arXiv subjects

Ola Spjuth

Publications and source records attributed to Ola Spjuth.

11 recordsLinked to original sources

arXiv2026

EMBL AI Librarian: Life-Sciences Knowledge Layer for AI Agents

The web is increasingly accessed by AI agents rather than humans. Every agent needs knowledge, especially in the life-sciences, where agentic pipelines are growing fast. Access to the literature is a crucial part of that need, and resources such as Europe PMC, with over 40M indexed records, are widely used to meet it. Yet these resources were not built for AI agents: they take keywords and complex syntax and return whole papers, so every agent must learn the syntax, issue several searches, and read full papers to find the evidence it needs. We introduce EMBL AI Librarian, a knowledge layer that upgrades the Europe PMC interface for AI agents: an agent asks in natural language and receives evidence that answers it. A single LLM orchestrates the whole knowledge retrieval process: it plans complementary subqueries executed by the live Europe PMC search engine, then reads the selected papers and locates the relevant evidence. We evaluate Librarian across four benchmarks: literature synthesis, claim verification, open-domain question answering, and downstream biology tasks such as protocol questions and sequence manipulation. On ScholarQABench, Librarian improves Citation F1 by more than $16$ points over strong recently published baselines. Used as the retrieval layer of an existing claim-verification pipeline, it increases agreement with expert consensus; and on the open-form LitQA2 benchmark, a GPT-5.4 agent scores about $8$ points higher when grounded in Librarian than with web search. Overall, our results show that equipping life-science agents with the Librarian knowledge layer improves performance across a range of tasks. We release our code publicly at https://github.com/petroni-lab/librarian

cs.CL↗

arXiv2025

AI Agents in Drug Discovery

Artificial intelligence (AI) agents are emerging as transformative tools in drug discovery, with the ability to autonomously reason, act, and learn through complicated research workflows. Building on large language models (LLMs) coupled with perception, computation, action, and memory tools, these agentic AI systems could integrate diverse biomedical data, execute tasks, carry out experiments via robotic platforms, and iteratively refine hypotheses in closed loops. We provide a conceptual and technical overview of agentic AI architectures, ranging from ReAct and Reflection to Supervisor and Swarm systems, and illustrate their applications across key stages of drug discovery, including literature synthesis, toxicity prediction, automated protocol generation, small-molecule synthesis, drug repurposing, and end-to-end decision-making. To our knowledge, this represents the first comprehensive work to present real-world implementations and quantifiable impacts of agentic AI systems deployed in operational drug discovery settings. Early implementations demonstrate substantial gains in speed, reproducibility, and scalability, compressing workflows that once took months into hours while maintaining scientific traceability. We discuss the current challenges related to data heterogeneity, system reliability, privacy, and benchmarking, and outline future directions towards technology in support of science and translation.

cs.LG↗

arXiv2024

A Decade in a Systematic Review: The Evolution and Impact of Cell Painting

High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions. Here, we systematically review the substantial methodological advancements and applications of Cell Painting. Advancements include improvements in the Cell Painting protocol, assay adaptations for different types of perturbations and applications, and improved methodologies for feature extraction, quality control, and batch effect correction. Moreover, machine learning methods recently surpassed classical approaches in their ability to extract biologically useful information from Cell Painting images. Cell Painting data have been used alone or in combination with other -omics data to decipher the mechanism of action of a compound, its toxicity profile, and many other biological effects. Overall, key methodological advances have expanded the ability of Cell Painting to capture cellular responses to various perturbations. Future advances will likely lie in advancing computational and experimental techniques, developing new publicly available datasets, and integrating them with other high-content data types.

q-bio.SC↗

arXiv2022

Scalable federated machine learning with FEDn

Federated machine learning has great promise to overcome the input privacy challenge in machine learning. The appearance of several projects capable of simulating federated learning has led to a corresponding rapid progress on algorithmic aspects of the problem. However, there is still a lack of federated machine learning frameworks that focus on fundamental aspects such as scalability, robustness, security, and performance in a geographically distributed setting. To bridge this gap we have designed and developed the FEDn framework. A main feature of FEDn is to support both cross-device and cross-silo training settings. This makes FEDn a powerful tool for researching a wide range of machine learning applications in a realistic setting.

cs.LG↗

arXiv2020

Smart Resource Management for Data Streaming using an Online Bin-packing Strategy

Data stream processing frameworks provide reliable and efficient mechanisms for executing complex workflows over large datasets. A common challenge for the majority of currently available streaming frameworks is efficient utilization of resources. Most frameworks use static or semi-static settings for resource utilization that work well for established use cases but lead to marginal improvements for unseen scenarios. Another pressing issue is the efficient processing of large individual objects such as images and matrices typical for scientific datasets. HarmonicIO has proven to be a good solution for streams of relatively large individual objects, as demonstrated in a benchmark comparison with the Spark and Kafka streaming frameworks. We here present an extension of the HarmonicIO framework based on the online bin-packing algorithm, to allow for efficient utilization of resources. Based on a real world use case from large-scale microscopy pipelines, we compare results of the new system to Spark's auto-scaling mechanism.

