arXiv subjects

Bernd Bischl

Publications and source records attributed to Bernd Bischl.

At least 91 records · Page 5Linked to original sources

arXiv2022

Improved proteasomal cleavage prediction with positive-unlabeled learning

Accurate in silico modeling of the antigen processing pathway is crucial to enable personalized epitope vaccine design for cancer. An important step of such pathway is the degradation of the vaccine into smaller peptides by the proteasome, some of which are going to be presented to T cells by the MHC complex. While predicting MHC-peptide presentation has received a lot of attention recently, proteasomal cleavage prediction remains a relatively unexplored area in light of recent advancesin high-throughput mass spectrometry-based MHC ligandomics. Moreover, as such experimental techniques do not allow to identify regions that cannot be cleaved, the latest predictors generate decoy negative samples and treat them as true negatives when training, even though some of them could actually be positives. In this work, we thus present a new predictor trained with an expanded dataset and the solid theoretical underpinning of positive-unlabeled learning, achieving a new state-of-the-art in proteasomal cleavage prediction. The improved predictive capabilities will in turn enable more precise vaccine development improving the efficacy of epitope-based vaccines. Pretrained models are available on GitHub

q-bio.QM↗

arXiv2022

What cleaves? Is proteasomal cleavage prediction reaching a ceiling?

Epitope vaccines are a promising direction to enable precision treatment for cancer, autoimmune diseases, and allergies. Effectively designing such vaccines requires accurate prediction of proteasomal cleavage in order to ensure that the epitopes in the vaccine are presented to T cells by the major histocompatibility complex (MHC). While direct identification of proteasomal cleavage \emph{in vitro} is cumbersome and low throughput, it is possible to implicitly infer cleavage events from the termini of MHC-presented epitopes, which can be detected in large amounts thanks to recent advances in high-throughput MHC ligandomics. Inferring cleavage events in such a way provides an inherently noisy signal which can be tackled with new developments in the field of deep learning that supposedly make it possible to learn predictors from noisy labels. Inspired by such innovations, we sought to modernize proteasomal cleavage predictors by benchmarking a wide range of recent methods, including LSTMs, transformers, CNNs, and denoising methods, on a recently introduced cleavage dataset. We found that increasing model scale and complexity appeared to deliver limited performance gains, as several methods reached about 88.5% AUC on C-terminal and 79.5% AUC on N-terminal cleavage prediction. This suggests that the noise and/or complexity of proteasomal cleavage and the subsequent biological processes of the antigen processing pathway are the major limiting factors for predictive performance rather than the specific modeling approach used. While biological complexity can be tackled by more data and better models, noise and randomness inherently limit the maximum achievable predictive performance. All our datasets and experiments are available at https://github.com/ziegler-ingo/cleavage_prediction.

q-bio.QM↗

arXiv2022

Benchmarking Online Sequence-to-Sequence and Character-based Handwriting Recognition from IMU-Enhanced Pens

Purpose. Handwriting is one of the most frequently occurring patterns in everyday life and with it come challenging applications such as handwriting recognition (HWR), writer identification, and signature verification. In contrast to offline HWR that only uses spatial information (i.e., images), online HWR (OnHWR) uses richer spatio-temporal information (i.e., trajectory data or inertial data). While there exist many offline HWR datasets, there is only little data available for the development of OnHWR methods on paper as it requires hardware-integrated pens. Methods. This paper presents data and benchmark models for real-time sequence-to-sequence (seq2seq) learning and single character-based recognition. Our data is recorded by a sensor-enhanced ballpoint pen, yielding sensor data streams from triaxial accelerometers, a gyroscope, a magnetometer and a force sensor at 100 Hz. We propose a variety of datasets including equations and words for both the writer-dependent and writer-independent tasks. Our datasets allow a comparison between classical OnHWR on tablets and on paper with sensor-enhanced pens. We provide an evaluation benchmark for seq2seq and single character-based HWR using recurrent and temporal convolutional networks and Transformers combined with a connectionist temporal classification (CTC) loss and cross-entropy (CE) losses. Results. Our convolutional network combined with BiLSTMs outperforms Transformer-based architectures, is on par with InceptionTime for sequence-based classification tasks, and yields better results compared to 28 state-of-the-art techniques. Time-series augmentation methods improve the sequence-based task, and we show that CE variants can improve the single classification task.

