Bernard De Baets

Leonardo Scabini, Kallil M. Zielinski, Lucas C. Ribas et al.

Texture analysis is a classical yet challenging task in computer vision for which deep neural networks are actively being applied. Most approaches are based on building feature aggregation modules around a pre-trained backbone and then fine-tuning the new architecture on specific texture recognition tasks. Here we propose a new method named \textbf{R}andom encoding of \textbf{A}ggregated \textbf{D}eep \textbf{A}ctivation \textbf{M}aps (RADAM) which extracts rich texture representations without ever changing the backbone. The technique consists of encoding the output at different depths of a pre-trained deep convolutional network using a Randomized Autoencoder (RAE). The RAE is trained locally to each image using a closed-form solution, and its decoder weights are used to compose a 1-dimensional texture representation that is fed into a linear SVM. This means that no fine-tuning or backpropagation is needed. We explore RADAM on several texture benchmarks and achieve state-of-the-art results with different computational budgets. Our results suggest that pre-trained backbones may not require additional fine-tuning for texture recognition if their learned representations are better encoded.

Leonardo Scabini, Bernard De Baets, Odemir M. Bruno

The deep learning literature is continuously updated with new architectures and training techniques. However, weight initialization is overlooked by most recent research, despite some intriguing findings regarding random weights. On the other hand, recent works have been approaching Network Science to understand the structure and dynamics of Artificial Neural Networks (ANNs) after training. Therefore, in this work, we analyze the centrality of neurons in randomly initialized networks. We show that a higher neuronal strength variance may decrease performance, while a lower neuronal strength variance usually improves it. A new method is then proposed to rewire neuronal connections according to a preferential attachment (PA) rule based on their strength, which significantly reduces the strength variance of layers initialized by common methods. In this sense, PA rewiring only reorganizes connections, while preserving the magnitude and distribution of the weights. We show through an extensive statistical analysis in image classification that performance is improved in most cases, both during training and testing, when using both simple and complex architectures and learning schedules. Our results show that, aside from the magnitude, the organization of the weights is also relevant for better initialization of deep ANNs.

Nicolas Dewolf, Bernard De Baets, Willem Waegeman

Conformal prediction, and split conformal prediction as a specific implementation, offer a distribution-free approach to estimating prediction intervals with statistical guarantees. Recent work has shown that split conformal prediction can produce state-of-the-art prediction intervals when focusing on marginal coverage, i.e. on a calibration dataset the method produces on average prediction intervals that contain the ground truth with a predefined coverage level. However, such intervals are often not adaptive, which can be problematic for regression problems with heteroskedastic noise. This paper tries to shed new light on how prediction intervals can be constructed, using methods such as normalized and Mondrian conformal prediction, in such a way that they adapt to the heteroskedasticity of the underlying process. Theoretical and experimental results are presented in which these methods are compared in a systematic way. In particular, it is shown how the conditional validity of a chosen conformal predictor can be related to (implicit) assumptions about the data-generating distribution.

Dimitrios Iliadis, Marcel Wever, Bernard De Baets et al.

As a result of the ever increasing complexity of configuring and fine-tuning machine learning models, the field of automated machine learning (AutoML) has emerged over the past decade. However, software implementations like Auto-WEKA and Auto-sklearn typically focus on classical machine learning (ML) tasks such as classification and regression. Our work can be seen as the first attempt at offering a single AutoML framework for most problem settings that fall under the umbrella of multi-target prediction, which includes popular ML settings such as multi-label classification, multivariate regression, multi-task learning, dyadic prediction, matrix completion, and zero-shot learning. Automated problem selection and model configuration are achieved by extending DeepMTP, a general deep learning framework for MTP problem settings, with popular hyperparameter optimization (HPO) methods. Our extensive benchmarking across different datasets and MTP problem settings identifies cases where specific HPO methods outperform others.

