Kai Puolamäki

Lauri Seppäläinen, Anton Björklund, Vitus Besel et al.

Manifold visualisation techniques are commonly used to visualise high-dimensional datasets in physical sciences. In this paper we apply a recently introduced manifold visualisation method, called Slise, on datasets from physics and chemistry. Slisemap combines manifold visualisation with explainable artificial intelligence. Explainable artificial intelligence is used to investigate the decision processes of black box machine learning models and complex simulators. With Slisemap we find an embedding such that data items with similar local explanations are grouped together. Hence, Slisemap gives us an overview of the different behaviours of a black box model. This makes Slisemap into a supervised manifold visualisation method, where the patterns in the embedding reflect a target property. In this paper we show how Slisemap can be used and evaluated on physical data and that Slisemap is helpful in finding meaningful information on classification and regression models trained on these datasets.

Arash Jamshidi, Lauri Seppäläinen, Katsiaryna Haitsiukevich et al.

Machine learning models are often learned by minimising a loss function on the training data using a gradient descent algorithm. These models often suffer from overfitting, leading to a decline in predictive performance on unseen data. A standard solution is early stopping using a hold-out validation set, which halts the minimisation when the validation loss stops decreasing. However, this hold-out set reduces the data available for training. This paper presents GRADSTOP, a novel stochastic early stopping method that only uses information in the gradients, which are produced by the gradient descent algorithm ``for free.'' Our main contributions are that we estimate the Bayesian posterior by the gradient information, define the early stopping problem as drawing sample from this posterior, and use the approximated posterior to obtain a stopping criterion. Our empirical evaluation shows that GRADSTOP achieves a small loss on test data and compares favourably to a validation-set-based stopping criterion. By leveraging the entire dataset for training, our method is particularly advantageous in data-limited settings, such as transfer learning. It can be incorporated as an optional feature in gradient descent libraries with only a small computational overhead. The source code is available at https://github.com/edahelsinki/gradstop.

Anton Björklund, Jarmo Mäkelä, Kai Puolamäki

Existing methods for explaining black box learning models often focus on building local explanations of model behaviour for a particular data item. It is possible to create global explanations for all data items, but these explanations generally have low fidelity for complex black box models. We propose a new supervised manifold visualisation method, SLISEMAP, that simultaneously finds local explanations for all data items and builds a (typically) two-dimensional global visualisation of the black box model such that data items with similar local explanations are projected nearby. We provide a mathematical derivation of our problem and an open source implementation implemented using the GPU-optimised PyTorch library. We compare SLISEMAP to multiple popular dimensionality reduction methods and find that SLISEMAP is able to utilise labelled data to create embeddings with consistent local white box models. We also compare SLISEMAP to other model-agnostic local explanation methods and show that SLISEMAP provides comparable explanations and that the visualisations can give a broader understanding of black box regression and classification models.

Kai Puolamäki, Emilia Oikarinen, Andreas Henelius

Efficient explorative data analysis systems must take into account both what a user knows and wants to know. This paper proposes a principled framework for interactive visual exploration of relations in data, through views most informative given the user's current knowledge and objectives. The user can input pre-existing knowledge of relations in the data and also formulate specific exploration interests, which are then taken into account in the exploration. The idea is to steer the exploration process towards the interests of the user, instead of showing uninteresting or already known relations. The user's knowledge is modelled by a distribution over data sets parametrised by subsets of rows and columns of data, called tile constraints. We provide a computationally efficient implementation of this concept based on constrained randomisation. Furthermore, we describe a novel dimensionality reduction method for finding the views most informative to the user, which at the limit of no background knowledge and with generic objectives reduces to PCA. We show that the method is suitable for interactive use and is robust to noise, outperforms standard projection pursuit visualisation methods, and gives understandable and useful results in analysis of real-world data. We provide an open-source implementation of the framework.

Kai Puolamäki, Emilia Oikarinen, Buse Atli et al.