cs.DC↗

arXiv2019

Combining Prediction Intervals on Multi-Source Non-Disclosed Regression Datasets

Conformal Prediction is a framework that produces prediction intervals based on the output from a machine learning algorithm. In this paper we explore the case when training data is made up of multiple parts available in different sources that cannot be pooled. We here consider the regression case and propose a method where a conformal predictor is trained on each data source independently, and where the prediction intervals are then combined into a single interval. We call the approach Non-Disclosed Conformal Prediction (NDCP), and we evaluate it on a regression dataset from the UCI machine learning repository using support vector regression as the underlying machine learning algorithm, with varying number of data sources and sizes. The results show that the proposed method produces conservatively valid prediction intervals, and while we cannot retain the same efficiency as when all data is used, efficiency is improved through the proposed approach as compared to predicting using a single arbitrarily chosen source.

stat.ML↗

arXiv2019

On-Demand Virtual Research Environments using Microservices

The computational demands for scientific applications are continuously increasing. The emergence of cloud computing has enabled on-demand resource allocation. However, relying solely on infrastructure as a service does not achieve the degree of flexibility required by the scientific community. Here we present a microservice-oriented methodology, where scientific applications run in a distributed orchestration platform as software containers, referred to as on-demand, virtual research environments. The methodology is vendor agnostic and we provide an open source implementation that supports the major cloud providers, offering scalable management of scientific pipelines. We demonstrate applicability and scalability of our methodology in life science applications, but the methodology is general and can be applied to other scientific domains.

cs.DC↗

arXiv2019

MaRe: a MapReduce-Oriented Framework for Processing Big Data with Application Containers

Background. Life science is increasingly driven by Big Data analytics, and the MapReduce programming model has been proven successful for data-intensive analyses. However, current MapReduce frameworks offer poor support for reusing existing processing tools in bioinformatics pipelines. Further, these frameworks do not have native support for application containers, which are becoming popular in scientific data processing. Results. Here we present MaRe, a programming model with an associated open-source implementation, which introduces support for application containers in MapReduce. MaRe is based on Apache Spark and Docker, the MapReduce framework and container engine that have collected the largest open source community, thus providing interoperability with the cutting-edge software ecosystem. We demonstrate MaRe on two data-intensive applications in life science, showing ease of use and scalability. Conclusions. MaRe enables scalable data-intensive processing in life science with MapReduce and application containers. When compared with current best practices, that involve the use of workflow systems, MaRe has the advantage of providing data locality, ingestion from heterogeneous storage systems and interactive processing. MaRe is generally-applicable and available as open source software.

cs.DC↗

arXiv2018

Aggregating Predictions on Multiple Non-disclosed Datasets using Conformal Prediction

Conformal Prediction is a machine learning methodology that produces valid prediction regions under mild conditions. In this paper, we explore the application of making predictions over multiple data sources of different sizes without disclosing data between the sources. We propose that each data source applies a transductive conformal predictor independently using the local data, and that the individual predictions are then aggregated to form a combined prediction region. We demonstrate the method on several data sets, and show that the proposed method produces conservatively valid predictions and reduces the variance in the aggregated predictions. We also study the effect that the number of data sources and size of each source has on aggregated predictions, as compared with equally sized sources and pooled data.

stat.ML↗

arXiv2018

conformalClassification: A Conformal Prediction R Package for Classification

The conformalClassification package implements Transductive Conformal Prediction (TCP) and Inductive Conformal Prediction (ICP) for classification problems. Conformal Prediction (CP) is a framework that complements the predictions of machine learning algorithms with reliable measures of confidence. TCP gives results with higher validity than ICP, however ICP is computationally faster than TCP. The package conformalClassification is built upon the random forest method, where votes of the random forest for each class are considered as the conformity scores for each data point. Although the main aim of the conformalClassification package is to generate CP errors (p-values) for classification problems, the package also implements various diagnostic measures such as deviation from validity, error rate, efficiency, observed fuzziness and calibration plots. In future releases, we plan to extend the package to use other machine learning algorithms, (e.g. support vector machines) for model fitting.

stat.ML↗

arXiv2018

Conformal Prediction in Learning Under Privileged Information Paradigm with Applications in Drug Discovery

This paper explores conformal prediction in the learning under privileged information (LUPI) paradigm. We use the SVM+ realization of LUPI in an inductive conformal predictor, and apply it to the MNIST benchmark dataset and three datasets in drug discovery. The results show that using privileged information produces valid models and improves efficiency compared to standard SVM, however the improvement varies between the tested datasets and is not substantial in the drug discovery applications. More importantly, using SVM+ in a conformal prediction framework enables valid prediction intervals at specified significance levels.

stat.ML↗