Frank Hutter

• University of Freiburg

Data repositories have accumulated a large number of tabular datasets from various domains. Machine Learning researchers are actively using these datasets to evaluate novel approaches. Consequently, data repositories have an important standing in tabular data research. They not only host datasets but also provide information on how to use them in s...

Linear Recurrent Neural Networks (linear RNNs) have emerged as competitive alternatives to Transformers for sequence modeling, offering efficient training and linear-time inference. However, existing architectures face a fundamental trade-off between expressivity and efficiency, dictated by the structure of their state-transition matrices. While di...

Recent foundational models for tabular data, such as TabPFN, have demonstrated remarkable effectiveness in adapting to new tasks through in-context learning. However, these models overlook a crucial equivariance property: the arbitrary ordering of target dimensions should not influence model predictions. In this study, we identify this oversight as...

Activation functions are fundamental elements of deep learning architectures as they significantly influence training dynamics. ReLU, while widely used, is prone to the dying neuron problem, which has been mitigated by variants such as LeakyReLU, PReLU, and ELU that better handle negative neuron outputs. Recently, self-gated activations like GELU a...

Large language models (LLMs) perform remarkably well on tabular datasets in zero- and few-shot settings, since they can extract meaning from natural language column headers that describe features and labels. Similarly, TabPFN, a recent non-LLM transformer pretrained on numerous tables for in-context learning, has demonstrated excellent performance...

Tools like S nipper or the Admixture Model count as state-of-the-art methods in forensic science for biogeographical ancestry. However, they have not been systematically compared to classifiers widely used in other disciplines. Noting that genetic data have a tabular form, this study addresses this gap by benchmarking forensic classifiers against T...

Evaluating Large Language Models (LLMs) often requires costly human annotations. To address this, LLM-based judges have been proposed, which compare the outputs of two LLMs enabling the ranking of models without human intervention. While several approaches have been proposed, many confounding factors are present between different papers. For instan...

Tabular data, spreadsheets organized in rows and columns, are ubiquitous across scientific fields, from biomedicine to particle physics to economics and climate science1,2. The fundamental prediction task of filling in missing values of a label column based on the rest of the columns is essential for various applications as diverse as biomedical ri...

Foundation models have become popular in forecasting due to their ability to make accurate predictions, even with minimal fine-tuning on specific datasets. In this paper, we demonstrate how the newly released regression variant of TabPFN, a general tabular foundation model, can be applied to time series forecasting. We propose a straightforward app...

Linear Recurrent Neural Networks (LRNNs) such as Mamba, RWKV, GLA, mLSTM, and DeltaNet have emerged as efficient alternatives to Transformers in large language modeling, offering linear scaling with sequence length and improved training efficiency. However, LRNNs struggle to perform state-tracking which may impair performance in tasks such as code...

While most ML models expect independent and identically distributed data, this assumption is often violated in real-world scenarios due to distribution shifts, resulting in the degradation of machine learning model performance. Until now, no tabular method has consistently outperformed classical supervised learning, which ignores these shifts. To a...

RNA-protein interactions (RPI) are ubiquitous in cellular organisms and essential for gene regulation. In particular, protein interactions with non-coding RNAs (ncRNAs) play a critical role in these processes. Experimental analysis of RPIs is time-consuming and expensive, and existing computational methods rely on small and limited datasets. This w...

Scaling model sizes to scale performance has worked remarkably well for the current large language models paradigm. The research and empirical findings of various scaling studies led to novel scaling results and laws that guides subsequent research. High training costs for contemporary scales of data and models result in a lack of thorough understa...

As the landscape of large language models expands, efficiently finetuning for specific tasks becomes increasingly crucial. At the same time, the landscape of parameter-efficient finetuning methods rapidly expands. Consequently, practitioners face a multitude of complex choices when searching for an optimal finetuning pipeline for large language mod...

Finetuning is a common practice widespread across different communities to adapt pretrained models to particular tasks. Text classification is one of these tasks for which many pretrained models are available. On the other hand, ensembles of neural networks are typically used to boost performance and provide reliable uncertainty estimates. However,...