An explorative data analysis system should be aware of what the user already knows and what the user wants to know of the data: otherwise the system cannot provide the user with the most informative and useful views of the data. We propose a principled way to do exploratory data analysis, where the user's background knowledge is modeled by a distribution parametrised by subsets of rows and columns in the data, called tiles. The user can also use tiles to describe his or her interests concerning relations in the data. We provide a computationally efficient implementation of this concept based on constrained randomisation. The implementation is used to model both the background knowledge and the user's information request and is a necessary prerequisite for any interactive system. Furthermore, we describe a novel linear projection pursuit method to find and show the views most informative to the user, which at the limit of no background knowledge and with generic objectives reduces to PCA. We show that our method is robust under noise and fast enough for interactive use. We also show that the method gives understandable and useful results when analysing real-world data sets. We will release an open source library implementing the idea, including the experiments presented in this paper. We show that our method can outperform standard projection pursuit visualisation methods in exploration tasks. Our framework makes it possible to construct human-guided data exploration systems which are fast, powerful, and give results that are easy to comprehend.

Andreas Henelius, Emilia Oikarinen, Kai Puolamäki

The outcome of the explorative data analysis (EDA) phase is vital for successful data analysis. EDA is more effective when the user interacts with the system used to carry out the exploration. In the recently proposed paradigm of iterative data mining the user controls the exploration by inputting knowledge in the form of patterns observed during the process. The system then shows the user views of the data that are maximally informative given the user's current knowledge. Although this scheme is good at showing surprising views of the data to the user, there is a clear shortcoming: the user cannot steer the process. In many real cases we want to focus on investigating specific questions concerning the data. This paper presents the Human Guided Data Exploration framework, generalising previous research. This framework allows the user to incorporate existing knowledge into the exploration process, focus on exploring a subset of the data, and compare different complex hypotheses concerning relations in the data. The framework utilises a computationally efficient constrained randomisation scheme. To showcase the framework, we developed a free open-source tool, using which the empirical evaluation on real-world datasets was carried out. Our evaluation shows that the ability to focus on particular subsets and being able to compare hypotheses are important additions to the interactive iterative data mining process.

Kai Puolamäki, Emilia Oikarinen, Bo Kang et al.

Visual exploration of high-dimensional real-valued datasets is a fundamental task in exploratory data analysis (EDA). Existing methods use predefined criteria to choose the representation of data. There is a lack of methods that (i) elicit from the user what she has learned from the data and (ii) show patterns that she does not know yet. We construct a theoretical model where identified patterns can be input as knowledge to the system. The knowledge syntax here is intuitive, such as "this set of points forms a cluster", and requires no knowledge of maths. This background knowledge is used to find a Maximum Entropy distribution of the data, after which the system provides the user data projections in which the data and the Maximum Entropy distribution differ the most, hence showing the user aspects of the data that are maximally informative given the user's current knowledge. We provide an open source EDA system with tailored interactive visualizations to demonstrate these concepts. We study the performance of the system and present use cases on both synthetic and real data. We find that the model and the prototype system allow the user to learn information efficiently from various data sources and the system works sufficiently fast in practice. We conclude that the information theoretic approach to exploratory data analysis where patterns observed by a user are formalized as constraints provides a principled, intuitive, and efficient basis for constructing an EDA system.

Matias Loukojärvi, Ananth Mahadevan, Katsiaryna Haitsiukevich et al.

Advances in computational chemistry have produced high-dimensional datasets on atmospherically relevant molecules. To aid exploration of such datasets, particularly for the study of atmospheric aerosol formation, we introduce PhiPlot: a web-based environment for interactive exploration and knowledge-based dimensionality reduction. The integration of visualisation, clustering, and domain knowledge-guided embedding refinement enables the discovery of patterns in the data and supports hypothesis generation. The application connects to an existing, evolving collection of molecular databases, offering an accessible interface for data-driven research in atmospheric chemistry.

