Tom Lenaerts

Tom Lenaerts
  • PhD
  • Professor at Université Libre de Bruxelles

About

222
Publications
27,562
Reads
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6,030
Citations
Current institution
Université Libre de Bruxelles
Current position
  • Professor
Additional affiliations
October 2018 - present
Université Libre de Bruxelles
Position
  • Professor
October 2007 - present
Vrije Universiteit Brussel
Position
  • Professor
October 2008 - September 2018
Université Libre de Bruxelles
Position
  • Professor (Associate)

Publications

Publications (222)
Preprint
Full-text available
Experimental evidence shows that in a repeated dilemma setting cooperation is more likely to become the norm in small matching groups than in large ones. This result holds even if cooperation is an equilibrium outcome for all investigated group sizes. But what happens if small matching groups are merged to become large ones? Our paper is based on t...
Preprint
Full-text available
Artificial intelligence (AI) has recently seen transformative breakthroughs in the life sciences, expanding possibilities for researchers to interpret biological information at an unprecedented capacity, with novel applications and advances being made almost daily. In order to maximise return on the growing investments in AI-based life science rese...
Article
Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The Data Optimization Model Evaluation (DOME) recommendations aim to enhance the validation and reproducibility of ML research by establishing standards for key aspects such as data handling and processing, optimization, evaluation, and model interpretabil...
Preprint
Full-text available
Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The DOME recommendations aim to enhance the validation and reproducibility of ML research by establishing standards for key aspects such as data handling and processing, optimization, evaluation, and model interpretability. The recommendations help to ensu...
Article
Full-text available
While biomedical relation extraction (bioRE) datasets have been instrumental in the development of methods to support biocuration of single variants from texts, no datasets are currently available for the extraction of digenic or even oligogenic variant relations, despite the reports in literature that epistatic effects between combinations of vari...
Article
Full-text available
While autonomous artificial agents are assumed to perfectly execute the strategies they are programmed with, humans who design them may make mistakes. These mistakes may lead to a misalignment between the humans’ intended goals and their agents’ observed behavior, a problem of value alignment. Such an alignment problem may have particularly strong...
Article
Motivation Whole exome sequencing (WES) has emerged as a powerful tool for genetic research, enabling the collection of a tremendous amount of data about human genetic variation. However, properly identifying which variants are causative of a genetic disease remains an important challenge, often due to the number of variants that need to be screene...
Article
Full-text available
RASopathies are syndromes caused by congenital defects in the Ras/mitogen-activated protein kinase (MAPK) pathway genes, with a population prevalence of 1 in 1,000. Patients are typically identified in childhood based on diverse characteristic features, including cryptorchidism (CR) in >50% of affected men. As CR predisposes to spermatogenic failur...
Article
Full-text available
In sequential social dilemmas with stranger matching, initiating cooperation is inherently risky for the first mover. The disclosure of the second mover’s past actions may be necessary to instigate cooperation. We experimentally compare the effect of mandatory and voluntary disclosure with non-disclosure in a sequential prisoner’s dilemma situation...
Article
Full-text available
It is widely known how the human ability to cooperate has influenced the thriving of our species. However, as we move towards a hybrid human-machine future, it is still unclear how the introduction of artificial agents in our social interactions affect this cooperative capacity. In a one-shot collective risk dilemma, where enough members of a group...
Article
Full-text available
Automatic biomedical relation extraction (bioRE) is an essential task in biomedical research in order to generate high-quality labelled data that can be used for the development of innovative predictive methods. However, building such fully labelled, high quality bioRE data sets of adequate size for the training of state-of-the-art relation extract...
Article
Full-text available
The development of high-throughput next-generation sequencing technologies and large-scale genetic association studies produced numerous advances in the biostatistics field. Various aggregation tests, i.e. statistical methods that analyze associations of a trait with multiple markers within a genomic region, have produced a variety of novel discove...
Article
Full-text available
Background Understanding the impact of gene interactions on disease phenotypes is increasingly recognised as a crucial aspect of genetic disease research. This trend is reflected by the growing amount of clinical research on oligogenic diseases, where disease manifestations are influenced by combinations of variants on a few specific genes. Althoug...
Conference Paper
Full-text available
In this paper, we present ALAMBIC, an open-source dockerized web-based platform for annotating text data through active learning for classification tasks. Active learning is known to reduce the need of labelling, a time-consuming task, by selecting the most informative instances among the unlabelled instances, reaching an optimal accuracy faster th...
Preprint
Experts advising decision-makers are likely to display expertise which varies as a function of the problem instance. In practice, this may lead to sub-optimal or discriminatory decisions against minority cases. In this work we model such changes in depth and breadth of knowledge as a partitioning of the problem space into regions of differing exper...
