Foundation models have shown remarkable success across scientific domains, yet their impact in chemistry remains limited due to the absence of diverse, large-scale, high-quality datasets that reflect the field's multifaceted nature. We present the ChemPile, an open dataset containing over 75 billion tokens of curated chemical data, specifically built for training and evaluating general-purpose models in the chemical sciences. The dataset mirrors the human learning journey through chemistry---from educational foundations to specialized expertise---spanning multiple modalities and content types including structured data in diverse chemical representations (SMILES, SELFIES, IUPAC names, InChI, molecular renderings), scientific and educational text, executable code, and chemical images. ChemPile integrates foundational knowledge (textbooks, lecture notes), specialized expertise (scientific articles and language-interfaced data), visual understanding (molecular structures, diagrams), and advanced reasoning (problem-solving traces and code)---mirroring how human chemists develop expertise through diverse learning materials and experiences. Constructed through hundreds of hours of expert curation, the ChemPile captures both foundational concepts and domain-specific complexity. We provide standardized training, validation, and test splits, enabling robust benchmarking. ChemPile is openly released via HuggingFace with a consistent API, permissive license, and detailed documentation. We hope the ChemPile will serve as a catalyst for chemical AI, enabling the development of the next generation of chemical foundation models.

SUMMARY: The lit-OTAR framework, developed through a collaboration between Europe PMC and Open Targets, leverages deep learning to revolutionize drug discovery by extracting evidence from scientific literature for drug target identification and validation. This novel framework combines named entity recognition for identifying gene/protein (target), disease, organism, and chemical/drug within scientific texts, and entity normalization to map these entities to databases like Ensembl, Experimental Factor Ontology, and ChEMBL. Continuously operational, it has processed over 39 million abstracts and 4.5 million full-text articles and preprints to date, identifying more than 48.5 million unique associations that significantly help accelerate the drug discovery process and scientific research >29.9 m distinct target-disease, 11.8 m distinct target-drug, and 8.3 m distinct disease-drug relationships. AVAILABILITY AND IMPLEMENTATION: The results are accessible through Europe PMC's SciLite web app (https://europepmc.org/) and its annotations API (https://europepmc.org/annotationsapi), as well as via the Open Targets Platform (https://platform.opentargets.org/). The daily pipeline is available at https://github.com/ML4LitS/otar-maintenance, and the Open Targets ETL processes are available at https://github.com/opentargets.

In many production clouds, with the notable exception of Google, aggregation-based VM placement policies are used to provision datacenter resources energy and performance efficiently. However, if VMs with similar workloads are placed onto the same machines, they might suffer from contention, particularly, if they are competing for similar resources. High levels of resource contention may degrade VMs performance, and, therefore, could potentially increase users’ costs and infrastructure's energy consumption. Furthermore, segregation-based methods result in stranded resources and, therefore, less economics. The recent industrial interest in segregating workloads opens new directions for research. In this article, we demonstrate how aggregation and segregation-based VM placement policies lead to variabilities in energy efficiency, workload performance, and users’ costs. We, then, propose various approaches to aggregation-based placement and migration. We investigate through a number of experiments, using Microsoft Azure and Google's workload traces for more than twelve thousand hosts and a million VMs, the impact of placement decisions on energy, performance, and costs. Our extensive simulations and empirical evaluation demonstrate that, for certain workloads, aggregation-based allocation and consolidation is$\sim$9.61% more energy and$\sim$20.0% more performance efficient than segregation-based policies. Moreover, various aggregation metrics, such as runtimes and workload types, offer variations in energy consumption and performance, therefore, users’ costs.

Shotgun sequencing has facilitated the analysis of complex microbial communities. Recently we have shown how local binary patterns (LBP) from image processing can be used to analyse the sequenced samples. LBP codes represent the data in a sparse high dimensional space. To improve the performance of our pipeline, marginalised stacked autoencoders are used here to learn frequent LBP codes and map the high dimensional space to a lower dimension dense space. We demonstrate its performance using both low and high complexity simulated metagenomic data and compare the performance of our method with several existing techniques including principal component analysis (PCA) in the dimension reduction step and fc-mer frequency in feature extraction step.

