The volume contains selected contributions from the Machine Learning Challenge "Discover the Mysteries of the Maya", presented at the Discovery Challenge Track of The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2021). Remote sensing has greatly accelerated traditional archaeological landscape surveys in the forested regions of the ancient Maya. Typical exploration and discovery attempts, beside focusing on whole ancient cities, focus also on individual buildings and structures. Recently, there have been several successful attempts of utilizing machine learning for identifying ancient Maya settlements. These attempts, while relevant, focus on narrow areas and rely on high-quality aerial laser scanning (ALS) data which covers only a fraction of the region where ancient Maya were once settled. Satellite image data, on the other hand, produced by the European Space Agency's (ESA) Sentinel missions, is abundant and, more importantly, publicly available. The "Discover the Mysteries of the Maya" challenge aimed at locating and identifying ancient Maya architectures (buildings, aguadas, and platforms) by performing integrated image segmentation of different types of satellite imagery (from Sentinel-1 and Sentinel-2) data and ALS (lidar) data.

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Much of our experiments are designed to uncover the cause(s) and effect(s) behind a data generating mechanism (i.e., phenomenon) we happen to be interested in. Uncovering such relationships allows us to identify the true working of a phenomenon and, most importantly, articulate a model that may enable us to further explore the phenomenon on hand and/or allow us to predict it accurately. Fundamentally, such models are likely to be derived via a causal approach (as opposed to an observational or empirical mean). In this approach, causal discovery is required to create a causal model, which can then be applied to infer the influence of interventions, and answer any hypothetical questions (i.e., in the form of What ifs? Etc.) that we might have. This paper builds a case for causal discovery and causal inference and contrasts that against traditional machine learning approaches; all from a civil and structural engineering perspective. More specifically, this paper outlines the key principles of causality and the most commonly used algorithms and packages for causal discovery and causal inference. Finally, this paper also presents a series of examples and case studies of how causal concepts can be adopted for our domain.

Cancer is one of the leading causes of death worldwide. Fast and safe early-stage, pre- and intra-operative diagnostics can significantly contribute to successful cancer identification and treatment. Artificial intelligence has played an increasing role in the enhancement of cancer diagnostics techniques in the last 15 years. This review covers the advances of artificial intelligence applications in well-established techniques such as MRI and CT. Also, it shows its high potential in combination with optical spectroscopy-based approaches that are under development for mobile, ultra-fast, and low-invasive diagnostics. I will show how spectroscopy-based approaches can reduce the time of tissue preparation for pathological analysis by making thin-slicing or haematoxylin-and-eosin staining obsolete. I will present examples of spectroscopic tools for fast and low-invasive ex- and in-vivo tissue classification for the determination of a tumour and its boundaries. Also, I will discuss that, contrary to MRI and CT, spectroscopic measurements do not require the administration of chemical agents to enhance the quality of cancer imaging which contributes to the development of more secure diagnostic methods. Overall, we will see that the combination of spectroscopy and artificial intelligence constitutes a highly promising and fast-developing field of medical technology that will soon augment available cancer diagnostic methods.

The discovery of drug-target interactions (DTIs) is a very promising area of research with great potential. The accurate identification of reliable interactions among drugs and proteins via computational methods, which typically leverage heterogeneous information retrieved from diverse data sources, can boost the development of effective pharmaceuticals. Although random walk and matrix factorization techniques are widely used in DTI prediction, they have several limitations. Random walk-based embedding generation is usually conducted in an unsupervised manner, while the linear similarity combination in matrix factorization distorts individual insights offered by different views. To tackle these issues, we take a multi-layered network approach to handle diverse drug and target similarities, and propose a novel optimization framework, called Multiple similarity DeepWalk-based Matrix Factorization (MDMF), for DTI prediction. The framework unifies embedding generation and interaction prediction, learning vector representations of drugs and targets that not only retain higher-order proximity across all hyper-layers and layer-specific local invariance, but also approximate the interactions with their inner product. Furthermore, we develop an ensemble method (MDMF2A) that integrates two instantiations of the MDMF model, optimizing the area under the precision-recall curve (AUPR) and the area under the receiver operating characteristic curve (AUC) respectively. The empirical study on real-world DTI datasets shows that our method achieves statistically significant improvement over current state-of-the-art approaches in four different settings. Moreover, the validation of highly ranked non-interacting pairs also demonstrates the potential of MDMF2A to discover novel DTIs.

Drug discovery is vitally important for protecting human against disease. Target-based screening is one of the most popular methods to develop new drugs in the past several decades. This method efficiently screens candidate drugs inhibiting target protein in vitro, but it often fails due to inadequate activity of the selected drugs in vivo. Accurate computational methods are needed to bridge this gap. Here, we propose a novel graph multi task deep learning model to identify compounds carrying both target inhibitory and cell active (MATIC) properties. On a carefully curated SARS-CoV-2 dataset, the proposed MATIC model shows advantages comparing with traditional method in screening effective compounds in vivo. Next, we explored the model interpretability and found that the learned features for target inhibition (in vitro) or cell active (in vivo) tasks are different with molecular property correlations and atom functional attentions. Based on these findings, we utilized a monte carlo based reinforcement learning generative model to generate novel multi-property compounds with both in vitro and in vivo efficacy, thus bridging the gap between target-based and cell-based drug discovery.