Article
Full-text available
Abstract Background Congenital hydrocephalus is characterized by ventriculomegaly, defined as a dilatation of cerebral ventricles, and thought to be due to impaired cerebrospinal fluid (CSF) homeostasis. Primary congenital hydrocephalus is a subset of cases with prenatal onset and absence of another primary cause, e.g., brain hemorrhage. Published...
Article
Evolutionary Game Theory (EGT) provides an important framework to study collective behavior. It combines ideas from evolutionary biology and population dynamics with the game theoretical modeling of strategic interactions. Its importance is highlighted by the numerous high level publications that have enriched different fields, ranging from biology...
Article
Full-text available
Although standards and guidelines for the interpretation of variants identified in genes that cause Mendelian disorders have been developed, this is not the case for more complex genetic models including variant combinations in multiple genes. During a large curation work conducted on 318 research articles presenting oligogenic variant combinations...
Article
Full-text available
People have different preferences for what they allocate for themselves and what they allocate to others in social dilemmas. These differences result from contextual reasons, intrinsic values, and social expectations. What is still an area of debate is whether these differences can be estimated from differences in each individual’s deliberation pro...
Preprint
Full-text available
In sequential social dilemmas with stranger matching, initiating cooperation is inherently risky for the first mover. The disclosure of the second mover’s past actions may be necessary to instigate cooperation. We experimentally compare the effect of mandatory and voluntary disclosure with non disclosure in a sequential prisoner's dilemma situation...
Article
Full-text available
Home assistant chat-bots, self-driving cars, drones or automated negotiation systems are some of the several examples of autonomous (artificial) agents that have pervaded our society. These agents enable the automation of multiple tasks, saving time and (human) effort. However, their presence in social settings raises the need for a better understa...
Preprint
Full-text available
It is widely known how the human ability to cooperate has influenced the thriving of our species. However, as we move towards a hybrid human-machine future, it is still unclear how the introduction of AI agents in our social interactions will affect this cooperative capacity. Within the context of the one-shot collective risk dilemma, where enough...
Article
Full-text available
While many theoretical studies have revealed the strategies that could lead to and maintain cooperation in the Iterated Prisoner’s dilemma, less is known about what human participants actually do in this game and how strategies change when being confronted with anonymous partners in each round. Previous attempts used short experiments, made differe...
Article
Full-text available
Improving the understanding of the oligogenic nature of diseases requires access to high-quality, well-curated Findable, Accessible, Interoperable, Reusable (FAIR) data. Although first steps were taken with the development of the Digenic Diseases Database, leading to novel computational advancements to assist the field, these were also linked with...
Preprint
Full-text available
While many theoretical studies have revealed the strategies that could lead to and maintain cooperation in the Iterated Prisoner's Dilemma, less is known about what human participants actually do in this game and how strategies change when being confronted with anonymous partners in each round. Previous attempts used short experiments, made differe...
Article
Full-text available
Regulation of advanced technologies such as Artificial Intelligence (AI) has become increasingly important, given the associated risks and apparent ethical issues. With the great benefits promised from being able to first supply such technologies, safety precautions and societal consequences might be ignored or shortchanged in exchange for speeding...
Article
With the introduction of Artificial Intelligence (AI) and related technologies in our daily lives, fear and anxiety about their misuse as well as their inherent biases, incorporated during their creation, have led to a demand for governance and associated regulation. Yet regulating an innovation process that is not well understood may stifle this p...
Conference Paper
Full-text available
We examine a social dilemma that arises with the advancement of technologies such as AI, where technologists can choose a safe (SAFE) vs risk-taking (UNSAFE) course of development. SAFE is costlier and takes more time to implement than UNSAFE, allowing UNSAFE strategists to further claim significant benefits from reaching supremacy in a certain tec...
Article
DOME is a set of community-wide recommendations for reporting supervised machine learning–based analyses applied to biological studies. Broad adoption of these recommendations will help improve machine learning assessment and reproducibility.
Preprint
Quite some real-world problems can be formulated as decision-making problems wherein one must repeatedly make an appropriate choice from a set of alternatives. Expert judgements, whether human or artificial, can help in taking correct decisions, especially when exploration of alternative solutions is costly. As expert opinions might deviate, the pr...
Preprint
Full-text available
With the introduction of Artificial Intelligence (AI) and related technologies in our daily lives, fear and anxiety about their misuse as well as the hidden biases in their creation have led to a demand for regulation to address such issues. Yet blindly regulating an innovation process that is not well understood, may stifle this process and reduce...
Preprint
Full-text available
Home assistant chat-bots, self-driving cars, drones or automated negotiations are some of the several examples of autonomous (artificial) agents that have pervaded our society. These agents enable the automation of multiple tasks, saving time and (human) effort. However, their presence in social settings raises the need for a better understanding o...