Pieter Dewulf, Michiel Stock, Bernard De Baets

Integral transforms are invaluable mathematical tools to map functions into spaces where they are easier to characterize. We introduce the hyperdimensional transform as a new kind of integral transform. It converts square-integrable functions into noise-robust, holographic, high-dimensional representations called hyperdimensional vectors. The central idea is to approximate a function by a linear combination of random functions. We formally introduce a set of stochastic, orthogonal basis functions and define the hyperdimensional transform and its inverse. We discuss general transform-related properties such as its uniqueness, approximation properties of the inverse transform, and the representation of integrals and derivatives. The hyperdimensional transform offers a powerful, flexible framework that connects closely with other integral transforms, such as the Fourier, Laplace, and fuzzy transforms. Moreover, it provides theoretical foundations and new insights for the field of hyperdimensional computing, a computing paradigm that is rapidly gaining attention for efficient and explainable machine learning algorithms, with potential applications in statistical modelling and machine learning. In addition, we provide straightforward and easily understandable code, which can function as a tutorial and allows for the reproduction of the demonstrated examples, from computing the transform to solving differential equations.

Pieter Dewulf, Bernard De Baets, Michiel Stock

Hyperdimensional computing (HDC) is an increasingly popular computing paradigm with immense potential for future intelligent applications. Although the main ideas already took form in the 1990s, HDC recently gained significant attention, especially in the field of machine learning and data science. Next to efficiency, interoperability and explainability, HDC offers attractive properties for generalization as it can be seen as an attempt to combine connectionist ideas from neural networks with symbolic aspects. In recent work, we introduced the hyperdimensional transform, revealing deep theoretical foundations for representing functions and distributions as high-dimensional holographic vectors. Here, we present the power of the hyperdimensional transform to a broad data science audience. We use the hyperdimensional transform as a theoretical basis and provide insight into state-of-the-art HDC approaches for machine learning. We show how existing algorithms can be modified and how this transform can lead to a novel, well-founded toolbox. Next to the standard regression and classification tasks of machine learning, our discussion includes various aspects of statistical modelling, such as representation, learning and deconvolving distributions, sampling, Bayesian inference, and uncertainty estimation.

Sina Borzooei, Leonardo Scabini, Gisele Miranda et al.

Microbial communities play a key role in biological wastewater treatment processes. Activated sludge settling characteristics, for example, are affected by microbial community composition, varying by changes in operating conditions and influent characteristics of wastewater treatment plants (WWTPs). Timely assessment and prediction of changes in microbial composition leading to settling problems, such as filamentous bulking (FB), can prevent operational challenges, reductions in treatment efficiency, and adverse environmental impacts. This study presents an innovative computer vision-based approach to assess activated sludge-settling characteristics based on the morphological properties of flocs and filaments in microscopy images. Implementing the transfer learning of deep convolutional neural network (CNN) models, this approach aims to overcome the limitations of existing quantitative image analysis techniques. The offline microscopy image dataset was collected over two years, with weekly sampling at a full-scale industrial WWTP in Belgium. Multiple data augmentation techniques were employed to enhance the generalizability of the CNN models. Various CNN architectures, including Inception v3, ResNet18, ResNet152, ConvNeXt-nano, and ConvNeXt-S, were tested to evaluate their performance in predicting sludge settling characteristics. The sludge volume index was used as the final prediction variable, but the method can easily be adjusted to predict any other settling metric of choice. The results showed that the suggested CNN-based approach provides less labour-intensive, objective, and consistent assessments, while transfer learning notably minimises the training phase, resulting in a generalizable system that can be employed in real-time applications.

Michiel Stock, Dimitri Boeckaerts, Pieter Dewulf et al.