cs.LG↗

arXiv2022

Joint Debiased Representation and Image Clustering Learning with Self-Supervision

Contrastive learning is among the most successful methods for visual representation learning, and its performance can be further improved by jointly performing clustering on the learned representations. However, existing methods for joint clustering and contrastive learning do not perform well on long-tailed data distributions, as majority classes overwhelm and distort the loss of minority classes, thus preventing meaningful representations to be learned. Motivated by this, we develop a novel joint clustering and contrastive learning framework by adapting the debiased contrastive loss to avoid under-clustering minority classes of imbalanced datasets. We show that our proposed modified debiased contrastive loss and divergence clustering loss improves the performance across multiple datasets and learning tasks. The source code is available at https://anonymous.4open.science/r/SSL-debiased-clustering

cs.CV↗

arXiv2022

Joint Debiased Representation Learning and Imbalanced Data Clustering

One of the most promising approaches for unsupervised learning is combining deep representation learning and deep clustering. Some recent works propose to simultaneously learn representation using deep neural networks and perform clustering by defining a clustering loss on top of embedded features. However, these approaches are sensitive to imbalanced data and out-of-distribution samples. As a consequence, these methods optimize clustering by pushing data close to randomly initialized cluster centers. This is problematic when the number of instances varies largely in different classes or a cluster with few samples has less chance to be assigned a good centroid. To overcome these limitations, we introduce a new unsupervised framework for joint debiased representation learning and image clustering. We simultaneously train two deep learning models, a deep representation network that captures the data distribution, and a deep clustering network that learns embedded features and performs clustering. Specifically, the clustering network and learning representation network both take advantage of our proposed statistics pooling block that represents mean, variance, and cardinality to handle the out-of-distribution samples and class imbalance. Our experiments show that using these representations, one can considerably improve results on imbalanced image clustering across a variety of image datasets. Moreover, the learned representations generalize well when transferred to the out-of-distribution dataset.

cs.CV↗

arXiv2022

Robust and Efficient Imbalanced Positive-Unlabeled Learning with Self-supervision

Learning from positive and unlabeled (PU) data is a setting where the learner only has access to positive and unlabeled samples while having no information on negative examples. Such PU setting is of great importance in various tasks such as medical diagnosis, social network analysis, financial markets analysis, and knowledge base completion, which also tend to be intrinsically imbalanced, i.e., where most examples are actually negatives. Most existing approaches for PU learning, however, only consider artificially balanced datasets and it is unclear how well they perform in the realistic scenario of imbalanced and long-tail data distribution. This paper proposes to tackle this challenge via robust and efficient self-supervised pretraining. However, training conventional self-supervised learning methods when applied with highly imbalanced PU distribution needs better reformulation. In this paper, we present \textit{ImPULSeS}, a unified representation learning framework for \underline{Im}balanced \underline{P}ositive \underline{U}nlabeled \underline{L}earning leveraging \underline{Se}lf-\underline{S}upervised debiase pre-training. ImPULSeS uses a generic combination of large-scale unsupervised learning with debiased contrastive loss and additional reweighted PU loss. We performed different experiments across multiple datasets to show that ImPULSeS is able to halve the error rate of the previous state-of-the-art, even compared with previous methods that are given the true prior. Moreover, our method showed increased robustness to prior misspecification and superior performance even when pretraining was performed on an unrelated dataset. We anticipate such robustness and efficiency will make it much easier for practitioners to obtain excellent results on other PU datasets of interest. The source code is available at \url{https://github.com/JSchweisthal/ImPULSeS}

cs.LG↗

arXiv2022

YAHPO Gym -- An Efficient Multi-Objective Multi-Fidelity Benchmark for Hyperparameter Optimization

