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Alexandru Floares

Alexandru Floares
Independent Researcher · Artificial Intelligence

MD, PhD

About

52
Publications
18,971
Reads
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448
Citations
Additional affiliations
March 2017 - January 2024
Artificial Intelligence Expert
Position
  • CEO
Description
  • I am the CEO of the company.

Publications

Publications (52)
Article
64 Background: Colorectal cancer (CRC), the second most deadly cancer, underscores the critical need for early detection to significantly improve treatment outcomes and survival rates. Colonoscopy, flexible sigmoidoscopy, and the fecal immunochemical tests (FIT), often fail to capture early disease, significantly decreasing the survival chance. Cir...
Chapter
Full-text available
Cancer is one of the most common and deadly diseases worldwide, claiming millions of lives yearly. Despite significant advances in treatment, the overall survival rate remains low, primarily due to late-stage diagnosis. In the high-throughput, high-dimensional omics data era, Biomedical Knowledge should be combined with Data Science best practices...
Article
5 Background: Breast cancer is requires early and accurate detection for effective treatment and improved patient outcomes. Current methods, such as mammography and biopsy, have limitations in accuracy, invasiveness, and accessibility. Circulating microRNAs (miRNAs) are promising non-invasive biomarkers for cancer detection, including breast cancer...
Article
Full-text available
High-quality omics tests can be developed by using machine learning. As high-throughput molecular determinations are costly, we want to build the best models, utilizing the minimal number of samples. Here, we specify a set of criteria for high-quality models and select the algorithms which best satisfy them. Boosted C5, Random Forest and Stochastic...
Presentation
Full-text available
This is the presentation of the paper with the same title
Presentation
Full-text available
This contribution, part of a larger project, was motivated by the fact that we want highly accurate OMICS tests, for diagnosis, prognosis, & response to treatment prediction, based on various omics data. e.g., microarray, NGS or PCR. For these goals, we should use machine learning and artificial intelligence (deep learning) tools to analyze the dat...
Conference Paper
Cancer signatures can be discovered from omics Big Data with machine learning. How big this costly data should be? For a given dataset and biomedical problem is the signature unique? We investigated the miRNA NGS data of the largest breast cancer cohort from TCGA, to develop decision trees (C5 and CART) models discriminating between cancer and norm...
Conference Paper
Precision Medicine’s goals cannot be reached without discovering molecular signatures from omics Big Data, using machine learning. The prevailing conception is that, for a given biomedical condition and class of biomolecules, there should be a unique, highly accurate signature. Following the best practice, for whet lab determinations and predictive...
Presentation
Full-text available
Functional redundancy is a fundamental property of living systems, ensuring their amazingly robust complexity. Both Cancer and Normal cells are robust, and this is partially due to the functional redundancy of their regulatory systems, e.g., many different microRNAs regulate the same mRNA. To explore the redundancy, we propose a computational intel...
Conference Paper
Full-text available
Functional redundancy is a fundamental property of living systems, ensuring their amazing robust complexity. Both cancer and normal cells are robust, and this is partially due to their regulatory subsystems which are functionally redundant, i.e. many different microRNAs regulate the same mRNA. To explore the redundancy, this paper proposes a comput...
Conference Paper
Full-text available
Most molecular diagnosis tests are based on small studies with about twenty patients, and use classical statistics. The prevailing conception is that such studies can indeed yield accurate tests with just one or two predictors, especially when using informative molecules like microRNA in cancer diagnosis. We investigated the relationship between ac...
Presentation
Full-text available
In this contribution, we investigated the relationship between the accuracy of a molecular test and the sample size of the study. Using some simple but powerful decision trees algorithms, we discovered some unexpected aspects. This paper received the ”Best Paper Award”.
Article
Full-text available
MicroRNAs (miRNAs) are small, noncoding RNA species with a length of 20–22 nucleotides that are recognized as essential regulators of relevant molecular mechanisms, including carcinogenesis. Current investigations show that miRNAs are detectable not only in different tissue types but also in a wide range of biological fluids, either free or trapped...
Conference Paper
Full-text available
This paper investigates the integration of clinico-pathological and microRNA data for breast cancer relapse prediction. Clinical and pathological data proved to be relevant in making predictions about cancer disease outcome. The most accurate predictive models can be obtained by using clinico-pathological information together with genomic informati...
Chapter
Full-text available
Reverse engineering of transcription networks is a challenging bioinformatics problem. Ordinary differential equation (ODEs) network models have their roots in the physicochemical base of these networks, but are difficult to build conventionally. Modeling automation is needed and knowledge discovery in data using computational intelligence methods...
Article
Full-text available
The purpose of the study is to identify and validate ultrasound criteria for parotid tumors evaluation, as well as to elaborate a multimodal, multi-criteria and integrative ultrasound approach for allowing tumor discrimination in a non-invasive manner. Twenty patients with solid parotid tumors (12 benign, 8 malignant) were examined by ultrasound: r...
