Computational Neuroscience & Bio-Inspired AI

Decoding Neural Dynamics
& Artificial Minds

I explore the meeting point of computational neuroscience and bio-inspired AI through open, testable projects.

Research in practice.

Three projects that connect neural systems, language models, and agent behavior.

CASE 01 // TRANSFORMER–BRAIN ALIGNMENT LLM × Neuroscience

AxonLM: probing neuroanatomy in a language model

Problem
Can transformer representations encode neuroanatomical connectivity?
My contribution
Built the modular PyTorch GPT-2 research codebase and FFN probing scripts.
Method
Linear probes on feed-forward activations, compared with Allen Brain Atlas connectivity.
Result
The repository reports AUC 0.963 for neuroanatomical decoding.
CASE 02 // COGNITIVE ARCHITECTURE Agent simulation

NeuroConscious: an extensible agent testbed

Problem
How can internal needs and mood shape an agent's decisions in a virtual world?
My contribution
Designed the modular agent architecture and its internal state, mood, and motivation components.
Method
Object-oriented Python modules connect changing internal state to action selection and environment interaction.
Result
An open-source testbed for experimenting with autonomous, biologically inspired behavior.
ARCHITECTURE SNAPSHOT
Internal stateMood & motivationAgent action
CASE 03 // SYNAPTIC PLASTICITY Neuromorphic simulation

STDP-SNN: exploring spike-driven learning

Problem
How do spike timing and lateral competition change synaptic weights?
My contribution
Built a spiking-network simulator with an interactive exploration interface.
Method
Leaky integrate-and-fire neurons, STDP learning, and winner-take-all inhibition.
Result
A simulator for observing spike activity and plasticity; no benchmark score is published here.
ARCHITECTURE SNAPSHOT
Input currentLIF spikesSTDP update

Make a neuron fire. Change a synapse.

Two small experiments show how input current produces spikes and how spike order changes a connection.

01 / LIFTeaching model

When does a neuron fire?

Increase the input current. Voltage rises to a threshold, then the neuron spikes and resets.

2.2 nA
0 nA3 nA
−55 mV
−60 mV−45 mV

Euler simulation: τ = 20 ms, R = 10 MΩ, rest/reset = −70 mV, refractory period = 4 ms.

02 / STDPTeaching model

Which spike comes first?

Move the postsynaptic spike. Pre before post strengthens this example synapse; reversing the order weakens it.

+12 ms
−40 ms0 ms+40 ms
EXAMPLE WEIGHT CHANGE+0.110Connection strengthens

Illustrative pair STDP: A+ = 0.20, A− = 0.22, τ = 20 ms. One pair; no network training or measured result.

Background reading: Neuronal Dynamics · Bi & Poo (1998)

About Me

I'm Efekan, a developer and computational neuroscience explorer focused on simulating artificial consciousness, neural decision-making, and biologically inspired systems through code.

Transitioning from backend systems to modeling neural mechanisms, I build biophysical spiking neural networks, transformer-brain alignment probes, and cognitive architectures simulating internal motivational drives.

AUC 0.963
Neuroanatomical decoding accuracy on Allen Brain Atlas (AxonLM)
LIF & SNN
Biophysical Spiking Neural Network & STDP synaptic plasticity

Other Projects

Multi-Agent ABM

ShipOfFools

AI-driven social agent-based modeling (ABM) exploring human psychology, power dynamics, trust network formation, and dynamic anomaly detection.

Neural Decoding

BrainDecode & Neural Dynamics

Decoding brain connectivity, cognitive confusion states, and EEG neural time-series data using Brian2 and signal processing pipelines.

Production MLOps

Production ML Systems

End-to-end production ML pipeline & Dockerized FastAPI service engineered with strict pre-commit validation, Pydantic data contracts, and predictive modeling.

Research & Identifiers

GitHub Telemetry

Streaming GitHub repository telemetry...

Skills & Technologies

Neuroscience & AI

Python / NumPy
92%
PyTorch / TensorFlow
82%
Scikit-Learn / SciPy
88%
MATLAB
75%

Systems & Engineering

C / Linux Systems
70%
OpenCV
72%
Git / CI Workflows
88%

Languages

Turkish
Native Proficiency
Native
English
Professional Working (B2)
B2
French
Elementary (A2)
A2
Dutch
Beginner (A1)
A1

Let's Connect

Open for collaborations on computational neuroscience, artificial consciousness research, and bio-inspired AI architectures.