When developing and analyzing new hyperparameter optimization methods, it is vital to empirically evaluate and compare them on well-curated benchmark suites. In this work, we propose a new set of challenging and relevant benchmark problems motivated by desirable properties and requirements for such benchmarks. Our new surrogate-based benchmark collection consists of 14 scenarios that in total constitute over 700 multi-fidelity hyperparameter optimization problems, which all enable multi-objective hyperparameter optimization. Furthermore, we empirically compare surrogate-based benchmarks to the more widely-used tabular benchmarks, and demonstrate that the latter may produce unfaithful results regarding the performance ranking of HPO methods. We examine and compare our benchmark collection with respect to defined requirements and propose a single-objective as well as a multi-objective benchmark suite on which we compare 7 single-objective and 7 multi-objective optimizers in a benchmark experiment. Our software is available at [https://github.com/slds-lmu/yahpo_gym].

cs.LG↗

arXiv2022

A Collection of Quality Diversity Optimization Problems Derived from Hyperparameter Optimization of Machine Learning Models

The goal of Quality Diversity Optimization is to generate a collection of diverse yet high-performing solutions to a given problem at hand. Typical benchmark problems are, for example, finding a repertoire of robot arm configurations or a collection of game playing strategies. In this paper, we propose a set of Quality Diversity Optimization problems that tackle hyperparameter optimization of machine learning models - a so far underexplored application of Quality Diversity Optimization. Our benchmark problems involve novel feature functions, such as interpretability or resource usage of models. To allow for fast and efficient benchmarking, we build upon YAHPO Gym, a recently proposed open source benchmarking suite for hyperparameter optimization that makes use of high performing surrogate models and returns these surrogate model predictions instead of evaluating the true expensive black box function. We present results of an initial experimental study comparing different Quality Diversity optimizers on our benchmark problems. Furthermore, we discuss future directions and challenges of Quality Diversity Optimization in the context of hyperparameter optimization.

cs.LG↗

arXiv2022

Tackling Neural Architecture Search With Quality Diversity Optimization

Neural architecture search (NAS) has been studied extensively and has grown to become a research field with substantial impact. While classical single-objective NAS searches for the architecture with the best performance, multi-objective NAS considers multiple objectives that should be optimized simultaneously, e.g., minimizing resource usage along the validation error. Although considerable progress has been made in the field of multi-objective NAS, we argue that there is some discrepancy between the actual optimization problem of practical interest and the optimization problem that multi-objective NAS tries to solve. We resolve this discrepancy by formulating the multi-objective NAS problem as a quality diversity optimization (QDO) problem and introduce three quality diversity NAS optimizers (two of them belonging to the group of multifidelity optimizers), which search for high-performing yet diverse architectures that are optimal for application-specific niches, e.g., hardware constraints. By comparing these optimizers to their multi-objective counterparts, we demonstrate that quality diversity NAS in general outperforms multi-objective NAS with respect to quality of solutions and efficiency. We further show how applications and future NAS research can thrive on QDO.

cs.LG↗

arXiv2022

HPO X ELA: Investigating Hyperparameter Optimization Landscapes by Means of Exploratory Landscape Analysis

Hyperparameter optimization (HPO) is a key component of machine learning models for achieving peak predictive performance. While numerous methods and algorithms for HPO have been proposed over the last years, little progress has been made in illuminating and examining the actual structure of these black-box optimization problems. Exploratory landscape analysis (ELA) subsumes a set of techniques that can be used to gain knowledge about properties of unknown optimization problems. In this paper, we evaluate the performance of five different black-box optimizers on 30 HPO problems, which consist of two-, three- and five-dimensional continuous search spaces of the XGBoost learner trained on 10 different data sets. This is contrasted with the performance of the same optimizers evaluated on 360 problem instances from the black-box optimization benchmark (BBOB). We then compute ELA features on the HPO and BBOB problems and examine similarities and differences. A cluster analysis of the HPO and BBOB problems in ELA feature space allows us to identify how the HPO problems compare to the BBOB problems on a structural meta-level. We identify a subset of BBOB problems that are close to the HPO problems in ELA feature space and show that optimizer performance is comparably similar on these two sets of benchmark problems. We highlight open challenges of ELA for HPO and discuss potential directions of future research and applications.