Tabular machine learning problems often require time-consuming and labor-intensive feature engineering. Recent efforts have focused on using large language models (LLMs) to capitalize on their potential domain knowledge. At the same time, researchers have observed ethically concerning negative biases in other LLM-related use cases, such as text gen...

Fairness-aware Machine Learning (FairML) applications are often characterized by complex social objectives and legal requirements, frequently involving multiple, potentially conflicting notions of fairness. Despite the well-known Impossibility Theorem of Fairness and extensive theoretical research on the statistical and socio-technical trade-offs b...

RNA is a dynamic biomolecule crucial for cellular regulation, with its function largely determined by its folding into complex structures, while misfolding can lead to multifaceted biological sequelae. During the folding process, RNA traverses through a series of intermediate structural states, with each transition occurring at variable rates that...

Fairness-aware Machine Learning (FairML) applications are often characterized by complex social objectives and legal requirements, frequently involving multiple, potentially conflicting notions of fairness. Despite the well-known Impossibility Theorem of Fairness and extensive theoretical research on the statistical and socio-technical trade-offs b...

This paper introduces Mamba4Cast, a zero-shot foundation model for time series forecasting. Based on the Mamba architecture and inspired by Prior-data Fitted Networks (PFNs), Mamba4Cast generalizes robustly across diverse time series tasks without the need for dataset specific fine-tuning. Mamba4Cast's key innovation lies in its ability to achieve...

Large language models (LLMs) exhibit remarkable reasoning abilities, allowing them to generalize across a wide range of downstream tasks, such as commonsense reasoning or instruction following. However, as LLMs scale, inference costs become increasingly prohibitive, accumulating significantly over their life cycle. This poses the question: Can we c...

Ensemble methods are known for enhancing the accuracy and robustness of machine learning models by combining multiple base learners. However, standard approaches like greedy or random ensembles often fall short, as they assume a constant weight across samples for the ensemble members. This can limit expressiveness and hinder performance when aggreg...

Generalized Additive Models (GAMs) are widely recognized for their ability to create fully interpretable machine learning models for tabular data. Traditionally, training GAMs involves iterative learning algorithms, such as splines, boosted trees, or neural networks, which refine the additive components through repeated error reduction. In this pap...

Traditionally, neural network training has been primarily viewed as an approximation of maximum likelihood estimation (MLE). This interpretation originated in a time when training for multiple epochs on small datasets was common and performance was data bound; but it falls short in the era of large-scale single-epoch trainings ushered in by large s...

Hyperparameters are a critical factor in reliably training well-performing reinforcement learning (RL) agents. Unfortunately, developing and evaluating automated approaches for tuning such hyperparameters is both costly and time-consuming. As a result, such approaches are often only evaluated on a single domain or algorithm, making comparisons diff...

Machine learning algorithms, and in particular deep learning approaches, have recently garnered attention in the field of molecular biology due to remarkable results. In this chapter, we describe machine learning approaches specifically developed for the design of RNAs, with a focus on the learna_tools Python package, a collection of automated deep...

A World Model is a compressed spatial and temporal representation of a real world environment that allows one to train an agent or execute planning methods. However, world models are typically trained on observations from the real world environment, and they usually do not enable learning policies for other real environments. We propose One-Shot Wo...

The importance of tuning hyperparameters in Machine Learning (ML) and Deep Learning (DL) is established through empirical research and applications, evident from the increase in new hyperparameter optimization (HPO) algorithms and benchmarks steadily added by the community. However, current benchmarking practices using averaged performance across m...

Machine Learning systems are increasingly prevalent across healthcare, law enforcement, and finance but often operate on historical data, which may carry biases against certain demographic groups. Causal and counterfactual fairness provides an intuitive way to define fairness that closely aligns with legal standards. Despite its theoretical benefit...

Motivation RNA design is a key technique to achieve new functionality in fields like synthetic biology or biotechnology. Computational tools could help to find such RNA sequences but they are often limited in their formulation of the search space. Results In this work, we propose partial RNA design, a novel RNA design paradigm that addresses the l...

