arXiv subjects

Agustinus Kristiadi

Publications and source records attributed to Agustinus Kristiadi.

At least 19 recordsLinked to original sources

arXiv2026

Out-Of-The-Loop Multi-Fidelity Bayesian Optimization

Black-box optimization is a ubiquitous problem in science and engineering, often dealing with expensive objective functions with cheaper lower-fidelity proxies available. Multi-fidelity Bayesian optimization (MF-BO) is a principled approach to this problem, leveraging correlations across different fidelities when querying the objective. However, for many important MF-BO tasks, the true highest-fidelity function is prohibitively expensive to be part of the optimization loop. Nevertheless, practitioners often have gold standard data (observations of the highest-fidelity function) obtained from previous experiments that might provide information for the current task. For instance, in molecular optimization, chemists often pick the top-$k$ candidate molecules using various computer simulations, and later reveal their true objective function values. In this work, we demonstrate the suboptimality of standard MF-BO algorithms in the real-world scenarios above, even under ideal assumptions. Next, we mitigate this problem by incorporating historical high-fidelity data accompanied by task descriptors---which can be explicitly given or extracted from unstructured metadata. We demonstrate the effectiveness of our methods on synthetic functions, as well as real-world problems in chemistry and hyperparameter optimization.

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arXiv2026

Benchmarking Instance-Dependent Label Noise with Controlled Corruptions

Synthetic instance-dependent label noise (IDN) benchmarks are widely used to evaluate noisy-label learning methods, yet existing approaches typically generate noise through imperfect annotators or classifier raters, leaving the source of ambiguity implicit. We introduce CILN, a benchmark generation framework that creates IDN through controlled input corruptions. A diverse voter pool labels corrupted instances, producing benchmark datasets in which both the source and severity of ambiguity are explicit and controllable. Using CIFAR10, MNIST, and Adult, we construct 90 benchmark settings spanning multiple corruption families and severity levels. Our experiments show that the resulting benchmarks exhibit genuine instance-dependent noise, provide diverse confusion structures, and, on CIFAR-10, can produce label distributions that are closer to human uncertainty than an existing synthetic IDN benchmark. We further demonstrate that corruption-mediated IDN can expose failure modes of popular noisy-label learning methods, including Co-Teaching and DivideMix, that are not observed under comparable levels of rater-fallibility noise. These findings suggest that noise structure, not only noise rate, plays an important role in benchmark difficulty and algorithm behavior. By making ambiguity generation explicit and controllable, CILN provides a complementary benchmarking framework for studying noisy-label learning under diverse sources of instance difficulty.

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arXiv2026

FlashMD: long-stride, universal prediction of molecular dynamics

Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD by providing inexpensive predictions of the forces, but they remain constrained to minuscule time integration steps, which are required by the fast time scale of atomic motion. In this work, we propose FlashMD, a method to predict the evolution of positions and momenta over strides that are between one and two orders of magnitude longer than typical MD time steps. We incorporate considerations on the mathematical and physical properties of Hamiltonian dynamics in the architecture, generalize the approach to allow the simulation of any thermodynamic ensemble, and carefully assess the possible failure modes of such a long-stride MD approach. We validate FlashMD's accuracy in reproducing equilibrium and time-dependent properties, using both system-specific and general-purpose models, extending the ability of MD simulation to reach the long time scales needed to model microscopic processes of high scientific and technological relevance.

physics.chem-ph↗

arXiv2025

Low-Rank Filtering and Smoothing for Sequential Deep Learning

Learning multiple tasks sequentially requires neural networks to balance retaining knowledge, yet being flexible enough to adapt to new tasks. Regularizing network parameters is a common approach, but it rarely incorporates prior knowledge about task relationships, and limits information flow to future tasks only. We propose a Bayesian framework that treats the network's parameters as the state space of a nonlinear Gaussian model, unlocking two key capabilities: (1) A principled way to encode domain knowledge about task relationships, allowing, e.g., control over which layers should adapt between tasks. (2) A novel application of Bayesian smoothing, allowing task-specific models to also incorporate knowledge from models learned later. This does not require direct access to their data, which is crucial, e.g., for privacy-critical applications. These capabilities rely on efficient filtering and smoothing operations, for which we propose diagonal plus low-rank approximations of the precision matrix in the Laplace approximation (LR-LGF). Empirical results demonstrate the efficiency of LR-LGF and the benefits of the unlocked capabilities.

