NEXUSLab

Neural Computation, Network and Storage Laboratory

Human-inspired intelligence, reliable systems, and data-centric computing

NEXUSLab is a research group at Boğaziçi University working at the intersection of neural computation, distributed systems, storage & coding, and human-centric AI. We build principled learning systems, scalable infrastructure, and scientifically grounded models that connect theory, experimentation, and real-world deployment.

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Mission

What we aim to build and why

Our mission is to develop robust, efficient, and human-aligned learning systems while advancing the theory and practice of distributed intelligence and storage-aware computing. We focus on methods that are not only accurate, but also interpretable, reliable, and deployable.

  • Human-inspired AI: biomimetic training, robustness under distribution shifts/degradations, visual neuroscience–inspired models.
  • Data-centric systems: information theory, data storage/coding, reliability modeling, scalable retrieval, and agentic RAG pipelines.
  • Networked intelligence: distributed storage and learning, privacy-aware coordination, and IoT-scale deployments.
Research pillars
  • Neural computation & cognitive inspiration
  • Distributed systems & trustworthy AI
  • Information, storage, coding, and reliability
  • Signal Processing and Systems
  • Multimodal learning & evaluations

Lab Members

Core team

  • Suayb S. Arslan — Principal Investigator
  • Feyza Özen — M.Sc. Student
    Thesis proposal: A HOLISTIC APPROACH TO BIOLOGICALLY PLAUSIBLE DEEP LEARNING: SYNERGISTIC EFFECTS OF BIO-PLAUSIBLE ALGORITHMS, ARCHITECTURES, AND TRAINING METHODS
  • Onuralp Guvercin — M.Sc. Student
  • Resul Kuru — M.Sc. Student
    Thesis proposal: Robustness in Vision Models via Stochastic Noise
  • Hannan Toprak — M.Sc. Student

Past Lab Members

  • M. Pourmandi — Ph.D. Student
    Ph.D. Thesis: “LDPC Code Design For Distributed Storage Systems”,
    Electrical & Electronics Engineering, Boğaziçi University, July 2023.

Projects

Selected directions

Blockchain-centered Security & Privacy · Self-Sovereign Identity and Management

Blockchain-centered security and privacy: Self-Sovereign Identity and Management. This project studies decentralized identity (SSI), privacy-preserving authentication, credential management, and trust frameworks built on blockchain and distributed ledger technologies, with particular relevance to IoT and large-scale networked systems.

Blockchain Self-Sovereign Identity Privacy Security
Brain Spatial Frequency Processing · Frequency‑decoupled computational models

Brain’s Spatial Frequency Processing and Frequency‑decoupled Computational Model Development. This project investigates biologically grounded spatial‑frequency processing mechanisms in the visual system and develops frequency‑decoupled computational models bridging neuroscience, signal processing, and learning.

Fully funded by BAP SUP (2025–2027) · Project No: 20411

Visual Neuroscience Spatial Frequency Signal Processing Bio‑inspired Models
Blockchain-centered Security & Privacy · Self-Sovereign Identity and Management

Blockchain-centered security and privacy: Self-Sovereign Identity and Management. This project focuses on decentralized identity architectures, privacy-preserving authentication, and trust management using blockchain and distributed ledger technologies, with applications to IoT and large-scale networked systems.

Blockchain Self-Sovereign Identity Privacy Trust & Security
Scalable Dataset Labeling & Cross-Modal Alignment · Multimodal foundation models

Scalable Dataset Labeling and Contrastive Alignment for Cross-Modal Inference and Data Generation with Multimodal Large Foundation Models. This project focuses on scalable annotation pipelines, contrastive learning, and cross-modal alignment for robust inference and data generation across vision, language, and other modalities.

Fully funded by YÖK-ADP (2025–2027) · Project No: 50192

Multimodal AI Contrastive Learning Foundation Models Data Generation
BIODeeprid · BIO-inspired deep neural & hybrid systems under degraded imaging

BIODeeprid: BIO-inspired Deep neural network and hybrid system design under degraded imaging conditions. The project focuses on biologically inspired architectures, signal-processing-aware learning, and robustness to real-world degradations.