Alzheimer's disease (AD) is a neurodegenerative disease caused by the progressive death of brain cells over time. It represents the most frequent cause of dementia in the western world, and affects an individual's cognitive ability and psychological capacity. While clinical diagnoses of AD are made primarily on the basis of clinical evaluation and mental health tests, diagnostic certainty is only possible through necropsy. One non-invasive approach to investigating AD is to use electroencephalograms (eEGs), which reflect brain electrical activity and so can be used to detect electrical abnormalities in brain signals with non-invasive cranial surface electrodes. Generally EEGs in AD patients show a shift to lower frequencies in spectral analysis and display less complexity and contain more regular patterns compared to those of control subjects. Here we present a method for differentiating AD patients from healthy ones based on their EEG signals using Benford's law and support vector machines (SVMs) with a radial basis function (RBF) kernel. EEG signals from eleven AD and eleven age-matched controls were divided into artefact-free 5-sec epochs and used to train an SVM. 10 fold cross validation was performed at both the epoch- and subject-level to evaluate the importance of each electrode in discriminating between AD and healthy subjects. Substantive variability was seen across the different electrodes, with electrodes O1, O2 and C4 particularly being important. Performance across the electrodes was reduced when subject-level cross validation was performed, but relative performance across the electrodes was consistent with that found using epoch-level cross validation.

Images of the kidneys using dynamic contrast-enhanced magnetic resonance renography (DCE-MRR) contains unwanted complex organ motion due to respiration. This gives rise to motion artefacts that hinder the clinical assessment of kidney function. However, due to the rapid change in contrast agent within the DCE-MR image sequence, commonly used intensity-based image registration techniques are likely to fail. While semi-automated approaches involving human experts are a possible alternative, they pose significant drawbacks including inter-observer variability, and the bottleneck introduced through manual inspection of the multiplicity of images produced during a DCE-MRR study. To address this issue, we present a novel automated, registration-free movement correction approach based on windowed and reconstruction variants of dynamic mode decomposition (WR-DMD). Our proposed method is validated on ten different healthy volunteers’ kidney DCE-MRI data sets. The results, using block-matching-block evaluation on the image sequence produced by WR-DMD, show the elimination of $$99\%$$ of mean motion magnitude when compared to the original data sets, thereby demonstrating the viability of automatic movement correction using WR-DMD.

Rendering a face recognition system robust is vital in order to safeguard it against spoof attacks carried out using printed pictures of a victim (also known as print attack) or a replayed video of the person (replay attack). A key property in distinguishing a live, valid access from printed media or replayed videos is by exploiting the information dynamics of the video content, such as blinking eyes, moving lips, and facial dynamics. We advance the state of the art in facial antispoofing by applying a recently developed algorithm called dynamic mode decomposition (DMD) as a general purpose, entirely data-driven approach to capture the above liveness cues. We propose a classification pipeline consisting of DMD, local binary patterns (LBPs), and support vector machines (SVMs) with a histogram intersection kernel. A unique property of DMD is its ability to conveniently represent the temporal information of the entire video as a single image with the same dimensions as those images contained in the video. The pipeline of DMD + LBP + SVM proves to be efficient, convenient to use, and effective. In fact only the spatial configuration for LBP needs to be tuned. The effectiveness of the methodology was demonstrated using three publicly available databases: (1) print-attack; (2) replay-attack; and (3) CASIA-FASD, attaining comparable results with the state of the art, following the respective published experimental protocols.

Survey questionnaires are often heterogeneous because they contain both quantitative (numeric) and qualitative (text) responses, as well as missing values. While traditional, model-based methods are commonly used by clinicians, we deploy Self Organizing Maps (SOM) as a means to visualise the data. In a survey study aiming at understanding the self-care behaviour of 611 patients with Type-1 Diabetes, we show that SOM can be used to (1) identify co-morbidities; (2) to link self-care factors that are dependent on each other; and (3) to visualise individual patient profiles; In evaluation with clinicians and experts in Type-1 Diabetes, the knowledge and insights extracted using SOM correspond well to clinical expectation. Furthermore, the output of SOM in the form of a U-matrix is found to offer an interesting alternative means of visualising patient profiles instead of a usual tabular form.