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arXiv2025

Limits of PRM-Guided Tree Search for Mathematical Reasoning with LLMs

While chain-of-thought prompting with Best-of-N (BoN) selection has become popular for mathematical reasoning in large language models (LLMs), its linear structure fails to capture the branching and exploratory nature of complex problem-solving. In this work, we propose an adaptive algorithm to maximize process reward model (PRM) scores over the intractable action space, and investigate whether PRM-guided tree search can improve mathematical reasoning by exploring multiple partial solution paths. Across $23$ diverse mathematical problems using Qwen2.5-Math-7B-Instruct with its associated PRM as a case study, we find that: (1) PRM-guided tree search shows no statistically significant improvements over BoN despite higher costs, (2) Monte Carlo tree search and beam search outperform other PRM-guided tree search methods, (3) PRMs poorly approximate state values and their reliability degrades with reasoning depth, and (4) PRMs generalize poorly out of distribution. This underperformance stems from tree search's greater reliance on unreliable PRM scores, suggesting different reward modeling is necessary before tree search can effectively enhance mathematical reasoning in LLMs.

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arXiv2025

A Critical Look At Tokenwise Reward-Guided Text Generation

Large language models (LLMs) can be improved by aligning with human preferences through fine-tuning -- the so-called reinforcement learning from human feedback (RLHF). However, the cost of fine-tuning an LLM is prohibitive for many users. Due to their ability to bypass LLM fine-tuning, prediction-time tokenwise reward-guided text generation (RGTG) methods have recently been proposed. They use a reward model trained on full sequences to score partial sequences during decoding in a bid to steer the generation towards sequences with high rewards. However, these methods have so far been only heuristically motivated and poorly analyzed. In this work, we show that reward models trained on full sequences are not compatible with scoring partial sequences. To alleviate this, we propose to train a Bradley-Terry reward model on partial sequences explicitly, and autoregressively sample from the implied tokenwise policy during decoding. We study the properties of this reward model and the resulting policy: we show that this policy is proportional to the ratio of two distinct RLHF policies. Our simple approach outperforms previous RGTG methods and performs similarly to strong offline baselines without large-scale LLM fine-tuning. Code for our work is available at https://github.com/ahmadrash/PARGS

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arXiv2025

Uncertainty-Guided Likelihood Tree Search

Tree search is a fundamental tool for planning, as many sequential decision-making problems can be framed as searching over tree-structured spaces. We propose an uncertainty-guided tree search algorithm for settings where the reward function is a log-likelihood function of the paths. Due to the combinatorial explosion of the tree size, the set of paths for which one can obtain rewards is sparse, particularly when the likelihood is obtained through expensive evaluations, such as by querying a large language model. We address this challenge by deriving an probabilistic search heuristic based on regularity assumptions for the likelihood. Unlike existing tree search methods, the proposed method can perform backtracking and trade-off exploration with exploitation, and yet does not require expensive roll-outs, or sophisticated Bayesian inference. Through extensive on-model and off-model experiments on timely, large-scale practical applications, we demonstrate that our method identifies paths with high likelihood while requiring fewer costly evaluations.

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arXiv2025

Introduction to the Analysis of Probabilistic Decision-Making Algorithms

Decision theories offer principled methods for making choices under various types of uncertainty. Algorithms that implement these theories have been successfully applied to a wide range of real-world problems, including materials and drug discovery. Indeed, they are desirable since they can adaptively gather information to make better decisions in the future, resulting in data-efficient workflows. In scientific discovery, where experiments are costly, these algorithms can thus significantly reduce the cost of experimentation. Theoretical analyses of these algorithms are crucial for understanding their behavior and providing valuable insights for developing next-generation algorithms. However, theoretical analyses in the literature are often inaccessible to non-experts. This monograph aims to provide an accessible, self-contained introduction to the theoretical analysis of commonly used probabilistic decision-making algorithms, including bandit algorithms, Bayesian optimization, and tree search algorithms. Only basic knowledge of probability theory and statistics, along with some elementary knowledge about Gaussian processes, is assumed.

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arXiv2025

Towards Cost-Effective Reward Guided Text Generation

Reward-guided text generation (RGTG) has emerged as a viable alternative to offline reinforcement learning from human feedback (RLHF). RGTG methods can align baseline language models to human preferences without further training like in standard RLHF methods. However, they rely on a reward model to score each candidate token generated by the language model at inference, incurring significant test-time overhead. Additionally, the reward model is usually only trained to score full sequences, which can lead to sub-optimal choices for partial sequences. In this work, we present a novel reward model architecture that is trained, using a Bradley-Terry loss, to prefer the optimal expansion of a sequence with just a \emph{single call} to the reward model at each step of the generation process. That is, a score for all possible candidate tokens is generated simultaneously, leading to efficient inference. We theoretically analyze various RGTG reward models and demonstrate that prior techniques prefer sub-optimal sequences compared to our method during inference. Empirically, our reward model leads to significantly faster inference than other RGTG methods. It requires fewer calls to the reward model and performs competitively compared to previous RGTG and offline RLHF methods.