Fully funded by TÜBİTAK 1001 (2025–2028) · Project No: 50192

Biomimetic AI Robust Vision Signal Processing Hybrid Systems
Brain Spatial Frequency Processing · Frequency-decoupled computational models

Brain’s Spatial Frequency Processing and Frequency-decoupled Computational Model Development. This project investigates biologically grounded spatial-frequency processing mechanisms in the visual system and develops frequency-decoupled computational models bridging neuroscience, signal processing, and learning.

Fully funded by BAP SUP (2025–2027) · Project No: 20411

Visual Neuroscience Spatial Frequency Signal Processing Bio-inspired Models
Biomimetic Training · Human-inspired curricula & robustness

Developing training protocols and architectures inspired by the human visual system to improve robustness under degradations (blur, downsampling, noise) and to enable fair comparisons between humans and machines.

Neuro-AI Robustness Vision
DNA Data Storage · Coding, sequencing, and system design

Reliable DNA storage pipelines combining coding theory, sequencing constraints, and practical system considerations (pooling, addressing, random access, and error mechanisms).

Coding Storage Systems
Agentic-RAG & Retrieval Systems · Document intelligence at scale

Building retrieval-augmented generation systems with semantic chunking, evaluation, and agentic workflows. Focus on quality, efficiency, and trustworthy answers for technical domains.

RAG Vector DB Evaluation
Distributed Intelligence & IoT · Privacy-aware learning and coordination

Methods and systems for scalable learning and decision-making across networked devices, including federation, identity, trust, and reliability constraints.

IoT Distributed ML Trust

Past Research

Selected prior research directions and industry experience

Quantum Corporation · Cloud & cold storage reliability, durability, and erasure coding

Our team at Quantum focused on cloud and cold storage technologies. Data integrity and protection are among the mainstream objectives of the data storage business. The reliability, durability, and availability of coded system architectures remain central (and often debated) concerns in the market.

Our aim was to develop algorithms and approximate random processes to predict the reliability and durability of Quantum’s product line, and to help other research groups assess their own systems by establishing a common set of tools. Erasure-correction coding is used to add redundancy and protect data against abnormalities and failures. Our research emphasized modern erasure codes with linear-time encoding/decoding when possible, spanning designs from Cauchy Reed–Solomon codes to fountain codes and locally decodable linear codes.

A key challenge was adapting elegant theory to real product constraints and system-level requirements, including efficient implementations that improve customer experience. Deliverables included patents, technical papers, and system-level implementations.

Reliability Erasure Codes Storage Systems Modeling
Wireless Multimedia · A cross-layer approach

Modern networked systems are typically designed as a stack of layers. In progressive multimedia coding, a base layer carries essential “skeleton” information, while enhancement layers refine reconstruction quality. In wireless environments, strict layering can lead to inefficiencies due to time-varying channels, interference, and heterogeneous receiver conditions. Cross-layer approaches have long been known to be beneficial, but are often avoided in practice due to complex inter-layer interactions and concerns about robustness. More recently, it has been shown that cross-layer optimization can be achieved while preserving robustness.

I studied progressive source transmission systems combining a progressive source coder, a rate-compatible punctured convolutional (RCPC) channel coder, and hierarchical modulation. Under bandwidth constraints, we developed a novel packetization strategy and optimized system parameters in a mean-distortion sense. See publications for details.

Cross-layer Design Progressive Coding RCPC Hierarchical Modulation
Coding for Embedded Bit Streams · Concatenated coding near capacity

A key contribution of my thesis was a simple, constructive concatenated coding method for embedded bit streams that achieved performance very close to Shannon-capacity limits for binary symmetric channels (BSCs), within approximately 0.25–0.3 dB in PSNR.

The method couples a novel packetization paradigm with RCPC and rate-compatible LDPC (RC-LDPC) codes, together with carefully designed interleavers for burst-error randomization. We developed a tractable functional optimization procedure enabling constrained exhaustive search to identify globally optimal designs for the stated objective.

Channel Coding RC-LDPC Optimization Embedded Streams
In the Absence of CSI or Multicast · The “fountain” idea

The above scenarios often assume the transmitter has perfect or imperfect channel state information (CSI). In many multimedia applications, CSI may be unavailable or unreliable; in multicast settings, receivers experience different channels, so there is no single CSI to adapt to.

