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H. Birkan Yilmaz

H. Birkan Yilmaz appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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Emerging TechnologiesInformation Theorymath.ITArtificial IntelligenceCryptography and SecurityMolecular NetworksNetworking and Internet Architecture

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Published work

20 published item(s)

preprint2026arXiv

Adversarial SQL Injection Generation with LLM-Based Architectures

SQL injection (SQLi) attacks are still one of the serious attacks ranked in the Open Worldwide Application Security Project (OWASP) Top 10 threats. Today, with advances in Artificial Intelligence (AI), especially in Large Language Models (LLMs), an opportunity has been created for automating adversarial attack tests to measure the defense mechanisms. In this paper, we aim to create a comprehensive evaluation of use cases that utilize LLMs for adversarial SQL injection generation. We introduce two novel LLM-based systems, Retrieval Augmented Generation for Adversarial SQLi (RADAGAS) and Reflective Chain-of-Thought SQLi (RefleXQLi), and compare them with existing baselines against 10 Web Application Firewalls (WAFs) and one execution-based MySQL validator. To perform a comprehensive test, we used six rule-based open-source WAFs (ModSecurity PL1--3, Coraza PL1--3), 2 AI/ML-based WAFs (WAF Brain, CNN-WAF), and 2 commercial WAFs (AWS WAF and Cloudflare WAF). For the LLM models, we used GPT-4o, Claude 3.7 Sonnet, and DeepSeek R1. Our tests consist of 240 experiments that generate 240,000 payloads and perform 2.2 million tests against WAFs. Our comprehensive evaluation reveals that RADAGAS-GPT4o outperforms other baseline models with a 22.73\% bypass rate. The proposed RADAGAS variants are highly successful on AI/ML-based WAFs (92.49\% on WAF-Brain by RADAGAS-DeepSeek, 80.48\% on CNN-WAF by RADAGAS-Claude), but struggle to bypass rule-based WAFs (0--5.70\% on ModSecurity and Coraza). In addition to these findings, another observation is that creating less diverse payloads achieves more bypasses, however they show poor results if the initially chosen payload is not successful. We observe that our findings provide a comprehensive view on using LLM-based approaches in security testing.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Simulation Study and Analysis of Diffusive Molecular Communications with an Apertured Plane

Molecular communication via diffusion (MCvD) is a method of achieving nano- and micro-scale connectivity by utilizing the free diffusion mechanism of information molecules. The randomness in diffusive propagation is the main cause of inter-symbol interference (ISI) and the limiting factor of high data rate MCvD applications. In this paper, an apertured plane is considered between the transmitter and the receiver of an MCvD link. Either after being artificially placed or occurring naturally, surfaces or volumes that resemble an apertured plane only allow a fraction of the molecules to pass. Contrary to intuition, it is observed that such topology may improve communication performance, given the molecules that can pass through the aperture are the ones that take more directed paths towards the receiver. Furthermore, through both computer simulations and a theoretical signal evaluation metric named signal-to-interference and noise amplitude ratio (SINAR), it is found that the size of the aperture imposes a trade-off between the received signal power and the ISI combating capability of an MCvD system, hinting to an optimal aperture size that minimizes the bit error rate (BER). It is observed that the trend of BER is accurately mirrored by SINAR, suggesting the proposed metric's applicability to optimization tasks in MCvD systems, including finding the optimal aperture size of an apertured plane. In addition, computer simulations and SINAR show that said optimal aperture size is affected by the location of the aperture and the bit rate. Lastly, the paper analyzes the effects of radial and angular offsets in the placement of the apertured plane, and finds that a reduction in BER is still in effect up to certain offset values. Overall, our results imply that apertured plane-like surfaces may actually help communication efficiency, even though they reduce the received signal power.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Two-Way Molecular Communications