Advances in bioinformatics are primarily due to new algorithms for processing diverse biological data sources. While sophisticated alignment algorithms have been pivotal in analyzing biological sequences, deep learning has substantially transformed bioinformatics, addressing sequence, structure, and functional analyses. However, these methods are incredibly data-hungry, compute-intensive and hard to interpret. Hyperdimensional computing (HDC) has recently emerged as an intriguing alternative. The key idea is that random vectors of high dimensionality can represent concepts such as sequence identity or phylogeny. These vectors can then be combined using simple operators for learning, reasoning or querying by exploiting the peculiar properties of high-dimensional spaces. Our work reviews and explores the potential of HDC for bioinformatics, emphasizing its efficiency, interpretability, and adeptness in handling multimodal and structured data. HDC holds a lot of potential for various omics data searching, biosignal analysis and health applications.

Leonardo Scabini, Andre Sacilotti, Kallil M. Zielinski et al.

Texture, a significant visual attribute in images, has been extensively investigated across various image recognition applications. Convolutional Neural Networks (CNNs), which have been successful in many computer vision tasks, are currently among the best texture analysis approaches. On the other hand, Vision Transformers (ViTs) have been surpassing the performance of CNNs on tasks such as object recognition, causing a paradigm shift in the field. However, ViTs have so far not been scrutinized for texture recognition, hindering a proper appreciation of their potential in this specific setting. For this reason, this work explores various pre-trained ViT architectures when transferred to tasks that rely on textures. We review 21 different ViT variants and perform an extensive evaluation and comparison with CNNs and hand-engineered models on several tasks, such as assessing robustness to changes in texture rotation, scale, and illumination, and distinguishing color textures, material textures, and texture attributes. The goal is to understand the potential and differences among these models when directly applied to texture recognition, using pre-trained ViTs primarily for feature extraction and employing linear classifiers for evaluation. We also evaluate their efficiency, which is one of the main drawbacks in contrast to other methods. Our results show that ViTs generally outperform both CNNs and hand-engineered models, especially when using stronger pre-training and tasks involving in-the-wild textures (images from the internet). We highlight the following promising models: ViT-B with DINO pre-training, BeiTv2, and the Swin architecture, as well as the EfficientFormer as a low-cost alternative. In terms of efficiency, although having a higher number of GFLOPs and parameters, ViT-B and BeiT(v2) can achieve a lower feature extraction time on GPUs compared to ResNet50.

Kallil M. Zielinski, Leonardo Scabini, Lucas C. Ribas et al.

In recent years, we have seen many advancements in wood species identification. Methods like DNA analysis, Near Infrared (NIR) spectroscopy, and Direct Analysis in Real Time (DART) mass spectrometry complement the long-established wood anatomical assessment of cell and tissue morphology. However, most of these methods have some limitations such as high costs, the need for skilled experts for data interpretation, and the lack of good datasets for professional reference. Therefore, most of these methods, and certainly the wood anatomical assessment, may benefit from tools based on Artificial Intelligence. In this paper, we apply two transfer learning techniques with Convolutional Neural Networks (CNNs) to a multi-view Congolese wood species dataset including sections from different orientations and viewed at different microscopic magnifications. We explore two feature extraction methods in detail, namely Global Average Pooling (GAP) and Random Encoding of Aggregated Deep Activation Maps (RADAM), for efficient and accurate wood species identification. Our results indicate superior accuracy on diverse datasets and anatomical sections, surpassing the results of other methods. Our proposal represents a significant advancement in wood species identification, offering a robust tool to support the conservation of forest ecosystems and promote sustainable forestry practices.

Nicolas Dewolf, Bernard De Baets, Willem Waegeman

Over the last few decades, various methods have been proposed for estimating prediction intervals in regression settings, including Bayesian methods, ensemble methods, direct interval estimation methods and conformal prediction methods. An important issue is the calibration of these methods: the generated prediction intervals should have a predefined coverage level, without being overly conservative. In this work, we review the above four classes of methods from a conceptual and experimental point of view. Results on benchmark data sets from various domains highlight large fluctuations in performance from one data set to another. These observations can be attributed to the violation of certain assumptions that are inherent to some classes of methods. We illustrate how conformal prediction can be used as a general calibration procedure for methods that deliver poor results without a calibration step.

