Patrick Filima

Patrick Filima

Research Software Engineer

Computational Neuroscientist

© 2026 Patrick Filima

Projects & Research Programs

Production software systems, open science infrastructure, and computational neuroscience studies

Production Platform

Brainlife Error Monitoring & Diagnostics Dashboard

Observability platform improving failure visibility across distributed HPC neuroimaging pipelines

Centralized observability dashboard aggregating failure logs, stack traces, and automated error classification across thousands of distributed containerized jobs on Brainlife.io.

ReactNext.jsELK StackNode.jsDockerHPC Telemetry
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Mobile Platform

Brainlife Mobile Companion Application

Real-time mobile status tracking and push alerts for long-running compute jobs

Cross-platform mobile application giving neuroscientists real-time visibility into multi-day pipeline execution status, error logs, and immediate completion alerts.

React NativePush NotificationsBrainlife REST APIiOS / Android
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Education & Admissions

ABDN Fellowship Evaluation Platform

Digitized admissions and multi-reviewer scoring workflows for pan-African programs

Full-stack evaluation platform supporting structured multi-reviewer assessment, reviewer assignment matrices, and score normalization for 1,000+ candidates across 50 countries.

Next.jsFirebaseTailwind CSSAccess Governance
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Digital Health

Lighthouse Digital Health Platform

Therapist discovery and appointment scheduling workflow system

Modern web platform connecting patients with certified mental health professionals through directory search, scheduling workflows, and administrative dashboards.

Next.jsNode.jsPostgreSQLTailwind CSS
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Functional Neuroimaging & Methodological Machine LearningActive Methodological Study / Project 8

GLM vs. Deep Learning Behavior in Small-Sample Task-Based fMRI of Cognitive Control

A Controlled Methodological Study of Predictive Generalization, Overfitting Dynamics, and Spatial Representation Alignment

Investigating model behavior under small-sample, high-dimensional fMRI conditions (NYU Slow Flanker task, N=26) to compare classical General Linear Models (GLM) and deep learning architectures across cross-subject generalization, statistical stability, and spatial correspondence (Pearson r / Dice).

Python 3.8+FSL 6.0+PyTorchTensorFlowNilearnNiPypeOpenNeuro ds000102LOSO CV
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Translational Medical AI & Clinical Protocol OptimizationActive Clinical Translational Study / Project 7

DeepAccess-MRI: AI-Assisted MRI Protocol Optimization via Missing Sequence Reconstruction

Clinically Validated Transfer Learning & Missing Sequence Synthesis for Shorter, Affordable Neuroimaging Protocols in Nigeria

Developing and clinically validating a transfer-learning framework that synthesizes missing structural MRI sequences (e.g. T1 -> FLAIR/T2) from heterogeneous Nigerian clinical scans, enabling shorter, non-inferior acquisition protocols without compromising diagnostic confidence.

Python 3.11+PyTorchMONAIDiffusion ModelscGANsU-NetSimpleITKMonte Carlo DropoutRadiologist Audit
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Medical Image Quality & AI ReliabilityActive Benchmark / Project 5

Quantifying Clinical MRI Quality Effects on Deep Learning Performance

Treating Real-World Image Quality Degradation as a Continuous Independent Variable to Define AI Safety Boundaries

Systematically quantifying how continuous objective Image Quality Metrics (SNR, CNR, blur, sharpness, edge strength) affect diagnostic accuracy, calibration error (ECE), and Grad-CAM saliency drift across 225 clinical scans.

Python 3.11+PyTorchMONAISimpleITKOpenCVScikit-ImageResNet-18DenseNet-121EfficientNet-B0
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Benchmark Ecosystem & Clinical DatasetActive Benchmark / Project 1

African Clinical Brain MRI Benchmark (Afri-Brain-Bench)

A Standardized Benchmark Ecosystem for Evaluating AI Generalization, Calibration, and Explainability on African Clinical Scans

Introducing Afri-Brain-Bench—a standardized multi-center benchmark dataset of 225 clinical MRI examinations across 3 Nigerian hospitals providing 7 standardized evaluation tasks, cross-hospital splits, ECE calibration scoring, and Grad-CAM spatial ROI auditing.

Python 3.11+PyTorchMONAITorchIOResNet-18DenseNet-121EfficientNet-B0ConvNeXt TinyScikit-Learn
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Explainable AI (XAI) & Clinical PlausibilityActive Benchmark / Project 6

Explainability & Clinical Plausibility of Deep Learning on Low-Field African Brain MRI

Evaluating Anatomical Attention vs. Shortcut Learning across Low-Field Scanners with Neuroradiology Expert Auditing

Evaluating whether deep learning models trained on heterogeneous low-field African clinical MRI base decisions on medically plausible neuroanatomy or spurious imaging shortcuts using a 5-point neuroradiologist rating rubric and quantitative anatomical IoU.

Python 3.11+PyTorchMONAIGrad-CAM++Integrated GradientsOcclusion SensitivityKernelSHAPResNet-18DenseNet-121ConvNeXt Tiny
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Data-Centric Medical AIActive Benchmark / Project 2

Data-Centric AI: Evaluating MRI Preprocessing on Low-Field African Brain MRI

A Multi-Center Factorial Study of Preprocessing Impact on Model Robustness, Calibration, and Explainability

Evaluating whether optimizing preprocessing quality via factorial experimental design (Pipelines A–G) yields greater classification accuracy, calibration, and cross-hospital generalization than increasing model complexity on 225 low-field African brain MRI scans.

Python 3.11+PyTorch 2.0+MONAI 1.2+ANTsPySimpleITKTorchIOResNet-18DenseNet-121EfficientNet-B0
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Scientific AI Ecosystem & InfrastructureActive 7-Phase Roadmap

African Brain MRI AI Research Ecosystem

A Multi-Project Research Program for Robust, Explainable & Clinically Validated AI in African Neuroimaging

Documents the architecture, dependency matrix, and 7-phase roadmap of a comprehensive research ecosystem designed to bridge the gap between idealized research MRI and real-world low-resource African clinical environments.

PythonPyTorchMONAISimpleITKDockerafri_brain_coreBIDSBayesian Models
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Neuroimaging & Medical AIActive Benchmark / Phase 3B

Beyond Research-Grade MRI: AI Robustness on Nigerian Clinical Scans

A Methodological Study of Model Calibration, Robustness, and Explainability under Real-World MRI Quality Constraints

Systematically characterizing AI model robustness, calibration error, and explainability maps across progressive real-world MRI degradations using a Nigerian clinical brain dataset.

Python 3.11+PyTorchMONAISimpleITKPyRadiomicsScikit-LearnResNet-18DenseNet-121
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Distributed Scientific InfrastructureIn Production

Brainlife.io Workflow Observability & Diagnostic Engine

Automated Pipeline Diagnostic & Performance Observability Platform for Distributed Scientific Workflows

Building observability tools that monitor, diagnose, and auto-triage HPC neuroimaging pipeline errors across thousands of distributed compute executions on Brainlife.io.

Node.jsPythonReactELK StackREST APIsDockerHPC Cluster Integration
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Digital Research PlatformIn Production

African Brain Data Network (ABDN) Platform

FAIR Data Management, Capacity Building & Participant Evaluation Platform for African Neuroscience

A digital research platform enabling neuroscientists across 50+ African institutions to collaborate, share FAIR datasets, and manage computational workshops.

Next.jsPythonPostgreSQLAppwriteTailwind CSSFAIR Data Protocols
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