For nano-scale communications, there must be cooperation and simultaneous communication between nano devices. To this end, in this paper we investigate two-way (a.k.a. bi-directional) molecular communications between nano devices. If different types of molecules are used for the communication links, the two-way system eliminates the need to consider self-interference. However, in many systems, it is not feasible to use a different type of molecule for each communication link. Thus, we propose a two-way molecular communication system that uses a single type of molecule. We develop a channel model for this system and use it to analyze the proposed system's bit error rate, throughput, and self-interference. Moreover, we propose analog- and digital- self-interference cancellation techniques. The enhancement of link-level performance using these techniques is confirmed with both numerical and analytical results.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

A Comprehensive Survey of Recent Advancements in Molecular Communication

With much advancement in the field of nanotechnology, bioengineering and synthetic biology over the past decade, microscales and nanoscales devices are becoming a reality. Yet the problem of engineering a reliable communication system between tiny devices is still an open problem. At the same time, despite the prevalence of radio communication, there are still areas where traditional electromagnetic waves find it difficult or expensive to reach. Points of interest in industry, cities, and medical applications often lie in embedded and entrenched areas, accessible only by ventricles at scales too small for conventional radio waves and microwaves, or they are located in such a way that directional high frequency systems are ineffective. Inspired by nature, one solution to these problems is molecular communication (MC), where chemical signals are used to transfer information. Although biologists have studied MC for decades, it has only been researched for roughly 10 year from a communication engineering lens. Significant number of papers have been published to date, but owing to the need for interdisciplinary work, much of the results are preliminary. In this paper, the recent advancements in the field of MC engineering are highlighted. First, the biological, chemical, and physical processes used by an MC system are discussed. This includes different components of the MC transmitter and receiver, as well as the propagation and transport mechanisms. Then, a comprehensive survey of some of the recent works on MC through a communication engineering lens is provided. The paper ends with a technology readiness analysis of MC and future research directions.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

A Machine Learning Approach to Model the Received Signal in Molecular Communications

A molecular communication channel is determined by the received signal. Received signal models form the basis for studies focused on modulation, receiver design, capacity, and coding depend on the received signal models. Therefore, it is crucial to model the number of received molecules until time $t$ analytically. Modeling the diffusion-based molecular communication channel with the first-hitting process is an open issue for a spherical transmitter. In this paper, we utilize the artificial neural networks technique to model the received signal for a spherical transmitter and a perfectly absorbing receiver (i.e., first hitting process). The proposed technique may be utilized in other studies that assume a spherical transmitter instead of a point transmitter.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Chemical Propagation Pattern for Molecular Communications

In a diffusion-based molecular communication system, molecules are employed to convey information. When propagation and reception processes are considered in a framework of first passage processes, we need to focus on absorbing receivers. For this kind of molecular communication system, the characteristics of the channel is also affected by the shape of the transmitter. In the literature, most studies focus on systems with a point transmitter due to circular symmetry. In this letter, we address propagation and reception pattern for chemical signals emitted from a spherical transmitter. We also investigate the directivity gain achieved by the reflecting spherical transmitter. We quantify the power gain by measuring the received power at different angles on a circular region. Moreover, we define three metrics, i.e., the half-power pattern-width, the directivity gain, and the peak time of the signal, for analyzing the received signal pattern.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Effective inter-symbol interference mitigation with a limited amount of enzymes in molecular communications

In molecular communication via diffusion (MCvD), the inter-symbol interference (ISI) is a well known severe problem that deteriorates both data rates and link reliability. ISI mainly occurs due to the slow and highly random propagation of the messenger molecules, which causes the emitted molecules from the previous symbols to interfere with molecules from the current symbol. An effective way to mitigate the ISI is using enzymes to degrade undesired molecules. Prior work on ISI mitigation by enzymes has assumed an infinite amount of enzymes randomly distributed around the molecular channel. Taking a different approach, this paper assumes an MCvD channel with a limited amount of enzymes. The main question this paper addresses is how to deploy these enzymes in an effective structure so that ISI mitigation is maximized. To find an effective MCvD channel environment, this study considers optimization of the shape of the transmitter node, the deployment location and structure, the size of the enzyme deployed area, and the half-lives of the enzymes. It also analyzes the dependence of the optimum size of the enzyme area on the distance and half-life.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Frequency Assignment Problem with Net Filter Discrimination Constraints