Arash Jamshidi, Katsiaryna Haitsiukevich, Kai Puolamäki

Second-order information -- such as curvature or data covariance -- is critical for optimisation, diagnostics, and robustness. However, in many modern settings, only the gradients are observable. We show that the gradients alone can reveal the Hessian, equalling the data covariance $Σ$ for the linear regression. Our key insight is a simple variance calibration: injecting Gaussian noise so that the total target noise variance equals the batch size ensures that the empirical gradient covariance closely approximates the Hessian, even when evaluated far from the optimum. We provide non-asymptotic operator-norm guarantees under sub-Gaussian inputs. We also show that without such calibration, recovery can fail by an $Ω(1)$ factor. The proposed method is practical (a "set target-noise variance to $n$" rule) and robust (variance $\mathcal{O}(n)$ suffices to recover $Σ$ up to scale). Applications include preconditioning for faster optimisation, adversarial risk estimation, and gradient-only training, for example, in distributed systems. We support our theoretical results with experiments on synthetic and real data.

Lauri Seppäläinen, Jakub Kubečka, Jonas Elm et al.

Understanding how atmospheric molecular clusters form and grow is key to resolving one of the biggest uncertainties in climate modelling: the formation of new aerosol particles. While quantum chemistry offers accurate insights into these early-stage clusters, its steep computational costs limit large-scale exploration. In this work, we present a fast, interpretable, and surprisingly powerful alternative: $k$-nearest neighbour ($k$-NN) regression model. By leveraging chemically informed distance metrics, including a kernel-induced metric and one learned via metric learning for kernel regression (MLKR), we show that simple $k$-NN models can rival more complex kernel ridge regression (KRR) models in accuracy, while reducing computational time by orders of magnitude. We perform this comparison with the well-established Faber-Christensen-Huang-Lilienfeld (FCHL19) molecular descriptor, but other descriptors (e.g., FCHL18, MBDF, and CM) can be shown to have similar performance. Applied to both simple organic molecules in the QM9 benchmark set and large datasets of atmospheric molecular clusters (sulphuric acid-water and sulphuric-multibase -base systems), our $k$-NN models achieve near-chemical accuracy, scale seamlessly to datasets with over 250,000 entries, and even appears to extrapolate to larger unseen clusters with minimal error (often nearing 1 kcal/mol). With built-in interpretability and straightforward uncertainty estimation, this work positions $k$-NN as a potent tool for accelerating discovery in atmospheric chemistry and beyond.

Lauri Seppäläinen, Mudong Guo, Kai Puolamäki

Most commonly used non-linear machine learning methods are closed-box models, uninterpretable to humans. The field of explainable artificial intelligence (XAI) aims to develop tools to examine the inner workings of these closed boxes. An often-used model-agnostic approach to XAI involves using simple models as local approximations to produce so-called local explanations; examples of this approach include LIME, SHAP, and SLISEMAP. This paper shows how a large set of local explanations can be reduced to a small "proxy set" of simple models, which can act as a generative global explanation. This reduction procedure, ExplainReduce, can be formulated as an optimisation problem and approximated efficiently using greedy heuristics.

Hoang Phuc Hau Luu, Hanlin Yu, Bernardo Williams et al.

We study a class of optimization problems in the Wasserstein space (the space of probability measures) where the objective function is nonconvex along generalized geodesics. Specifically, the objective exhibits some difference-of-convex structure along these geodesics. The setting also encompasses sampling problems where the logarithm of the target distribution is difference-of-convex. We derive multiple convergence insights for a novel semi Forward-Backward Euler scheme under several nonconvex (and possibly nonsmooth) regimes. Notably, the semi Forward-Backward Euler is just a slight modification of the Forward-Backward Euler whose convergence is -- to our knowledge -- still unknown in our very general non-geodesically-convex setting.

Anri Patron, Ayush Prasad, Hoang Phuc Hau Luu et al.

A fundamental problem in supervised learning is to find a good set of features or distance measures. If the new set of features is of lower dimensionality and can be obtained by a simple transformation of the original data, they can make the model understandable, reduce overfitting, and even help to detect distribution drift. We propose a supervised dimensionality reduction method Gradient Boosting Mapping (GBMAP), where the outputs of weak learners -- defined as one-layer perceptrons -- define the embedding. We show that the embedding coordinates provide better features for the supervised learning task, making simple linear models competitive with the state-of-the-art regressors and classifiers. We also use the embedding to find a principled distance measure between points. The features and distance measures automatically ignore directions irrelevant to the supervised learning task. We also show that we can reliably detect out-of-distribution data points with potentially large regression or classification errors. GBMAP is fast and works in seconds for dataset of million data points or hundreds of features. As a bonus, GBMAP provides a regression and classification performance comparable to the state-of-the-art supervised learning methods.