Fountain codes are a natural fit in such cases. They are rateless: an essentially unbounded number of encoded packets can be generated, and the actual number transmitted can be determined on the fly. In my thesis, we proposed a general fountain-code design suited to multimedia transmissions, showing how to tune parameters for progressive transmission and emphasizing unequal iteration time (URI) performance via a joint design of the distributions governing code behavior. We also investigated limiting performance bounds for simple LT-code designs under representative source-transmission scenarios.

Fountain Codes LT Codes Multicast No-CSI
Object Tracking · “Visible or Invisible?” (MERL, 2009)

In summer 2009, I worked with the imaging group at Mitsubishi Electric Research Laboratories (MERL), Cambridge, MA. I first developed a tissue simulation program (C-based engine) using a finite element method to morph an object (a tumor) within a volume. This enabled the generation of synthetic images and videos for testing tracking and classification pipelines.

We evaluated algorithms for detection and tracking in both visible and invisible tumor scenarios, focusing on accuracy and reliability. I also developed additional methods including: (1) improved temporal random-walk tracking, (2) seedless image segmentation using repeated random walks or graph cuts, and (3) learning and tracking via regression on different Lie groups.

Tracking FEM Simulation Segmentation MERL
Founsure · Erasure coding for reliable distributed storage

Founsure is an open-source erasure coding library for fault-tolerant distributed storage systems. It implements multi-dimensional, graph-based erasure codes using efficient XOR-based operations and multi-core optimizations, enabling fast encoding, decoding, repair, and update in large-scale storage architectures.

The library supports fountain-style (LT) coding with flexible parameterization, bridging elegant erasure-coding theory with practical, deployable system-level implementations for modern distributed storage platforms.

Erasure Coding Fountain Codes Distributed Storage Open Source

Posters

Selected research posters and visual summaries

Enhancing RAG with Semantic Chunking and Chain-of-Thought Reasoning

Presented at IEEE MLSP 2025 · August 31–September 3, 2025 · Istanbul, Türkiye

We present a novel RAG architecture that combines LLM-driven semantic chunking, metadata augmentation, and Chain-of-Thought reasoning to improve document retrieval and generation. Unlike traditional fixed-length chunking, our method aligns retrieval units with semantic boundaries and enriches them with context-aware metadata. Results show substantial improvements in retrieval effectiveness and answer coherence, validating the importance of reasoning-aware chunk design in scalable document processing systems.

Internal Neural Noise Progression for Emergent Classification Robustness

Presented at Cognitive Computational Neuroscience (CCN) 2024 · August 6–9, 2024 · Boston, Massachusetts

Utilization of low spatial frequencies and internal noise, whether it be input-dependent or input-independent, when applied progressively (high to low noise) during training, has the potential to enhance classification robustness performance of networks under degraded (noisy and/or blurry) input. While the progression from high to low noise may appear contrary to some existing studies, our approach focuses on noise manipulation at the neuronal level. We hypothesize that noise should be considered together with dynamic network changes through architectural processes such as proliferation and pruning.

Spatial Frequency Decoupling: A Bio-Inspired Strategy for Robust Visual Recognition

Presented at Vision Sciences Society (VSS) 2024 · St. Pete Beach, FL, USA

This poster explores spatial frequency decoupling as a biologically inspired architectural principle for improving robustness in visual recognition networks. Motivated by evidence from human vision—where low and high spatial frequencies are processed along partially distinct pathways with different temporal dynamics—we introduce network designs that explicitly separate and later fuse low- and high-frequency information. EEG analyses and machine robustness experiments show that such decoupling improves resilience to blur, noise, and turbulence, while yielding internal dynamics that align with known neurophysiological processing patterns.

Biomimetic Progressive Chromatic Training for Robust Face Recognition

Presented at Vision Sciences Society (VSS) 2024 · St. Pete Beach, FL, USA

This poster investigates whether biologically inspired, developmental progression of color information can improve the robustness of deep face recognition systems. Motivated by human visual development—where chromatic sensitivity emerges gradually—we introduce progressive chromatic training regimes that transition models from grayscale to color in a controlled manner. Experiments on face recognition tasks demonstrate that such biomimetic training enhances resilience to chromatic distortions and hue variations, particularly under moderate degradation, highlighting the value of developmentally grounded learning strategies for robust computer vision.