Managing radio spectrum resources is a crucial issue. The frequency assignment problem (FAP) basically aims to allocate, in an efficient manner, limited number of frequencies to communication links. Geographically close links, however, cause interference, which complicates the assignment, imposing frequency separation constraints. The FAP is closely related to the graph-coloring problem and it is an NP-hard problem. In this paper, we propose to incorporate the randomization into greedy and fast heuristics. As far as being implemented, the proposed algorithms are very straight forward and are without system parameters that need tuned. The proposed algorithms significantly improve, quickly and effectively, the solutions obtained by greedy algorithms in terms of the number of assigned frequencies and the range. The enhanced versions of proposed algorithms perform close to the lower bounds while running for a reasonable duration. Another novelty of our study is its consideration of the net filter discrimination effects in the communication model. Performance analysis is done by synthetic and measured data, where the measurement data includes the effect of the real 3-dimensional (3D) geographical features in the Daejeon region in Korea. In both cases, we observe a significant improvement by employing randomized heuristics.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

ISI-Aware Modeling and Achievable Rate Analysis of the Diffusion Channel

Analyzing the achievable rate of molecular communication via diffusion (MCvD) inherits intricacies due to its nature: MCvD channel has memory, and the heavy tail of the signal causes inter symbol interference (ISI). Therefore, using Shannon's channel capacity formulation for memoryless channel is not appropriate for the MCvD channel. Instead, a more general achievable rate formulation and system model must be considered to make this analysis accurately. In this letter, we propose an effective ISI-aware MCvD modeling technique in 3-D medium and properly analyze the achievable rate.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Molecular MIMO: From Theory to Prototype

In diffusion-based molecular communication, information transport is governed by diffusion through a fluid medium. The achievable data rates for these channels are very low compared to the radio-based communication system, since diffusion can be a slow process. To improve the data rate, a novel multiple-input multiple-output (MIMO) design for molecular communication is proposed that utilizes multiple molecular emitters at the transmitter and multiple molecular detectors at the receiver (in RF communication these all correspond to antennas). Using particle-based simulators, the channel's impulse response is obtained and mathematically modeled. These models are then used to determine inter-link interference (ILI) and inter-symbol interference (ISI). It is assumed that when the receiver has incomplete information regarding the system and the channel state, low complexity symbol detection methods are preferred since the receiver is small and simple. Thus four detection algorithms are proposed---adaptive thresholding, practical zero forcing with channel models excluding/including the ILI and ISI, and Genie-aided zero forcing. The proposed algorithms are evaluated extensively using numerical and analytical evaluations.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

SMIET: Simultaneous Molecular Information and Energy Transfer

The performance of communication systems is fundamentally limited by the loss of energy through propagation and circuit inefficiencies. In this article, we show that it is possible to achieve ultra low energy communications at the nano-scale, if diffusive molecules are used for carrying data. Whilst the energy of electromagnetic waves will inevitably decay as a function of transmission distance and time, the energy in individual molecules does not. Over time, the receiver has an opportunity to recover some, if not all of the molecular energy transmitted. The article demonstrates the potential of ultra-low energy simultaneous molecular information and energy transfer (SMIET) through the design of two different nano-relay systems, and the discusses how molecular communications can benefit more from crowd energy harvesting than traditional wave-based systems.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Detection Algorithms for Molecular MIMO