Dimitrios Iliadis, Bernard De Baets, Willem Waegeman

Multi-target prediction (MTP) serves as an umbrella term for machine learning tasks that concern the simultaneous prediction of multiple target variables. Classical instantiations are multi-label classification, multivariate regression, multi-task learning, dyadic prediction, zero-shot learning, network inference, and matrix completion. Despite the significant similarities, all these domains have evolved separately into distinct research areas over the last two decades. This led to the development of a plethora of highly-engineered methods, and created a substantially-high entrance barrier for machine learning practitioners that are not experts in the field. In this work we present a generic deep learning methodology that can be used for a wide range of multi-target prediction problems. We introduce a flexible multi-branch neural network architecture, partially configured via a questionnaire that helps end-users to select a suitable MTP problem setting for their needs. Experimental results for a wide range of domains illustrate that the proposed methodology manifests a competitive performance compared to methods from specific MTP domains.

Michiel Stock, Tapio Pahikkala, Antti Airola et al.

Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction or network inference problems. During the last decade kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify existing kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency and spectral filtering properties. Our theoretical results provide valuable insights in assessing the advantages and limitations of existing pairwise learning methods.

Michiel Stock, Krzysztof Dembczynski, Bernard De Baets et al.

Many complex multi-target prediction problems that concern large target spaces are characterised by a need for efficient prediction strategies that avoid the computation of predictions for all targets explicitly. Examples of such problems emerge in several subfields of machine learning, such as collaborative filtering, multi-label classification, dyadic prediction and biological network inference. In this article we analyse efficient and exact algorithms for computing the top-$K$ predictions in the above problem settings, using a general class of models that we refer to as separable linear relational models. We show how to use those inference algorithms, which are modifications of well-known information retrieval methods, in a variety of machine learning settings. Furthermore, we study the possibility of scoring items incompletely, while still retaining an exact top-K retrieval. Experimental results in several application domains reveal that the so-called threshold algorithm is very scalable, performing often many orders of magnitude more efficiently than the naive approach.

Michiel Stock, Tapio Pahikkala, Antti Airola et al.

Pairwise learning or dyadic prediction concerns the prediction of properties for pairs of objects. It can be seen as an umbrella covering various machine learning problems such as matrix completion, collaborative filtering, multi-task learning, transfer learning, network prediction and zero-shot learning. In this work we analyze kernel-based methods for pairwise learning, with a particular focus on a recently-suggested two-step method. We show that this method offers an appealing alternative for commonly-applied Kronecker-based methods that model dyads by means of pairwise feature representations and pairwise kernels. In a series of theoretical results, we establish correspondences between the two types of methods in terms of linear algebra and spectral filtering, and we analyze their statistical consistency. In addition, the two-step method allows us to establish novel algorithmic shortcuts for efficient training and validation on very large datasets. Putting those properties together, we believe that this simple, yet powerful method can become a standard tool for many problems. Extensive experimental results for a range of practical settings are reported.

Witold Bołt, Jan M. Baetens, Bernard De Baets

In this paper we consider the identification problem of Cellular Automata (CAs). The problem is defined and solved in the context of partial observations with time gaps of unknown length, i.e. pre-recorded, partial configurations of the system at certain, unknown time steps. A solution method based on a modified variant of a Genetic Algorithm (GA) is proposed and illustrated with brief experimental results.

Jeaneth Machicao, Jan M. Baetens, Anderson G. Marco et al.

Evidence of signatures associated with cryptographic modes of operation is established. Motivated by some analogies between cryptographic and dynamical systems, in particular with chaos theory, we propose an algorithm based on Lyapunov exponents of discrete dynamical systems to estimate the divergence among ciphertexts as the encryption algorithm is applied iteratively. The results allow to distinguish among six modes of operation, namely ECB, CBC, OFB, CFB, CTR and PCBC using DES, IDEA, TEA and XTEA block ciphers of 64 bits, as well as AES, RC6, Twofish, Seed, Serpent and Camellia block ciphers of 128 bits. Furthermore, the proposed methodology enables a classification of modes of operation of cryptographic systems according to their strength.