Articles

Static notes and research articles (PDF downloads)

These articles are intended to cover both fundamental principles and advanced concepts across several core topics. While many applications are motivated by storage and data recording systems, the presented methods and algorithms have found wide use in digital communications, computer vision, parallel computing, and related fields.

I encourage readers to also explore other high‑quality resources available online for successful applications of these techniques. I would appreciate any corrections or feedback regarding the uploaded documents—please share your comments via the Contact page.

Research Articles on Error Correction Codes

  • Introduction to Information Theory and Bounds PDF — 12 pages, Version 0.1
  • Algebraic Code Constructions: Linear Codes PDF — 35 pages, Version 0.1
  • Convolutional and Turbo Codes PDF Not available yet
  • LDPC Codes PDF — 18 pages, Version 0.1
  • Incremental Redundancy and Fountain Codes PDF — 57 pages, Version 0.2
  • Erasure Codes for Storage PDF Not available yet
  • Modes of Tape C1–C2 Product Code Decoding PDF (LTO Tape Technology) — Version 1.0
  • Performance Analysis of C1–C2 Product Codes under Different Settings PDF (LTO Tape Technology) — Version 2.0

Research Articles on Artificial Intelligence

  • A novel paradigm at the intersection of Machines and Humans: Artificial Human Intelligence PDF — 26 pages, Version 0.2

Research Articles on Data Compression & Deduplication

  • Introduction to Coded Deduplication Systems PDF Not available yet

Research Articles on Constrained Codes

  • Constraint Systems PDF Not available yet
  • RLL and MTR Codes PDF Not available yet

Research Articles on Digital Communication Systems

  • Introduction to Communication Theory: Fundamentals PDF — 33 pages, Version 0.1

Research Articles on Reliability Theory

  • Reliability Engineering PDF Not available yet
  • Durability and Availability of Erasure‑Coded Systems with Concurrent Maintenance PDF — 30 pages, Version 0.1

Articles on Time Series Analysis

  • Hidden Markov Models: Evaluation, Decoding, and Learning PDF Not available yet

Review Articles on Multimedia Communications

  • Wireless Progressive / Scalable Multimedia Communications PDF (Intended for IEEE Potentials)

Review Articles on Relay Protocols

  • BER Calculations for Hierarchical 4‑PAM under Truncate‑and‑Forward Relaying PDF

Publications (recent)

Selected highlights (keep full list on the main Publications section)

For the complete and up-to-date list, see the Publications (recent) section on the main page or your Google Scholar.

Artificial Human Intelligence: The Role of Humans in the Development of Next Generation AI
Suayb S. Arslan · IEEE Transactions on Emerging Topics in Computational Intelligence, vol. 10, no. 1, pp. 4–20, Feb. 2026 · IEEE Xplore
Blockchain-Based Self-Sovereign Identity: Taking Control of Identity in Federated Learning
Engin Zeydan, Josep Mangues-Bafalluy,Suayb S. Arslan, et al. · IEEE Open Journal of the Communications Society · 2024
Decentralizing Authentication for Mobile Networks: Opportunities and Challenges in Web 3.0 Era
Engin Zeydan, Josep Mangues-Bafalluy,Suayb S. Arslan, Yekta Turk · IEEE Communications Society (Contents Digest / magazine listing) · 2025
Minimum Repair Bandwidth LDPC Codes for Distributed Storage Systems
Massoud Pourmandi, Ali Emre Pusane,Suayb S. Arslan, Elif Haytaoglu · IEEE Communications Letters · 2023
Data Repair-Efficient Fault Tolerance for Cellular Networks Using LDPC Codes
E. Haytaoglu, E. Kaya and S. S. Arslan, “Data Repair-Efficient Fault Tolerance for Cellular Networks Using LDPC Codes,” IEEE Transactions on Communications, vol. 70, no. 1, pp. 19–31, Jan. 2022 · IEEE Xplore
Blockchain-based self-sovereign identity solution for aerial base stations in multi-operator environments
Engin Zeydan, Josep Mangues-Bafalluy,Suayb S. Arslan, et al. · Internet of Things · 2024
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