In this paper, we present the Fast Optimizer Benchmark (FOB), a tool designed for evaluating deep learning optimizers during their development. The benchmark supports tasks from multiple domains such as computer vision, natural language processing, and graph learning. The focus is on convenient usage, featuring human-readable YAML configurations, S...

Automated machine learning (AutoML) was formed around the fundamental objectives of automatically and efficiently configuring machine learning (ML) workflows, aiding the research of new ML algorithms, and contributing to the democratization of ML by making it accessible to a broader audience. Over the past decade, commendable achievements in AutoML...

The expanding size of language models has created the necessity for a comprehensive examination across various dimensions that reflect the desiderata with respect to the tradeoffs between various hardware metrics, such as latency, energy consumption, GPU memory usage, and performance. There is a growing interest in establishing Pareto frontiers for...

A bstract The design of RNAs that fulfill desired functions is one of the major challenges in computational biology. The function of an RNA molecule depends on its structure and a strong structure-to-function relationship is already achieved on the secondary structure level of RNA. Therefore, computational RNA design is often interpreted as the inv...

The field of automated machine learning (AutoML) introduces techniques that automate parts of the development of machine learning (ML) systems, accelerating the process and reducing barriers for novices. However, decisions derived from ML models can reproduce, amplify, or even introduce unfairness in our societies, causing harm to (groups of) indiv...

A bstract Predicting RNA secondary structure is essential for understanding RNA function and developing RNA-based therapeutics. Despite recent advances in deep learning for structural biology, its application to RNA secondary structure prediction remains contentious. A primary concern is the control of homology between training and test data. Moreo...

RNA is a crucial regulator in living organisms and malfunctions can lead to severe diseases. To explore RNA-based therapeutics and applications, computational structure prediction and design approaches play a vital role. Among these approaches, deep learning (DL) algorithms show great promise. However, the adoption of DL methods in the RNA communit...

In this work, we propose partial RNA design, a novel RNA design paradigm formulated as a constraint satisfaction problem. Partial RNA design describes the problem of designing RNA sequences from arbitrary RNA sequence and structure motifs. Our formulation enables RNA design of variable-lengths candidates, while still allowing precise control over s...

Many Self-Supervised Learning (SSL) methods aim for model invariance to different image augmentations known as views. To achieve this invariance, conventional approaches make use of random sampling operations within the image augmentation pipeline. We hypothesize that the efficacy of pretraining pipelines based on conventional random view sampling...

The recent rise in popularity of Hyperparameter Optimization (HPO) for deep learning has highlighted the role that good hyperparameter (HP) space design can play in training strong models. In turn, designing a good HP space is critically dependent on understanding the role of different HPs. This motivates research on HP Importance (HPI), e.g., with...

Hyperparameter optimization (HPO) is a vital step in improving performance in deep learning (DL). Practitioners are often faced with the trade-off between multiple criteria, such as accuracy and latency. Given the high computational needs of DL and the growing demand for efficient HPO, the acceleration of multi-objective (MO) optimization becomes e...

Hyperparameter optimization (HPO) is crucial for strong performance of deep learning algorithms and real-world applications often impose some constraints, such as memory usage, or latency on top of the performance requirement. In this work, we propose constrained TPE (c-TPE), an extension of the widely-used versatile Bayesian optimization method, t...

Experimental screening and selection pipelines for the discovery of novel riboswitches are expensive, time-consuming, and inefficient. Using computational methods to reduce the number of candidates for the screen could drastically decrease these costs. However, existing computational approaches do not fully satisfy all requirements for the design o...

The field of RNA secondary structure prediction has made significant progress with the adoption of deep learning techniques. In this work, we present the RNAformer, a lean deep learning model using axial attention and recycling in the latent space. We gain performance improvements by designing the architecture for modeling the adjacency matrix dire...

We present MDP Playground, a testbed for Reinforcement Learning (RL) agents with dimensions of hardness that can be controlled independently to challenge agents in different ways and obtain varying degrees of hardness in toy and complex RL environments. We consider and allow control over a wide variety of dimensions, including delayed rewards, sequ...