In this paper, we propose a novel design for molecular communication in which both the transmitter and the receiver have, in a 3-dimensional environment, multiple bulges (in RF communication this corresponds to antenna). The proposed system consists of a fluid medium, information molecules, a transmitter, and a receiver. We simulate the system with a one-shot signal to obtain the channel's finite impulse response. We then incorporate this result within our mathematical analysis to determine interference. Molecular communication has a great need for low complexity, hence, the receiver may have incomplete information regarding the system and the channel state. Thus, for the cases of limited information set at the receiver, we propose three detection algorithms, namely adaptive thresholding, practical zero forcing, and Genie-aided zero forcing.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Energy Model for Vesicle-Based Active Transport Molecular Communication

In active transport molecular communication (ATMC), information particles are actively transported from a transmitter to a receiver using special proteins. Prior work has demonstrated that ATMC can be an attractive and viable solution for on-chip applications. The energy consumption of an ATMC system plays a central role in its design and engineering. In this work, an energy model is presented for ATMC and the model is used to provide guidelines for designing energy efficient systems. The channel capacity per unit energy is analyzed and maximized. It is shown that based on the size of the symbol set and the symbol duration, there is a vesicle size that maximizes rate per unit energy. It is also demonstrated that maximizing rate per unit energy yields very different system parameters compared to maximizing the rate only.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Molecular Communications: Channel Model and Physical Layer Techniques

This article examines recent research in molecular communications from a telecommunications system design perspective. In particular, it focuses on channel models and state-of-the-art physical layer techniques. The goal is to provide a foundation for higher layer research and motivation for research and development of functional prototypes. In the first part of the article, we focus on the channel and noise model, comparing molecular and radio-wave pathloss formulae. In the second part, the article examines, equipped with the appropriate channel knowledge, the design of appropriate modulation and error correction coding schemes. The third reviews transmitter and receiver side signal processing methods that suppress inter-symbol-interference. Taken together, the three parts present a series of physical layer techniques that are necessary to producing reliable and practical molecular communications.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

3-D Channel Characteristics for Molecular Communications with an Absorbing Receiver

Within the domain of molecular communications, researchers mimic the techniques in nature to come up with alternative communication methods for collaborating nanomachines. This work investigates the channel transfer function for molecular communication via diffusion. In nature, information-carrying molecules are generally absorbed by the target node via receptors. Using the concentration function, without considering the absorption process, as the channel transfer function implicitly assumes that the receiver node does not affect the system. In this letter, we propose a solid analytical formulation and analyze the signal metrics (attenuation and propagation delay) for molecular communication via diffusion channel with an absorbing receiver in a 3-D environment. The proposed model and the formulation match well with the simulations without any normalization.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Arrival Modeling and Error Analysis for Molecular Communication via Diffusion with Drift

The arrival of molecules in molecular communication via diffusion (MCvD) is a counting process, exhibiting by its nature binomial distribution. Even if the binomial process describes well the arrival of molecules, when considering consecutively sent symbols, the process struggles to work with the binomial cumulative distribution function (CDF). Therefore, in the literature, Poisson and Gaussian approximations of the binomial distribution are used. In this paper, we analyze these two approximations of the binomial model of the arrival process in MCvD with drift. Considering the distance, drift velocity, and the number of emitted molecules, we investigate the regions in which either Poisson or Gaussian model is better in terms of root mean squared error (RMSE) of the CDFs; we confirm the boundaries of the region via numerical simulations. Moreover, we derive the error probabilities for continuous communication and analyze which model approximates it more accurately.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Effect of Degradation in Molecular Communication: Impairment or Enhancement?