cs.LG↗

arXiv2025

Simplifying Bayesian Optimization Via In-Context Direct Optimum Sampling

The optimization of expensive black-box functions is ubiquitous in science and engineering. A common solution to this problem is Bayesian optimization (BO), which is generally comprised of two components: (i) a surrogate model and (ii) an acquisition function, which generally require expensive re-training and optimization steps at each iteration, respectively. Although recent work enabled in-context surrogate models that do not require re-training, virtually all existing BO methods still require acquisition function maximization to select the next observation, which introduces many knobs to tune, such as Monte Carlo samplers and multi-start optimizers. In this work, we propose a completely in-context, zero-shot solution for BO that does not require surrogate fitting or acquisition function optimization. This is done by using a pre-trained deep generative model to directly sample from the posterior over the optimum point. We show that this process is equivalent to Thompson sampling and demonstrate the capabilities and cost-effectiveness of our foundation model on a suite of real-world benchmarks. We achieve an efficiency gain of more than 35x in terms of wall-clock time when compared with Gaussian process-based BO, enabling efficient parallel and distributed BO, e.g., for high-throughput optimization.

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arXiv2025

Bayesian Optimization for General Reaction Conditions

General chemical reaction conditions that achieve consistently high performance across multiple substrates are important for practical applications such as library synthesis and high-throughput experimentation. However, identifying such conditions efficiently has been a longstanding challenge, as it requires decision making under uncertainty with respect to both conditions and substrates, while minimizing the number of required experiments. Here, we introduce CurryBO, a high-level framework for generality-oriented optimization. By formalizing the problem as Bayesian optimization over curried functions, CurryBO provides a unified framework that accommodates different generality definitions (e.g., mean yield across substrates), and supports a range of substrate and condition selection strategies. We evaluate this framework on four benchmark tasks in experimental reaction optimization, and systematically analyze key algorithmic components. Our results show that efficient experiment planning can be achieved by emphasizing exploration when selecting reaction conditions, followed by the uncertainty-guided prioritization of substrates in a sequential decison-making scheme. Based on these insights, we design and validate an optimization policy that substantially improves sample efficiency relative to previously reported approaches across all benchmarks. Overall, the flexibility and modularity of CurryBO facilitate the integration of generality-oriented optimization into experimental settings, enabling more efficient identification of solutions that perform robustly across diverse tasks.

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arXiv2025

Position: Curvature Matrices Should Be Democratized via Linear Operators

Structured large matrices are prevalent in machine learning. A particularly important class is curvature matrices like the Hessian, which are central to understanding the loss landscape of neural nets (NNs), and enable second-order optimization, uncertainty quantification, model pruning, data attribution, and more. However, curvature computations can be challenging due to the complexity of automatic differentiation, and the variety and structural assumptions of curvature proxies, like sparsity and Kronecker factorization. In this position paper, we argue that linear operators -- an interface for performing matrix-vector products -- provide a general, scalable, and user-friendly abstraction to handle curvature matrices. To support this position, we developed $\textit{curvlinops}$, a library that provides curvature matrices through a unified linear operator interface. We demonstrate with $\textit{curvlinops}$ how this interface can hide complexity, simplify applications, be extensible and interoperable with other libraries, and scale to large NNs.

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arXiv2024

Position: Bayesian Deep Learning is Needed in the Age of Large-Scale AI

In the current landscape of deep learning research, there is a predominant emphasis on achieving high predictive accuracy in supervised tasks involving large image and language datasets. However, a broader perspective reveals a multitude of overlooked metrics, tasks, and data types, such as uncertainty, active and continual learning, and scientific data, that demand attention. Bayesian deep learning (BDL) constitutes a promising avenue, offering advantages across these diverse settings. This paper posits that BDL can elevate the capabilities of deep learning. It revisits the strengths of BDL, acknowledges existing challenges, and highlights some exciting research avenues aimed at addressing these obstacles. Looking ahead, the discussion focuses on possible ways to combine large-scale foundation models with BDL to unlock their full potential.