Advanced programmatic hyperparameter optimization (HPO) methods, such as Bayesian optimization, have high sample efficiency in reproducibly finding optimal hyperparameter values of machine learning (ML) models. Yet, ML practitioners often apply less sample-efficient HPO methods, such as grid search, which often results in under-optimized ML models....

Hyperparameters of Deep Learning (DL) pipelines are crucial for their downstream performance. While a large number of methods for Hyperparameter Optimization (HPO) have been developed, their incurred costs are often untenable for modern DL. Consequently, manual experimentation is still the most prevalent approach to optimize hyperparameters, relyin...

In this paper, we use Prior-data Fitted Networks (PFNs) as a flexible surrogate for Bayesian Optimization (BO). PFNs are neural processes that are trained to approximate the posterior predictive distribution (PPD) for any prior distribution that can be efficiently sampled from. We describe how this flexibility can be exploited for surrogate modelin...

Hyperparameter optimization (HPO) is a powerful technique for automating the tuning of machine learning (ML) models. However, in many real-world applications, accuracy is only one of multiple performance criteria that must be considered. Optimizing these objectives simultaneously on a complex and diverse search space remains a challenging task. In...

As the field of automated machine learning (AutoML) advances, it becomes increasingly important to include domain knowledge within these systems. We present an approach for doing so by harnessing the power of large language models (LLMs). Specifically, we introduce Context-Aware Automated Feature Engineering (CAAFE), a feature engineering method fo...

Gaussian processes are cemented as the model of choice in Bayesian optimization and active learning. Yet, they are severely dependent on cleverly chosen hyperparameters to reach their full potential, and little effort is devoted to finding the right hyperparameters in the literature. We demonstrate the impact of selecting good hyperparameters for G...

The recent rise in popularity of Hyperparameter Optimization (HPO) for deep learning has highlighted the role that good hyperparameter (HP) space design can play in training strong models. In turn, designing a good HP space is critically dependent on understanding the role of different HPs. This motivates research on HP Importance (HPI), e.g., with...

The success of deep learning in recent years has lead to a rising demand for neural network architecture engineering. As a consequence, neural architecture search (NAS), which aims at automatically designing neural network architectures in a data-driven manner rather than manually, has evolved as a popular field of research. With the advent of weig...

Modern machine learning models are often constructed taking into account multiple objectives, e.g., minimizing inference time while also maximizing accuracy. Multi-objective hyperparameter optimization (MHPO) algorithms return such candidate models, and the approximation of the Pareto front is used to assess their performance. In practice, we also...

Recent years have witnessed tremendously improved efficiency of Automated Machine Learning (AutoML), especially Automated Deep Learning (AutoDL) systems, but recent work focuses on tabular, image, or NLP tasks. So far, little attention has been paid to general AutoDL frameworks for time series forecasting, despite the enormous success in applying d...

The field of automated machine learning (AutoML) introduces techniques that automate parts of the development of machine learning (ML) systems, accelerating the process and reducing barriers for novices. However, decisions derived from ML models can reproduce, amplify, or even introduce unfairness in our societies, causing harm to (groups of) indiv...

In the past decade, advances in deep learning have resulted in breakthroughs in a variety of areas, including computer vision, natural language understanding, speech recognition, and reinforcement learning. Specialized, high-performing neural architectures are crucial to the success of deep learning in these areas. Neural architecture search (NAS),...

The performance of an algorithm often critically depends on its parameter configuration. While a variety of automated algorithm configuration methods have been proposed to relieve users from the tedious and error-prone task of manually tuning parameters, there is still a lot of untapped potential as the learned configuration is static, i.e., parame...

Hyperparameter optimization (HPO) is essential for the better performance of deep learning, and practitioners often need to consider the trade-off between multiple metrics, such as error rate, latency, memory requirements, robustness, and algorithmic fairness. Due to this demand and the heavy computation of deep learning, the acceleration of multi-...