In the nanonetworking literature, many solutions have been suggested to enable the nanomachine-to-nanomachine communication. Among these solutions, we focus on what constitutes the basis for molecular communication paradigms --molecular communication via diffusion (MCvD). In this paper, we start with an analytical modeling of a spherical absorbing receiver under messenger molecule degradation and show that our formulations are in agreement with the simulation results of a similar topology. Next, we identify how such signal characteristics as pulse peak time and pulse amplitude are affected by degradation. Indeed, we show analytically how in MCvD, signal shaping is achieved through degradation. We also compare communication under messenger molecule degradation with the case of no-degradation and electromagnetic communication in terms of channel characteristics. Lastly, we evaluate the communication performance of the scenarios having various degradation rates. Here, we assess the system performance according to traditional network metrics such as the level of inter-symbol interference, detection performance, bit error rate, and channel capacity. Our results indicate that introducing degradation significantly improves the system performance when the rate of degradation is appropriately selected. We make a thorough analysis of the communication scenario by taking into account different detection thresholds, symbol durations, and communication distances.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Effect of ISI Mitigation on Modulation Techniques in Communication via Diffusion

Communication via diffusion (CvD) is an effective and energy efficient method for transmitting information in nanonetworks. In this work, we focus on a diffusion-based communication system where the reception process is an absorption via receptors. Whenever a molecule hits to the receiver it is removed from the environment. This kind of reception process is called first passage process and it is more complicated compared to diffusion process only. In 3-D environments, obtaining analytical solution for hitting time distribution for realistic cases is complicated, hence we develop an end-to-end simulator for he diffusion-based communication system that sends consecutive symbols. In CvD, each symbol is modulated and demodulated in a time slot called symbol duration, however the long tail distribution of hitting time is the main challenge that affects the symbol detection error. The molecules arriving in the following slots become an interference source when detection takes place. End-to-end simulator enables us to analyze the effect of inter symbol interference (ISI) without making any assumptions on the ISI. We propose an ISI cancellation technique that utilizes decision feedback for compensating the effect of previously demodulated symbol. Three different modulation types are considered with pulse, square, and cosine carrier waves. In case of constraints on transmitter or receiver node it may not be possible to use pulse as a carrier, and peak-to-average messenger molecule metric is defined for this purpose. Results show that, the proposed ISI mitigation technique improves the symbol detection performance and the amplitude-based modulations are improved more than frequency-based modulations.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Effect of Receptor Density and Size on Signal Reception in Molecular Communication via Diffusion with an Absorbing Receiver

The performance of molecular communication is significantly impacted by the reception process of the messenger molecules. The receptors' size and density, however, have yet to be investigated. In this letter, we analyze the effect of receptor density and size on the signal reception of an absorbing receiver with receptors. The results show that, when the total receptor area is the same, better hitting probability is achieved by using a higher number of relatively small receptors. In addition, deploying receptors, which cover a small percentage of the receiver surface, is able to create an effective communication channel that has a detectable signal level.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

ISI Mitigation Techniques in Molecular Communication

Molecular communication is a new field of communication where molecules are used to transfer information. Among the proposed methods, molecular communication via diffusion (MCvD) is particularly effective. One of the main challenges in MCvD is the intersymbol interference (ISI), which inhibits communication at high data rates. Furthermore, at the nano scale, energy efficiency becomes an essential problem. Before addressing these problems, a pre-determined threshold for the received signal must be calculated to make a decision. In this paper, an analytical technique is proposed to determine the optimum threshold, whereas in the literature, these thresholds are generally calculated empirically. Since the main goal of this paper is to build an MCvD system suitable for operating at high data rates without sacrificing quality, new modulation and filtering techniques are proposed to decrease the effects of ISI and enhance energy efficiency. As a transmitter-based solution, a modulation technique for MCvD, molecular transition shift keying (MTSK), is proposed in order to increase the data rate via suppressing the ISI. Furthermore, for energy efficiency, a power adjustment technique that utilizes the residual molecules is proposed. Finally, as a receiver-based solution, a new energy efficient decision feedback filter (DFF) is proposed as a substitute for the decoders such as minimum mean squared error (MMSE) and decision feedback equalizer (DFE). The error performance of DFF and MMSE equalizers are compared in terms of bit error rates, and it is concluded that DFF may be more advantageous when energy efficiency is concerned, due to its lower computational complexity.

0 citations0 reviewsNo code linkedOpen access