Conference Paper
Early and non-invasive diagnosis and prognosis are important but challenging problems in cancer clinical management.Our results suggest that the most accurate solutions could be developed combining Artificial Intelligence with OMICS technologies. The new i-Biomarker concept and the methodology for developing panels of i-Biomarkers will be presented...
Conference Paper
Understanding and eventually controlling the dynamics of microRNA (miRNA) networks via drug treatments are important yet challenging biomedical research issues. Ordinary differential equations (ODEs), the main mathematical framework of dynamical systems theory, even though considered adequate models for such biomedical networks, are difficult to bu...
Chapter
Full-text available
Modeling complex networks with ordinary differential equations systems is an appropriate approach, particularly suited for dynamical systems represented by time series data. The main challenge of this approach is the difficulty of determining the suitable form of the differential equations which represent the network. In this chapter, we propose...
Book
Computational intelligence aims to emulate aspects of biological systems for developing software and/or hardware that learns and adapts. Such systems primarily include neural networks, fuzzy logic systems and evolutionary computation each of them including multiple active and fast growing research directions. This book presents new and ground-break...
Conference Paper
Full-text available
The aim of this study is to propose a methodology for developing intelligent systems for cancer diagnosis and evaluate it on bladder cancer. Owing to recent advances in high-throughput experiments, large data repositories are now freely available for use. However, the process of extracting information from these data and transforming it into clinic...
Conference Paper
Full-text available
Bladder cancer is the fourth most common malignancy in men in the western countries. The aim of this study was to develop intelligent systems for invasive bladder cancer progression prediction. The proposed methodology combines knowledge discov- ery in data using artificial intelligence and knowledge mining. These are used both in feature selection...
Conference Paper
Bladder cancer is the fourth most common malignancy in men in the western countries. The aim of this study was to develop intelligent systems for invasive bladder cancer progression prediction. The proposed methodology combines knowledge discovery in data using artificial intelligence and knowledge mining. These are used both in feature selection a...
Conference Paper
Full-text available
Currently, there are some paradigm shifts in medicine, from the search for a single ideal biomarker, to the search for panels of molecules, and from a reductionistic to a systemic view, placing these molecules on functional networks. There is also a general trend to favor non-invasive biomarkers. Identifying non-invasive biomarkers in high- through...
Conference Paper
Currently, there are some paradigm shifts in medicine, from the search for a single ideal biomarker, to the search for panels of molecules, and from a reductionistic to a systemic view, placing these molecules on functional networks. There is also a general trend to favor non-invasive biomarkers. Identifying non-invasive biomarkers in high-throughp...
Conference Paper
Full-text available
Currently, there are some paradigm shifts in medicine, from the search for a single ideal biomarker, to the search for panels of molecules, and from a reductionistic to a systemic view, placing these molecules on functional networks. There is also a general trend to favor non-invasive biomarkers. Identifying non-invasive biomarkers in high-throughp...
Conference Paper
Clinical Decision Support Systems have the potential to optimize medical decisions, improve medical care, and reduce costs. An effective strategy to reach these goals is by transforming conventional Clinical Decision Support in Intelligent Clinical Decision Support, using knowledge discovery in data and computational intelligence tools. In this pap...
Conference Paper
Full-text available
In chronic hepatitis C and B, which can progress to cirrhosis and liver cancer, Interferon is the only effective treatment, for carefully selected patients, but it is very expensive. Some of the selection criteria are based on liver biopsy, an invasive, costly and painful medical procedure. Developing an efficient selection system, based on non-inv...
Conference Paper
Full-text available
Mathematical modeling gene regulatory networks is important for understanding and controlling them, with various drugs and their dosage regimens. The ordinary differential equations approach is sensible but also very difficult. Our reverse engineering algorithm (RODES), based on neural networks feedback linearization and genetic programming, takes...
Conference Paper
An important goal of modern medicine is to replace invasive, painful procedures with non-invasive techniques for diagnosis. We investigated the possibility of a knowledge discovery in data approach, based on computational intelligence tools, to integrate information from various data sources - imaging data, clinical and laboratory data, to predict...
Article
Motivation: Various drugs and their dosage regimens. The ordinary differential equations approach is probably the most sensible. Unfortunately, this is also the most difficult, tedious, expensive, and time-consuming approach. There is a need for algorithms to automatically infer such models from high-throughput temporal series data. Computational i...
Conference Paper
Automatically inferring drug gene regulatory networks models from microarray time series data is a challenging task. The ordinary differential equations models are sensible, but difficult to build. We extended our reverse engineering algorithm for gene networks (RODES), based on genetic programming, by adding a neural networks feedback linearizatio...
Article