The automated machine learning (AutoML) process can require searching through complex configuration spaces of not only machine learning (ML) components and their hyperparameters but also ways of composing them together, i.e. forming ML pipelines. Optimisation efficiency and the model accuracy attainable for a fixed time budget suffer if this pipeline configuration space is excessively large. A key research question is whether it is both possible and practical to preemptively avoid costly evaluations of poorly performing ML pipelines by leveraging their historical performance for various ML tasks, i.e. meta-knowledge. The previous experience comes in the form of classifier/regressor accuracy rankings derived from either (1) a substantial but non-exhaustive number of pipeline evaluations made during historical AutoML runs, i.e. 'opportunistic' meta-knowledge, or (2) comprehensive cross-validated evaluations of classifiers/regressors with default hyperparameters, i.e. 'systematic' meta-knowledge. Numerous experiments with the AutoWeka4MCPS package suggest that (1) opportunistic/systematic meta-knowledge can improve ML outcomes, typically in line with how relevant that meta-knowledge is, and (2) configuration-space culling is optimal when it is neither too conservative nor too radical. However, the utility and impact of meta-knowledge depend critically on numerous facets of its generation and exploitation, warranting extensive analysis; these are often overlooked/underappreciated within AutoML and meta-learning literature. In particular, we observe strong sensitivity to the `challenge' of a dataset, i.e. whether specificity in choosing a predictor leads to significantly better performance. Ultimately, identifying `difficult' datasets, thus defined, is crucial to both generating informative meta-knowledge bases and understanding optimal search-space reduction strategies.

Early detection of cancers has been much explored due to its paramount importance in biomedical fields. Among different types of data used to answer this biological question, studies based on T cell receptors (TCRs) are under recent spotlight due to the growing appreciation of the roles of the host immunity system in tumor biology. However, the one-to-many correspondence between a patient and multiple TCR sequences hinders researchers from simply adopting classical statistical/machine learning methods. There were recent attempts to model this type of data in the context of multiple instance learning (MIL). Despite the novel application of MIL to cancer detection using TCR sequences and the demonstrated adequate performance in several tumor types, there is still room for improvement, especially for certain cancer types. Furthermore, explainable neural network models are not fully investigated for this application. In this article, we propose multiple instance neural networks based on sparse attention (MINN-SA) to enhance the performance in cancer detection and explainability. The sparse attention structure drops out uninformative instances in each bag, achieving both interpretability and better predictive performance in combination with the skip connection. Our experiments show that MINN-SA yields the highest area under the ROC curve (AUC) scores on average measured across 10 different types of cancers, compared to existing MIL approaches. Moreover, we observe from the estimated attentions that MINN-SA can identify the TCRs that are specific for tumor antigens in the same T cell repertoire.

Understanding human behavior is an important task and has applications in many domains such as targeted advertisement, health analytics, security, and entertainment, etc. For this purpose, designing a system for activity recognition (AR) is important. However, since every human can have different behaviors, understanding and analyzing common patterns become a challenging task. Since smartphones are easily available to every human being in the modern world, using them to track the human activities becomes possible. In this paper, we extracted different human activities using accelerometer, magnetometer, and gyroscope sensors of android smartphones by building an android mobile applications. Using different social media applications, such as Facebook, Instagram, Whatsapp, and Twitter, we extracted the raw sensor values along with the attributes of $29$ subjects along with their attributes (class labels) such as age, gender, and left/right/both hands application usage. We extract features from the raw signals and use them to perform classification using different machine learning (ML) algorithms. Using statistical analysis, we show the importance of different features towards the prediction of class labels. In the end, we use the trained ML model on our data to extract unknown features from a well known activity recognition data from UCI repository, which highlights the potential of privacy breach using ML models. This security analysis could help researchers in future to take appropriate steps to preserve the privacy of human subjects.

Autonomous bin picking poses significant challenges to vision-driven robotic systems given the complexity of the problem, ranging from various sensor modalities, to highly entangled object layouts, to diverse item properties and gripper types. Existing methods often address the problem from one perspective. Diverse items and complex bin scenes require diverse picking strategies together with advanced reasoning. As such, to build robust and effective machine-learning algorithms for solving this complex task requires significant amounts of comprehensive and high quality data. Collecting such data in real world would be too expensive and time prohibitive and therefore intractable from a scalability perspective. To tackle this big, diverse data problem, we take inspiration from the recent rise in the concept of metaverses, and introduce MetaGraspNet, a large-scale photo-realistic bin picking dataset constructed via physics-based metaverse synthesis. The proposed dataset contains 217k RGBD images across 82 different article types, with full annotations for object detection, amodal perception, keypoint detection, manipulation order and ambidextrous grasp labels for a parallel-jaw and vacuum gripper. We also provide a real dataset consisting of over 2.3k fully annotated high-quality RGBD images, divided into 5 levels of difficulties and an unseen object set to evaluate different object and layout properties. Finally, we conduct extensive experiments showing that our proposed vacuum seal model and synthetic dataset achieves state-of-the-art performance and generalizes to real world use-cases.