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arXiv2024

Structured Inverse-Free Natural Gradient: Memory-Efficient & Numerically-Stable KFAC

Second-order methods such as KFAC can be useful for neural net training. However, they are often memory-inefficient since their preconditioning Kronecker factors are dense, and numerically unstable in low precision as they require matrix inversion or decomposition. These limitations render such methods unpopular for modern mixed-precision training. We address them by (i) formulating an inverse-free KFAC update and (ii) imposing structures in the Kronecker factors, resulting in structured inverse-free natural gradient descent (SINGD). On modern neural networks, we show that SINGD is memory-efficient and numerically robust, in contrast to KFAC, and often outperforms AdamW even in half precision. Our work closes a gap between first- and second-order methods in modern low-precision training.

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arXiv2024

How Useful is Intermittent, Asynchronous Expert Feedback for Bayesian Optimization?

Bayesian optimization (BO) is an integral part of automated scientific discovery -- the so-called self-driving lab -- where human inputs are ideally minimal or at least non-blocking. However, scientists often have strong intuition, and thus human feedback is still useful. Nevertheless, prior works in enhancing BO with expert feedback, such as by incorporating it in an offline or online but blocking (arrives at each BO iteration) manner, are incompatible with the spirit of self-driving labs. In this work, we study whether a small amount of randomly arriving expert feedback that is being incorporated in a non-blocking manner can improve a BO campaign. To this end, we run an additional, independent computing thread on top of the BO loop to handle the feedback-gathering process. The gathered feedback is used to learn a Bayesian preference model that can readily be incorporated into the BO thread, to steer its exploration-exploitation process. Experiments on toy and chemistry datasets suggest that even just a few intermittent, asynchronous expert feedback can be useful for improving or constraining BO. This can especially be useful for its implication in improving self-driving labs, e.g. making them more data-efficient and less costly.

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arXiv2024

On the Disconnect Between Theory and Practice of Neural Networks: Limits of the NTK Perspective

The neural tangent kernel (NTK) has garnered significant attention as a theoretical framework for describing the behavior of large-scale neural networks. Kernel methods are theoretically well-understood and as a result enjoy algorithmic benefits, which can be demonstrated to hold in wide synthetic neural network architectures. These advantages include faster optimization, reliable uncertainty quantification and improved continual learning. However, current results quantifying the rate of convergence to the kernel regime suggest that exploiting these benefits requires architectures that are orders of magnitude wider than they are deep. This assumption raises concerns that architectures used in practice do not exhibit behaviors as predicted by the NTK. Here, we supplement previous work on the NTK by empirically investigating whether the limiting regime predicts practically relevant behavior of large-width architectures. Our results demonstrate that this is not the case across multiple domains. This observed disconnect between theory and practice further calls into question to what degree NTK theory should inform architectural and algorithmic choices.

cs.LG↗

arXiv2024

A Sober Look at LLMs for Material Discovery: Are They Actually Good for Bayesian Optimization Over Molecules?

Automation is one of the cornerstones of contemporary material discovery. Bayesian optimization (BO) is an essential part of such workflows, enabling scientists to leverage prior domain knowledge into efficient exploration of a large molecular space. While such prior knowledge can take many forms, there has been significant fanfare around the ancillary scientific knowledge encapsulated in large language models (LLMs). However, existing work thus far has only explored LLMs for heuristic materials searches. Indeed, recent work obtains the uncertainty estimate -- an integral part of BO -- from point-estimated, non-Bayesian LLMs. In this work, we study the question of whether LLMs are actually useful to accelerate principled Bayesian optimization in the molecular space. We take a sober, dispassionate stance in answering this question. This is done by carefully (i) viewing LLMs as fixed feature extractors for standard but principled BO surrogate models and by (ii) leveraging parameter-efficient finetuning methods and Bayesian neural networks to obtain the posterior of the LLM surrogate. Our extensive experiments with real-world chemistry problems show that LLMs can be useful for BO over molecules, but only if they have been pretrained or finetuned with domain-specific data.

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arXiv2024

Preventing Arbitrarily High Confidence on Far-Away Data in Point-Estimated Discriminative Neural Networks

Discriminatively trained, deterministic neural networks are the de facto choice for classification problems. However, even though they achieve state-of-the-art results on in-domain test sets, they tend to be overconfident on out-of-distribution (OOD) data. For instance, ReLU networks - a popular class of neural network architectures - have been shown to almost always yield high confidence predictions when the test data are far away from the training set, even when they are trained with OOD data. We overcome this problem by adding a term to the output of the neural network that corresponds to the logit of an extra class, that we design to dominate the logits of the original classes as we move away from the training data.This technique provably prevents arbitrarily high confidence on far-away test data while maintaining a simple discriminative point-estimate training. Evaluation on various benchmarks demonstrates strong performance against competitive baselines on both far-away and realistic OOD data.

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