Núbia Rosa da Silva, Pieter Van der Weeën, Bernard De Baets et al.

In this paper, the problem of classifying synthetic and natural texture images is addressed. To tackle this problem, an innovative method is proposed that combines concepts from corrosion modeling and cellular automata to generate a texture descriptor. The core processes of metal (pitting) corrosion are identified and applied to texture images by incorporating the basic mechanisms of corrosion in the transition function of the cellular automaton. The surface morphology of the image is analyzed before and during the application of the transition function of the cellular automaton. In each iteration the cumulative mass of corroded product is obtained to construct each of the attributes of the texture descriptor. In a final step, this texture descriptor is used for image classification by applying Linear Discriminant Analysis. The method was tested on the well-known Brodatz and Vistex databases. In addition, in order to verify the robustness of the method, its invariance to noise and rotation were tested. To that end, different variants of the original two databases were obtained through addition of noise to and rotation of the images. The results showed that the method is effective for texture classification according to the high success rates obtained in all cases. This indicates the potential of employing methods inspired on natural phenomena in other fields.

Tapio Pahikkala, Michiel Stock, Antti Airola et al.

Dyadic prediction methods operate on pairs of objects (dyads), aiming to infer labels for out-of-sample dyads. We consider the full and almost full cold start problem in dyadic prediction, a setting that occurs when both objects in an out-of-sample dyad have not been observed during training, or if one of them has been observed, but very few times. A popular approach for addressing this problem is to train a model that makes predictions based on a pairwise feature representation of the dyads, or, in case of kernel methods, based on a tensor product pairwise kernel. As an alternative to such a kernel approach, we introduce a novel two-step learning algorithm that borrows ideas from the fields of pairwise learning and spectral filtering. We show theoretically that the two-step method is very closely related to the tensor product kernel approach, and experimentally that it yields a slightly better predictive performance. Moreover, unlike existing tensor product kernel methods, the two-step method allows closed-form solutions for training and parameter selection via cross-validation estimates both in the full and almost full cold start settings, making the approach much more efficient and straightforward to implement.

Michiel Stock, Thomas Fober, Eyke Hüllermeier et al.

Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored. In this work we show that rankings of that kind can be substantially improved by applying kernel-based learning algorithms. This approach enables the detection of statistical dependencies between similarities of the active cleft and the biological function of annotated enzymes. This is in contrast to search-based approaches, which do not take annotated training data into account. Similarity measures based on the active cleft are known to outperform sequence-based or structure-based measures under certain conditions. We consider the Enzyme Commission (EC) classification hierarchy for obtaining annotated enzymes during the training phase. The results of a set of sizeable experiments indicate a consistent and significant improvement for a set of similarity measures that exploit information about small cavities in the surface of enzymes.

Tapio Pahikkala, Antti Airola, Michiel Stock et al.

In domains like bioinformatics, information retrieval and social network analysis, one can find learning tasks where the goal consists of inferring a ranking of objects, conditioned on a particular target object. We present a general kernel framework for learning conditional rankings from various types of relational data, where rankings can be conditioned on unseen data objects. We propose efficient algorithms for conditional ranking by optimizing squared regression and ranking loss functions. We show theoretically, that learning with the ranking loss is likely to generalize better than with the regression loss. Further, we prove that symmetry or reciprocity properties of relations can be efficiently enforced in the learned models. Experiments on synthetic and real-world data illustrate that the proposed methods deliver state-of-the-art performance in terms of predictive power and computational efficiency. Moreover, we also show empirically that incorporating symmetry or reciprocity properties can improve the generalization performance.