Modern machine learning models are often constructed taking into account multiple objectives, e.g., to minimize inference time while also maximizing accuracy. Multi-objective hyperparameter optimization (MHPO) algorithms return such candidate models and the approximation of the Pareto front is used to assess their performance. However, when estimat...

Hyperparameter optimization (HPO) is crucial for strong performance of deep learning algorithms. A widely-used versatile HPO method is a variant of Bayesian optimization called tree-structured Parzen estimator (TPE), which splits data into good and bad groups and uses the density ratio of those groups as an acquisition function (AF). However, real-...

The discovery of neural architectures from scratch is the long-standing goal of Neural Architecture Search (NAS). Searching over a wide spectrum of neural architectures can facilitate the discovery of previously unconsidered but well-performing architectures. In this work, we take a large step towards discovering neural architectures from scratch b...

Face recognition systems are deployed across the world by government agencies and contractors for sensitive and impactful tasks, such as surveillance and database matching. Despite their widespread use, these systems are known to exhibit bias across a range of sociodemographic dimensions, such as gender and race. Nonetheless, an array of works prop...

Zero-cost proxies (ZC proxies) are a recent architecture performance prediction technique aiming to significantly speed up algorithms for neural architecture search (NAS). Recent work has shown that these techniques show great promise, but certain aspects, such as evaluating and exploiting their complementary strengths, are under-studied. In this w...

For autonomous skill acquisition, robots have to learn about the physical rules governing the 3D world dynamics from their own past experience to predict and reason about plausible future outcomes. To this end, we propose a transformation-based 3D video prediction (T3VIP) approach that explicitly models the 3D motion by decomposing a scene into its...

Self-Supervised Learning (SSL) has become a very active area of Deep Learning research where it is heavily used as a pre-training method for classification and other tasks. However, the rapid pace of advancements in this area comes at a price: training pipelines vary significantly across papers, which presents a potentially crucial confounding fact...

We present TabPFN, an AutoML method that is competitive with the state of the art on small tabular datasets while being over 1,000$\times$ faster. Our method is very simple: it is fully entailed in the weights of a single neural network, and a single forward pass directly yields predictions for a new dataset. Our AutoML method is meta-learned using...

Given a new dataset D and a low compute budget , how should we choose a pre-trained model to fine-tune to D, and set the fine-tuning hyperpa-rameters without risking overfitting, particularly if D is small? Here, we extend automated machine learning (AutoML) to best make these choices. Our domain-independent meta-learning approach learns a zero-sho...

Given a new dataset D and a low compute budget, how should we choose a pre-trained model to fine-tune to D, and set the fine-tuning hyperparameters without risking overfitting, particularly if D is small? Here, we extend automated machine learning (AutoML) to best make these choices. Our domain-independent meta-learning approach learns a zero-shot...

Although deep neural networks are capable of achieving performance superior to humans on various tasks, they are notorious for requiring large amounts of data and computing resources, restricting their success to domains where such resources are available. Metalearning methods can address this problem by transferring knowledge from related tasks, t...

Information-theoretic Bayesian optimization techniques have become popular for optimizing expensive-to-evaluate black-box functions due to their non-myopic qualities. Entropy Search and Predictive Entropy Search both consider the entropy over the optimum in the input space, while the recent Max-value Entropy Search considers the entropy over the op...

Automated Machine Learning (AutoML) is used more than ever before to support users in determining efficient hyperparameters, neural architectures, or even full machine learning pipelines. However, users tend to mistrust the optimization process and its results due to a lack of transparency, making manual tuning still widespread. We introduce DeepCA...

The combination of Reinforcement Learning (RL) with deep learning has led to a series of impressive feats, with many believing (deep) RL provides a path towards generally capable agents. However, the success of RL agents is often highly sensitive to design choices in the training process, which may require tedious and error-prone manual tuning. Thi...

Our world is ambiguous and this is reflected in the data we use to train our algorithms. This is especially true when we try to model natural processes where collected data is affected by noisy measurements and differences in measurement techniques. Sometimes, the process itself can be ambiguous, such as in the case of RNA folding, where a single n...