Article
Full-text available
This paper investigates how the possibility of affecting group composition combined with the possibility of repeated interaction impacts cooperation within groups and surplus distribution. We developed and tested experimentally a Surplus Allocation Game where cooperation of four agents is needed to produce surplus, but only two have the power to al...
Article
From climate action to public health measures, human collective endeavors are often shaped by different uncertainties. Here we introduce a novel population-based learning model wherein a group of individuals facing a collective risk dilemma acquire their strategies over time through reinforcement learning, while handling different sources of uncert...
Article
Full-text available
Human hematopoiesis is surprisingly resilient to disruptions, providing suitable responses to severe bleeding, long lasting immune activation, and even bone marrow transplants. Still, many blood disorders exist which push the system past its natural plasticity, resulting in abnormalities in the circulating blood. While proper treatment of such dise...
Article
Full-text available
The field of Artificial Intelligence (AI) is going through a period of great expectations, introducing a certain level of anxiety in research, business and also policy. This anxiety is further energised by an AI race narrative that makes people believe they might be missing out. Whether real or not, a belief in this narrative may be detrimental as...
Preprint
Full-text available
The field of Artificial Intelligence (AI) has been introducing a certain level of anxiety in research, business and also policy. Tensions are further heightened by an AI race narrative which makes many stakeholders fear that they might be missing out. Whether real or not, a belief in this narrative may be detrimental as some stakeholders will feel...
Article
Objective The study aimed to identify the genetic basis of partial gonadal dysgenesis (PGD) in a non‐consanguineous family from Estonia. Patients Cousins P (proband) 1 (12 years; 46,XY) and P2 (18 years; 46,XY) presented bilateral cryptorchidism, severe penoscrotal hypospadias, low bitesticular volume and azoospermia in P2. Their distant relative,...
Article
Full-text available
Social dilemmas are often shaped by actions involving uncertain returns only achievable in the future, such as climate action or voluntary vaccination. In this context, uncertainty may produce non-trivial effects. Here, we assess experimentally — through a collective risk dilemma — the effect of timing uncertainty, i.e. how uncertainty about when a...
Article
Full-text available
Rapid technological advancements in Artificial Intelligence (AI), as well as the growing deployment of intelligent technologies in new application domains, have generated serious anxiety and a fear of missing out among different stake-holders, fostering a racing narrative. Whether real or not, the belief in such a race for domain supremacy through...
Chapter
In collective decision-making (CDM) a group of experts with a shared set of values and a common goal must combine their knowledge to make a collectively optimal decision. Whereas existing research on CDM primarily focuses on making binary decisions, we focus here on CDM applied to solving contextual multi-armed bandit (CMAB) problems, where the goa...
Chapter
Collective decision-making (CDM) processes – wherein the knowledge of a group of individuals with a common goal must be combined to make optimal decisions – can be formalized within the framework of the deciding with expert advice setting. Traditional approaches to tackle this problem focus on finding appropriate weights for the individuals in the...
Preprint
Full-text available
The field of Artificial Intelligence (AI) is going through a period of great expectations, introducing a certain level of anxiety in research, business and also policy. This anxiety is further energised by an AI race narrative that makes people believe they might be missing out. Whether real or not, a belief in this narrative may be detrimental as...
Preprint
Full-text available
Human hematopoiesis is surprisingly resilient to disruptions, providing suitable responses to severe bleeding, long lasting immune activation, and even bone marrow transplants. Still, many blood disorders exist which push the system past its natural plasticity, resulting in abnormalities in the circulating blood. While proper treatment of such dise...
Article
Full-text available
How do people decide which action to take? This question is best answered using Game Theory, which has proposed a series of decision-making mechanisms that people potentially use. In network simulations, wherein games are repeated and pay-off differences can be observed, those mechanisms often rely on imitation of successful behaviour. Surprisingly...
Article
Full-text available
Objective Oesophageal cancer (OEC) is an aggressive disease with a poor survival rate. Prognostic markers are thus urgently needed. Due to the demonstrated prognostic value of histopathological growth pattern (HGP) in other cancers, we performed a retrospective assessment of HGP in patients suffering from invasive OEC. Design A first cohort compos...
Article
Full-text available
Methicillin-resistant Staphylococcus aureus (MRSA) is a difficult-to-treat infection. Increasing efforts have been taken to mitigate the epidemics and to avoid potential outbreaks in low endemic settings. Understanding the population dynamics of MRSA is essential to identify the causal mechanisms driving the epidemics and to generalise conclusions...
Preprint
Full-text available
Human social dilemmas are often shaped by actions involving uncertain goals and returns that may only be achieved in the future. Climate action, voluntary vaccination and other prospective choices stand as paramount examples of this setting. In this context, as well as in many other social dilemmas, uncertainty may produce non-trivial effects. Wher...