Laila Melkas, Rafael Savvides, Suyog Chandramouli et al.

Causal structure discovery (CSD) models are making inroads into several domains, including Earth system sciences. Their widespread adaptation is however hampered by the fact that the resulting models often do not take into account the domain knowledge of the experts and that it is often necessary to modify the resulting models iteratively. We present a workflow that is required to take this knowledge into account and to apply CSD algorithms in Earth system sciences. At the same time, we describe open research questions that still need to be addressed. We present a way to interactively modify the outputs of the CSD algorithms and argue that the user interaction can be modelled as a greedy finding of the local maximum-a-posteriori solution of the likelihood function, which is composed of the likelihood of the causal model and the prior distribution representing the knowledge of the expert user. We use a real-world data set for examples constructed in collaboration with our co-authors, who are the domain area experts. We show that finding maximally usable causal models in the Earth system sciences or other similar domains is a difficult task which contains many interesting open research questions. We argue that taking the domain knowledge into account has a substantial effect on the final causal models discovered.

Sami Hanhijärvi, Markus Ojala, Niko Vuokko et al.

There is a wide variety of data mining methods available, and it is generally useful in exploratory data analysis to use many different methods for the same dataset. This, however, leads to the problem of whether the results found by one method are a reflection of the phenomenon shown by the results of another method, or whether the results depict in some sense unrelated properties of the data. For example, using clustering can give indication of a clear cluster structure, and computing correlations between variables can show that there are many significant correlations in the data. However, it can be the case that the correlations are actually determined by the cluster structure. In this paper, we consider the problem of randomizing data so that previously discovered patterns or models are taken into account. The randomization methods can be used in iterative data mining. At each step in the data mining process, the randomization produces random samples from the set of data matrices satisfying the already discovered patterns or models. That is, given a data set and some statistics (e.g., cluster centers or co-occurrence counts) of the data, the randomization methods sample data sets having similar values of the given statistics as the original data set. We use Metropolis sampling based on local swaps to achieve this. We describe experiments on real data that demonstrate the usefulness of our approach. Our results indicate that in many cases, the results of, e.g., clustering actually imply the results of, say, frequent pattern discovery.

Francesco Concas, Julien Mineraud, Eemil Lagerspetz et al.

The significance of air pollution and the problems associated with it are fueling deployments of air quality monitoring stations worldwide. The most common approach for air quality monitoring is to rely on environmental monitoring stations, which unfortunately are very expensive both to acquire and to maintain. Hence environmental monitoring stations are typically sparsely deployed, resulting in limited spatial resolution for measurements. Recently, low-cost air quality sensors have emerged as an alternative that can improve the granularity of monitoring. The use of low-cost air quality sensors, however, presents several challenges: they suffer from cross-sensitivities between different ambient pollutants; they can be affected by external factors, such as traffic, weather changes, and human behavior; and their accuracy degrades over time. Periodic re-calibration can improve the accuracy of low-cost sensors, particularly with machine-learning-based calibration, which has shown great promise due to its capability to calibrate sensors in-field. In this article, we survey the rapidly growing research landscape of low-cost sensor technologies for air quality monitoring and their calibration using machine learning techniques. We also identify open research challenges and present directions for future research.

Henri Tiittanen, Emilia Oikarinen, Andreas Henelius et al.

Regression analysis is a standard supervised machine learning method used to model an outcome variable in terms of a set of predictor variables. In most real-world applications we do not know the true value of the outcome variable being predicted outside the training data, i.e., the ground truth is unknown. It is hence not straightforward to directly observe when the estimate from a model potentially is wrong, due to phenomena such as overfitting and concept drift. In this paper we present an efficient framework for estimating the generalization error of regression functions, applicable to any family of regression functions when the ground truth is unknown. We present a theoretical derivation of the framework and empirically evaluate its strengths and limitations. We find that it performs robustly and is useful for detecting concept drift in datasets in several real-world domains.