cs.LG↗

arXiv2022

Efficient Automated Deep Learning for Time Series Forecasting

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 different novel architectures to such tasks. In this paper, we propose an efficient approach for the joint optimization of neural architecture and hyperparameters of the entire data processing pipeline for time series forecasting. In contrast to common NAS search spaces, we designed a novel neural architecture search space covering various state-of-the-art architectures, allowing for an efficient macro-search over different DL approaches. To efficiently search in such a large configuration space, we use Bayesian optimization with multi-fidelity optimization. We empirically study several different budget types enabling efficient multi-fidelity optimization on different forecasting datasets. Furthermore, we compared our resulting system, dubbed \system, against several established baselines and show that it significantly outperforms all of them across several datasets.

cs.LG↗

arXiv2022

Domain Adaptation for Time-Series Classification to Mitigate Covariate Shift

The performance of a machine learning model degrades when it is applied to data from a similar but different domain than the data it has initially been trained on. To mitigate this domain shift problem, domain adaptation (DA) techniques search for an optimal transformation that converts the (current) input data from a source domain to a target domain to learn a domain-invariant representation that reduces domain discrepancy. This paper proposes a novel supervised DA based on two steps. First, we search for an optimal class-dependent transformation from the source to the target domain from a few samples. We consider optimal transport methods such as the earth mover's distance, Sinkhorn transport and correlation alignment. Second, we use embedding similarity techniques to select the corresponding transformation at inference. We use correlation metrics and higher-order moment matching techniques. We conduct an extensive evaluation on time-series datasets with domain shift including simulated and various online handwriting datasets to demonstrate the performance.

cs.LG↗

arXiv2022

Uncertainty-aware Evaluation of Time-Series Classification for Online Handwriting Recognition with Domain Shift

For many applications, analyzing the uncertainty of a machine learning model is indispensable. While research of uncertainty quantification (UQ) techniques is very advanced for computer vision applications, UQ methods for spatio-temporal data are less studied. In this paper, we focus on models for online handwriting recognition, one particular type of spatio-temporal data. The data is observed from a sensor-enhanced pen with the goal to classify written characters. We conduct a broad evaluation of aleatoric (data) and epistemic (model) UQ based on two prominent techniques for Bayesian inference, Stochastic Weight Averaging-Gaussian (SWAG) and Deep Ensembles. Next to a better understanding of the model, UQ techniques can detect out-of-distribution data and domain shifts when combining right-handed and left-handed writers (an underrepresented group).

cs.CV↗

arXiv2022

Factorized Structured Regression for Large-Scale Varying Coefficient Models

Recommender Systems (RS) pervade many aspects of our everyday digital life. Proposed to work at scale, state-of-the-art RS allow the modeling of thousands of interactions and facilitate highly individualized recommendations. Conceptually, many RS can be viewed as instances of statistical regression models that incorporate complex feature effects and potentially non-Gaussian outcomes. Such structured regression models, including time-aware varying coefficients models, are, however, limited in their applicability to categorical effects and inclusion of a large number of interactions. Here, we propose Factorized Structured Regression (FaStR) for scalable varying coefficient models. FaStR overcomes limitations of general regression models for large-scale data by combining structured additive regression and factorization approaches in a neural network-based model implementation. This fusion provides a scalable framework for the estimation of statistical models in previously infeasible data settings. Empirical results confirm that the estimation of varying coefficients of our approach is on par with state-of-the-art regression techniques, while scaling notably better and also being competitive with other time-aware RS in terms of prediction performance. We illustrate FaStR's performance and interpretability on a large-scale behavioral study with smartphone user data.