The performance of an algorithm often critically depends on its parameter configuration. While a variety of automated algorithm configuration methods have been proposed to relieve users from the tedious and error-prone task of manually tuning parameters, there is still a lot of untapped potential as the learned configuration is static, i.e., parame...

Recent years have witnessed tremendously improved efficiency of Automated Machine Learning (AutoML), especially Automated Deep Learning (AutoDL) systems, but recent work focuses on tabular, image, or NLP tasks. So far, little attention has been paid to general AutoDL frameworks for time series forecasting, despite the enormous success in applying d...

Bayesian optimization (BO) has become an established framework and popular tool for hyperparameter optimization (HPO) of machine learning (ML) algorithms. While known for its sample-efficiency, vanilla BO can not utilize readily available prior beliefs the practitioner has on the potential location of the optimum. Thus, BO disregards a valuable sou...

The success of deep learning in recent years has lead to a rising demand for neural network architecture engineering. As a consequence, neural architecture search (NAS), which aims at automatically designing neural network architectures in a data-driven manner rather than manually, has evolved as a popular field of research. With the advent of weig...

We introduce Synthetic Environments (SEs) and Reward Networks (RNs), represented by neural networks, as proxy environment models for training Reinforcement Learning (RL) agents. We show that an agent, after being trained exclusively on the SE, is able to solve the corresponding real environment. While an SE acts as a full proxy to a real environmen...

While Reinforcement Learning (RL) has made great strides towards solving increasingly complicated problems, many algorithms are still brittle to even slight changes in environments. Contextual Reinforcement Learning (cRL) provides a theoretical framework to model such changes in a principled manner, thereby enabling flexible, precise and interpreta...

It has long been observed that the performance of evolutionary algorithms and other randomized search heuristics can benefit from a non-static choice of the parameters that steer their optimization behavior. Mechanisms that identify suitable configurations on the fly ("parameter control") or via a dedicated training process ("dynamic algorithm conf...

We introduce Synthetic Environments (SEs) and Reward Networks (RNs), represented by neural networks, as proxy environment models for training Reinforcement Learning (RL) agents. We show that an agent, after being trained exclusively on the SE, is able to solve the corresponding real environment. While an SE acts as a full proxy to a real environmen...

The release of tabular benchmarks, such as NAS-Bench-101 and NAS-Bench-201, has significantly lowered the computational overhead for conducting scientific research in neural architecture search (NAS). Although they have been widely adopted and used to tune real-world NAS algorithms, these benchmarks are limited to small search spaces and focus sole...

The combination of Reinforcement Learning (RL) with deep learning has led to a series of impressive feats, with many believing (deep) RL provides a path towards generally capable agents. However, the success of RL agents is often highly sensitive to design choices in the training process, which may require tedious and error-prone manual tuning. Thi...

This paper reports the results and post-challenge analyses of ChaLearn's AutoDL challenge series, which helped sorting out a profusion of AutoML solutions for Deep Learning (DL) that had been introduced in a variety of settings, but lacked fair comparisons. All input data modalities (time series, images, videos, text, tabular) were formatted as ten...

Currently, it is hard to reap the benefits of deep learning for Bayesian methods, which allow the explicit specification of prior knowledge and accurately capture model uncertainty. We present Prior-Data Fitted Networks (PFNs). PFNs leverage large-scale machine learning techniques to approximate a large set of posteriors. The only requirement for P...

While early research in neural architecture search (NAS) required extreme computational resources, the recent releases of tabular and surrogate benchmarks have greatly increased the speed and reproducibility of NAS research. However, two of the most popular benchmarks do not provide the full training information for each architecture. As a result,...

While Reinforcement Learning has made great strides towards solving ever more complicated tasks, many algorithms are still brittle to even slight changes in their environment. This is a limiting factor for real-world applications of RL. Although the research community continuously aims at improving both robustness and generalization of RL algorithm...

Tabular datasets are the last "unconquered castle" for deep learning, with traditional ML methods like Gradient-Boosted Decision Trees still performing strongly even against recent specialized neural architectures. In this paper, we hypothesize that the key to boosting the performance of neural networks lies in rethinking the joint and simultaneous...