhtman et al.

Missing value imputation is crucial for real-world data science workflows. Imputation is harder in the online setting, as it requires the imputation method itself to be able to evolve over time. For practical applications, imputation algorithms should produce imputations that match the true data distribution, handle data of mixed types, including ordinal, boolean, and continuous variables, and scale to large datasets. In this work we develop a new online imputation algorithm for mixed data using the Gaussian copula. The online Gaussian copula model meets all the desiderata: its imputations match the data distribution even for mixed data, improve over its offline counterpart on the accuracy when the streaming data has a changing distribution, and on the speed (up to an order of magnitude) especially on large scale datasets. By fitting the copula model to online data, we also provide a new method to detect change points in the multivariate dependence structure with missing values. Experimental results on synthetic and real world data validate the performance of the proposed methods.

Elizabeth A. Ricci, Madeleine Udell, Ross A. Knepper

Robots can be used to collect environmental data in regions that are difficult for humans to traverse. However, limitations remain in the size of region that a robot can directly observe per unit time. We introduce a method for selecting a limited number of observation points in a large region, from which we can predict the state of unobserved points in the region. We combine a low rank model of a target attribute with an information-maximizing path planner to predict the state of the attribute throughout a region. Our approach is agnostic to the choice of target attribute and robot monitoring platform. We evaluate our method in simulation on two real-world environment datasets, each containing observations from one to two million possible sampling locations. We compare against a random sampler and four variations of a baseline sampler from the ecology literature. Our method outperforms the baselines in terms of average Fisher information gain per samples taken and performs comparably for average reconstruction error in most trials.

William T. Stephenson, Madeleine Udell, Tamara Broderick

Many recent advances in machine learning are driven by a challenging trifecta: large data size $N$; high dimensions; and expensive algorithms. In this setting, cross-validation (CV) serves as an important tool for model assessment. Recent advances in approximate cross validation (ACV) provide accurate approximations to CV with only a single model fit, avoiding traditional CV's requirement for repeated runs of expensive algorithms. Unfortunately, these ACV methods can lose both speed and accuracy in high dimensions -- unless sparsity structure is present in the data. Fortunately, there is an alternative type of simplifying structure that is present in most data: approximate low rank (ALR). Guided by this observation, we develop a new algorithm for ACV that is fast and accurate in the presence of ALR data. Our first key insight is that the Hessian matrix -- whose inverse forms the computational bottleneck of existing ACV methods -- is ALR. We show that, despite our use of the \emph{inverse} Hessian, a low-rank approximation using the largest (rather than the smallest) matrix eigenvalues enables fast, reliable ACV. Our second key insight is that, in the presence of ALR data, error in existing ACV methods roughly grows with the (approximate, low) rank rather than with the (full, high) dimension. These insights allow us to prove theoretical guarantees on the quality of our proposed algorithm -- along with fast-to-compute upper bounds on its error. We demonstrate the speed and accuracy of our method, as well as the usefulness of our bounds, on a range of real and simulated data sets.

Lijun Ding, Jicong Fan, Madeleine Udell

This paper proposes a new variant of Frank-Wolfe (FW), called $k$FW. Standard FW suffers from slow convergence: iterates often zig-zag as update directions oscillate around extreme points of the constraint set. The new variant, $k$FW, overcomes this problem by using two stronger subproblem oracles in each iteration. The first is a $k$ linear optimization oracle ($k$LOO) that computes the $k$ best update directions (rather than just one). The second is a $k$ direction search ($k$DS) that minimizes the objective over a constraint set represented by the $k$ best update directions and the previous iterate. When the problem solution admits a sparse representation, both oracles are easy to compute, and $k$FW converges quickly for smooth convex objectives and several interesting constraint sets: $k$FW achieves finite $\frac{4L_f^3D^4}{γδ^2}$ convergence on polytopes and group norm balls, and linear convergence on spectrahedra and nuclear norm balls. Numerical experiments validate the effectiveness of $k$FW and demonstrate an order-of-magnitude speedup over existing approaches.

Yuxuan Zhao, Madeleine Udell

Modern large scale datasets are often plagued with missing entries. For tabular data with missing values, a flurry of imputation algorithms solve for a complete matrix which minimizes some penalized reconstruction error. However, almost none of them can estimate the uncertainty of its imputations. This paper proposes a probabilistic and scalable framework for missing value imputation with quantified uncertainty. Our model, the Low Rank Gaussian Copula, augments a standard probabilistic model, Probabilistic Principal Component Analysis, with marginal transformations for each column that allow the model to better match the distribution of the data. It naturally handles Boolean, ordinal, and real-valued observations and quantifies the uncertainty in each imputation. The time required to fit the model scales linearly with the number of rows and the number of columns in the dataset. Empirical results show the method yields state-of-the-art imputation accuracy across a wide range of data types, including those with high rank. Our uncertainty measure predicts imputation error well: entries with lower uncertainty do have lower imputation error (on average). Moreover, for real-valued data, the resulting confidence intervals are well-calibrated.

Chengrun Yang, Jicong Fan, Ziyang Wu et al.

Data scientists seeking a good supervised learning model on a new dataset have many choices to make: they must preprocess the data, select features, possibly reduce the dimension, select an estimation algorithm, and choose hyperparameters for each of these pipeline components. With new pipeline components comes a combinatorial explosion in the number of choices! In this work, we design a new AutoML system to address this challenge: an automated system to design a supervised learning pipeline. Our system uses matrix and tensor factorization as surrogate models to model the combinatorial pipeline search space. Under these models, we develop greedy experiment design protocols to efficiently gather information about a new dataset. Experiments on large corpora of real-world classification problems demonstrate the effectiveness of our approach.

Iddo Drori, Anant Kharkar, William R. Sickinger et al.

Combinatorial optimization algorithms for graph problems are usually designed afresh for each new problem with careful attention by an expert to the problem structure. In this work, we develop a new framework to solve any combinatorial optimization problem over graphs that can be formulated as a single player game defined by states, actions, and rewards, including minimum spanning tree, shortest paths, traveling salesman problem, and vehicle routing problem, without expert knowledge. Our method trains a graph neural network using reinforcement learning on an unlabeled training set of graphs. The trained network then outputs approximate solutions to new graph instances in linear running time. In contrast, previous approximation algorithms or heuristics tailored to NP-hard problems on graphs generally have at least quadratic running time. We demonstrate the applicability of our approach on both polynomial and NP-hard problems with optimality gaps close to 1, and show that our method is able to generalize well: (i) from training on small graphs to testing on large graphs; (ii) from training on random graphs of one type to testing on random graphs of another type; and (iii) from training on random graphs to running on real world graphs.