Jefrey Lijffijt, Bo Kang, Wouter Duivesteijn et al.

Deriving insights from high-dimensional data is one of the core problems in data mining. The difficulty mainly stems from the fact that there are exponentially many variable combinations to potentially consider, and there are infinitely many if we consider weighted combinations, even for linear combinations. Hence, an obvious question is whether we can automate the search for interesting patterns and visualizations. In this paper, we consider the setting where a user wants to learn as efficiently as possible about real-valued attributes. For example, to understand the distribution of crime rates in different geographic areas in terms of other (numerical, ordinal and/or categorical) variables that describe the areas. We introduce a method to find subgroups in the data that are maximally informative (in the formal Information Theoretic sense) with respect to a single or set of real-valued target attributes. The subgroup descriptions are in terms of a succinct set of arbitrarily-typed other attributes. The approach is based on the Subjective Interestingness framework FORSIED to enable the use of prior knowledge when finding most informative non-redundant patterns, and hence the method also supports iterative data mining.

Andreas Henelius, Kai Puolamäki, Antti Ukkonen

In this work we present the novel ASTRID method for investigating which attribute interactions classifiers exploit when making predictions. Attribute interactions in classification tasks mean that two or more attributes together provide stronger evidence for a particular class label. Knowledge of such interactions makes models more interpretable by revealing associations between attributes. This has applications, e.g., in pharmacovigilance to identify interactions between drugs or in bioinformatics to investigate associations between single nucleotide polymorphisms. We also show how the found attribute partitioning is related to a factorisation of the data generating distribution and empirically demonstrate the utility of the proposed method.

Jussi Korpela, Emilia Oikarinen, Kai Puolamäki et al.

Confidence intervals are a popular way to visualize and analyze data distributions. Unlike p-values, they can convey information both about statistical significance as well as effect size. However, very little work exists on applying confidence intervals to multivariate data. In this paper we define confidence intervals for multivariate data that extend the one-dimensional definition in a natural way. In our definition every variable is associated with its own confidence interval as usual, but a data vector can be outside of a few of these, and still be considered to be within the confidence area. We analyze the problem and show that the resulting confidence areas retain the good qualities of their one-dimensional counterparts: they are informative and easy to interpret. Furthermore, we show that the problem of finding multivariate confidence intervals is hard, but provide efficient approximate algorithms to solve the problem.

Andreas Henelius, Kai Puolamäki, Henrik Boström et al.

Clustering is a widely used unsupervised learning method for finding structure in the data. However, the resulting clusters are typically presented without any guarantees on their robustness; slightly changing the used data sample or re-running a clustering algorithm involving some stochastic component may lead to completely different clusters. There is, hence, a need for techniques that can quantify the instability of the generated clusters. In this study, we propose a technique for quantifying the instability of a clustering solution and for finding robust clusters, termed core clusters, which correspond to clusters where the co-occurrence probability of each data item within a cluster is at least $1 - α$. We demonstrate how solving the core clustering problem is linked to finding the largest maximal cliques in a graph. We show that the method can be used with both clustering and classification algorithms. The proposed method is tested on both simulated and real datasets. The results show that the obtained clusters indeed meet the guarantees on robustness.

Andreas Henelius, Antti Ukkonen, Kai Puolamäki

In many data exploration tasks it is meaningful to identify groups of attribute interactions that are specific to a variable of interest. For instance, in a dataset where the attributes are medical markers and the variable of interest (class variable) is binary indicating presence/absence of disease, we would like to know which medical markers interact with respect to the binary class label. These interactions are useful in several practical applications, for example, to gain insight into the structure of the data, in feature selection, and in data anonymisation. We present a novel method, based on statistical significance testing, that can be used to verify if the data set has been created by a given factorised class-conditional joint distribution, where the distribution is parametrised by a partition of its attributes. Furthermore, we provide a method, named ASTRID, for automatically finding a partition of attributes describing the distribution that has generated the data. State-of-the-art classifiers are utilised to capture the interactions present in the data by systematically breaking attribute interactions and observing the effect of this breaking on classifier performance. We empirically demonstrate the utility of the proposed method with examples using real and synthetic data.