Background and aims: The gold standard in evaluating fibrosis stage in chronic hepatitis C (CHC) patients is liver biopsy, a costly and invasive procedure. Alternatively, transient elastography (FibroScan®) performs well in identifying severe fibrosis or cirrhosis, but is less accurate in identifying lower degrees of fibrosis. We recently built a p...
Article
Modeling neural networks with ordinary differential equations systems is a sensible approach, but also very difficult. This paper describes a new algorithm based on linear genetic programming which can be used to reverse engineer neural networks. The RODES algorithm automatically discovers the structure of the network, including neural connections,...
Article
Full-text available
Chronic hepatitis B can evolve to cirrhosis and liver cancer. Interferon is the only effective treatment, for carefully selected patients, but it is very expensive. Some of the selection criteria are based on liver biopsy, an invasive, costly and painful medical proce-dure. Therefore, developing efficient non-invasive selection systems, could be in...
Conference Paper
The ordinary differential equations approach to neutral networks modeling is one of the most sensible approach but also very difficult. We proposed a reverse engineering algorithm for neural networks based on linear genetic programming. This algorithm allows the automatic discovery of the structure, estimation of the parameters, and even identifica...
Article
Full-text available
Automatically inferring gene regulating networks models from microarray time series data is one of the most challenging tasks of bioinformatics. The ordinary differential equations models are the most sensible, but very difficult to build. We introduced the more general concept of drug gene regulating networks, where the regulation is exerted also...
Conference Paper
Full-text available
Modern pharmacology, combining pharmacokinetic, pharmacodynamic, and pharmacogenomic data, is dealing with high dimensional, nonlinear, stiff systems. Mathematical modeling of these systems is very difficult, but important for understanding them. At least as important is to adequately control them through inputs – drugs’ dosage regimens. Genetic pr...
Conference Paper
Recently, magnetic resonance imaging and proton magnetic resonance spectroscopy studies of major depression identified structural and neurochemical alterations in several brain regions, including the hippocampus and prefrontal cortex. However, many contradictory endings exist. Most previous studies used a few cases and features, and conventional st...
Conference Paper
Full-text available
Pharmacogenomic systems (PG) are very high dimensional, nonlinear, and stiff systems. Mathematical modeling of these systems, as systems of nonlinear coupled ordinary differential equations (ODE), is considered important for understanding them; unfortunately, it is also a very difficult task. At least as important is to adequately control them thro...
Conference Paper
Full-text available
Pharmacogenomic systems (PG) are very high dimensional, nonlinear, and stiff systems. Mathematical modeling of these systems, as systems of nonlinear coupled ordinary differential equations (ODE), is considered important for understanding them; unfortunately, it is also a very difficult task. At least as important is to adequately control them thro...
Conference Paper
Recently, magnetic resonance imaging and proton magnetic resonance spectroscopy studies of major depression identified structural and neurochemical alterations in several brain regions, including the hippocampus and prefrontal cortex. However, many contradictory endings exist. Most previous studies used a few cases and features, and conventional st...
Conference Paper
Full-text available
Pharmacological modeling is developing from an empirical discipline into a mechanistic science. Also, new and important fields like pharmacogenomics appeared. As a consequence, pharmacology is dealing with high dimensional, nonlinear, control systems. The intent of this paper is to show that all this systems, being based on a limited array of mecha...
Article
2134 Background: An important problem in cancer chemotherapy is the design of drug dosage regimens such that at the end of treatment, the tumor burden is minimized, and the benefits are balanced against the toxic effects. We propose an approach based on neural networks (NN) control to optimize chemotherapy regimens. Methods: The tumor growth and th...
Conference Paper
Full-text available
This paper presents the optimal control chemotherapy scheduling in cancer using neural networks. Unlike conventional methods, the proposed neural networks methodology, feedback linearization, is simple and capable of automatically finding the optimal solutions for complex cancer chemotherapy problems. Also, it allows the application of the well dev...

Questions

Questions (4)
Question
It is clear that miRNA are informative molecules for cancer diagnosis, and there is a desire for non-invasive tests. It is also clear that NGS is a real progress. However, the known advantages of miRNA NGS vs microarray are not important for my study, as I do not want to discover new miRNAs or isoforms. I want just to discriminate, with the highest possible accuracy, between cancer and normal, using advanced Artificial Intelligence (AI) methods. Prelimiary results suggest that microrna data are better than NGS. Moreover, microarray profiling is cheaper. Searching the literature, I found some papers corroborationg this idea: microarray is a better choice if you are interested in miRNA cuantification. What is your opinion? Thank you!
Question
I would like to know your answer to the following questions:  
Why most omics (e.g., microarray, NGS, PCR) studies concerning disease diagnosis, or prognosis, or response to treatment end up with lists of differentially expressed molecules. Is this the most relevant and/or practically useful result?  
I will tell you my opinion later, as I do not want to influence your answers. 
Thank you 

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