stat.ML↗

arXiv2022

Analyzing the Effects of Handling Data Imbalance on Learned Features from Medical Images by Looking Into the Models

One challenging property lurking in medical datasets is the imbalanced data distribution, where the frequency of the samples between the different classes is not balanced. Training a model on an imbalanced dataset can introduce unique challenges to the learning problem where a model is biased towards the highly frequent class. Many methods are proposed to tackle the distributional differences and the imbalanced problem. However, the impact of these approaches on the learned features is not well studied. In this paper, we look deeper into the internal units of neural networks to observe how handling data imbalance affects the learned features. We study several popular cost-sensitive approaches for handling data imbalance and analyze the feature maps of the convolutional neural networks from multiple perspectives: analyzing the alignment of salient features with pathologies and analyzing the pathology-related concepts encoded by the networks. Our study reveals differences and insights regarding the trained models that are not reflected by quantitative metrics such as AUROC and AP and show up only by looking at the models through a lens.

eess.IV↗

arXiv2022

deepregression: a Flexible Neural Network Framework for Semi-Structured Deep Distributional Regression

In this paper we describe the implementation of semi-structured deep distributional regression, a flexible framework to learn conditional distributions based on the combination of additive regression models and deep networks. Our implementation encompasses (1) a modular neural network building system based on the deep learning library \pkg{TensorFlow} for the fusion of various statistical and deep learning approaches, (2) an orthogonalization cell to allow for an interpretable combination of different subnetworks, as well as (3) pre-processing steps necessary to set up such models. The software package allows to define models in a user-friendly manner via a formula interface that is inspired by classical statistical model frameworks such as \pkg{mgcv}. The packages' modular design and functionality provides a unique resource for both scalable estimation of complex statistical models and the combination of approaches from deep learning and statistics. This allows for state-of-the-art predictive performance while simultaneously retaining the indispensable interpretability of classical statistical models.

stat.ML↗

arXiv2022

Regularized target encoding outperforms traditional methods in supervised machine learning with high cardinality features

Since most machine learning (ML) algorithms are designed for numerical inputs, efficiently encoding categorical variables is a crucial aspect in data analysis. A common problem are high cardinality features, i.e. unordered categorical predictor variables with a high number of levels. We study techniques that yield numeric representations of categorical variables which can then be used in subsequent ML applications. We focus on the impact of these techniques on a subsequent algorithm's predictive performance, and -- if possible -- derive best practices on when to use which technique. We conducted a large-scale benchmark experiment, where we compared different encoding strategies together with five ML algorithms (lasso, random forest, gradient boosting, k-nearest neighbors, support vector machine) using datasets from regression, binary- and multiclass- classification settings. In our study, regularized versions of target encoding (i.e. using target predictions based on the feature levels in the training set as a new numerical feature) consistently provided the best results. Traditionally widely used encodings that make unreasonable assumptions to map levels to integers (e.g. integer encoding) or to reduce the number of levels (possibly based on target information, e.g. leaf encoding) before creating binary indicator variables (one-hot or dummy encoding) were not as effective in comparison.

stat.ML↗

arXiv2022

Deep Semi-Supervised Learning for Time Series Classification

While Semi-supervised learning has gained much attention in computer vision on image data, yet limited research exists on its applicability in the time series domain. In this work, we investigate the transferability of state-of-the-art deep semi-supervised models from image to time series classification. We discuss the necessary model adaptations, in particular an appropriate model backbone architecture and the use of tailored data augmentation strategies. Based on these adaptations, we explore the potential of deep semi-supervised learning in the context of time series classification by evaluating our methods on large public time series classification problems with varying amounts of labelled samples. We perform extensive comparisons under a decidedly realistic and appropriate evaluation scheme with a unified reimplementation of all algorithms considered, which is yet lacking in the field. We find that these transferred semi-supervised models show significant performance gains over strong supervised, semi-supervised and self-supervised alternatives, especially for scenarios with very few labelled samples.

cs.LG↗