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Jonathan Warrell is a Researcher in the Machine Learning Department at NEC Laboratories America. He received his BA in Music from the University of Cambridge, his Master’s as well as his PhD in Music Theory and Analysis from King’s College London, an MS in Computer Science (Distinction) from the University College London, and he went on to postdoctoral work in computational genomics and neuroscience in Yale’s Department of Molecular Biophysics and Biochemistry.
His research focuses particularly on computational biology, spatial genomics, and optimization theory. At NEC, Dr. Warrell contributes to projects involving molecular design, large-scale genomic reasoning, compositionality of diffusion models, biomarker discovery, reinforcement learning, and variational methods. His work leverages hybrid approaches that combine symbolic and neural methods, particularly for solving discrete optimization problems in genomics.
He collaborates closely with NEC Bio, NEC OncoImmunity, and NEC’s Biometric Research Laboratories on developing interpretable and efficient methods for solving biological and medical problems. He has published widely in high impact journals such as Science, Cell, Nature Genetics and Nature Machine Intelligence.
Overview: We are focused on developing advanced LMMs that integrate explainable reasoning and safe generation to optimize healthcare workflows. These models are designed to process and analyze multiple data modalities—such as text, images, and structured data—enabling them to assist in complex tasks like diagnostics, treatment planning, and patient management with exceptional accuracy.
Overview: Since 2019, the parameters of large deep learning models have increased by over 300 times every 18 months. However, the future ML progress cannot continue simply based on using more data or creating larger models, because the growing gap between the model demand and resource supply is not sustainable.
AI interpretability has long been the focus, but what if it’s only part of the story? New research introduces model semantics, a framework for understanding what AI systems truly represent and how their internal structures connect to real-world phenomena.
We introduce a framework to analyse interpretability in deep learning, by drawing on a formal notion of model semantics from the philosophy of science. We argue that interpretability is only one aspect of a models semantics and illustrate our framework with examples from biomedicine.
We propose LOGDIFF (Logical Guidance for the Exact Composition of Diffusion Models), a guidance framework for diffusion models that enables principled constrained generation with complex logical expressions at inference time. We study when exact score-based guidance for complex logical formulas can
Tumor-infiltrating lymphocytes (TILs) are a provocative biomarker in melanoma, influencing diagnosis, prognosis, and immunotherapy outcomes; however, traditional pathologistreadTIL assessment on hematoxylin and eosin–stained slides is prone to interobserver variability, leading to inconsistent clinical
A major challenge in near-term quantum computing is its application to large real-world datasets due to scarce quantum hardware resources. One approach to enabling tractable quantum models for such datasets involves finding low-dimensional representations that preserve essential information for downstream
Non-small cell lung cancer (NSCLC) shows variable responses to immunotherapy, highlighting the need for biomarkers to guide patient selection. We applied a spatial multi-omics approach to 234 advanced NSCLC patients treated with programmed death 1-based immunotherapy across three cohorts to identify
Variational optimization (VO) offers a general approach for handling objectives which may involve discontinuities, or whose gradients are difficult to calculate. By introducing a variational distribution over the parameter space, such objectives are smoothed, and rendered amenable to VO methods. Local
NEC Labs America is proud to attend NeurIPS 2024 in Vancouver, Canada from December 10-15. Zachary Izzo will present Subgroup Discovery with the Cox Model, Shaobo Han will present VB-LoRA: Extreme Parameter Efficient Fine-Tuning with Vector Banks and Jonathan Warrell will present Discrete-Continuous
Graph neural networks (GNNs) have emerged as powerful tools for representation learning. Their efficacy depends on their having an optimal underlying graph. In many cases, the most relevant information comes from specific subgraphs. In this work, we introduce a GNN-based framework (graph-partitioned
Levels of selection and multilevel evolutionary processes are essential concepts in evolutionary theory, and yet there is a lack of common mathematical models for these core ideas. Here, we propose a unified mathematical framework for formulating and optimizing multilevel evolutionary processes and genetic
Spatial transcriptomics technologies, which generate a spatial map of gene activity, can deepen the understanding of tissue architecture and its molecular underpinnings in health and disease. However, the high cost makes these technologies difficult to use in practice. Histological images co-registered
We aim to improve the prediction of response or resistance to immunotherapies in patients with melanoma. This goal is based on the hypothesis that current gene signatures predicting immunotherapy outcomes show only modest accuracy due to the lack of spatial information about cellular functions and molecular
A major challenge in near-term quantum computing is its application to large real-world datasets due to scarce quantum hardware resources. One approach to enabling tractable quantum models for such datasets involves compressing the original data to manageable dimensions while still representing essential
Motivation Spatial transcriptomics technologies, which generate a spatial map of gene activity, can deepen the understanding of tissue architecture and its molecular underpinnings in health and disease. However, the high cost makes these technologies difficult to use in practice. Histological images