Chapter
One of the cornerstones in combating the HIV pandemic is the ability to assess the current state and evolution of local HIV epidemics. This remains a complex problem, as many HIV infected individuals remain unaware of their infection status, leading to parts of HIV epidemics being undiagnosed and under-reported. We first present a method to learn e...
Book
This book contains a selection of the best papers of the 31st Benelux Conference on Artificial Intelligence, BNAIC 2019, and 28th Belgian Dutch Machine Learning Conference, BENELEARN 2019, held in Brussels, Belgium in November 2019. The 11 papers presented in this volume were carefully reviewed and selected from 50 regular submissions. They addres...
Article
Full-text available
Primary Microcephaly (PM) is characterized by a small head since birth and is vastly heterogeneous both genetically and phenotypically. While most cases are monogenic, genetic interactions between Aspm and Wdr62 have recently been described in a mouse model of PM. Here, we used two complementary, holistic in vivo approaches: high throughput DNA seq...
Preprint
Full-text available
One of the cornerstones in combating the HIV pandemic is being able to assess the current state and evolution of local HIV epidemics. This remains a complex problem, as many HIV infected individuals remain unaware of their infection status, leading to parts of HIV epidemics being undiagnosed and under-reported. To that end, we firstly present a met...
Poster
Full-text available
The vast amount of DNA sequencing data collected from large patient cohorts have helped in identifying a wide number of disease related mutations relevant for diagnosis and therapy. Although these approaches have greatly improved our understanding of Mendelian cases, many difficulties remain in identifying the causes of a large amount of human gene...
Preprint
Full-text available
Innovation, creativity, and competition are some of the fundamental underlying forces driving the advances in Artificial Intelligence (AI). This race for technological supremacy creates a complex ecology of choices that may lead to negative consequences, in particular, when ethical and safety procedures are underestimated or even ignored. Here we r...
Article
In order to gain insight into oligogenic disorders, understanding those involving bi-locus variant combinations appears to be key. In prior work, we showed that features at multiple biological scales can already be used to discriminate among two types, i.e. disorders involving true digenic and modifier combinations. The current study expands this m...
Article
Full-text available
A tremendous amount of DNA sequencing data is being produced around the world with the ambition to capture in more detail the mechanisms underlying human diseases. While numerous bioinformatics tools exist that allow the discovery of causal variants in Mendelian diseases, little to no support is provided to do the same for variant combinations, an...
Article
Full-text available
Notwithstanding important advances in the context of single-variant pathogenicity identification, novel breakthroughs in discerning the origins of many rare diseases require methods able to identify more complex genetic models. We present here the Variant Combinations Pathogenicity Predictor (VarCoPP), a machine-learning approach that identifies pa...
Conference Paper
Full-text available
A race for technological supremacy in AI could lead to serious negative consequences, especially whenever ethical and safety procedures are underestimated or even ignored, leading potentially to the rejection of AI in general. For all to enjoy the benefits provided by safe, ethical and trustworthy AI systems, it is crucial to incentivise participan...
Preprint
Full-text available
Notwithstanding important advances in the context of single-variant pathogenicity identification, novel breakthroughs in discerning the origins of many rare diseases require methods able to identify more complex genetic models. We present here the Variant Combinations Pathogenicity Predictor (VarCoPP), a machine-learning approach that identifies pa...
Chapter
Full-text available
The Iterated Prisoner’s Dilemma (IPD) game is a one of the most popular subjects of study in game theory. Numerous experiments have investigated many properties of this game over the last decades. However, topics related to the simulation scale did not always play a significant role in such experimental work. The main contribution of this paper is...
Article
Full-text available
Next generation sequencing technologies are providing increasing amounts of sequencing data, paving the way for improvements in clinical genetics and precision medicine. The interpretation of the observed genomic variants in the light of their phenotypic effects is thus emerging as a crucial task to solve in order to advance our understanding of ho...
Preprint
Full-text available
Many real-world decision problems are characterized by multiple objectives which must be balanced based on their relative importance. In the dynamic weights setting this relative importance changes over time, as recognized by Natarajan and Tadepalli (2005) who proposed a tabular Reinforcement Learning algorithm to deal with this problem. However, t...
Article
Full-text available
Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal blood disorder characterized by hemolysis and a high risk of thrombosis, that is due to a deficiency in several cell surface proteins that prevent complement activation. Its origin has been traced to a somatic mutation in the PIG-A gene within hematopoietic stem cells (HSC). However, t...
Article
Full-text available
Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the S...
Article
Full-text available
A metaheuristic proposed by us recently, Ant Colony Optimization (ACO) hybridized with socio-cognitive inspirations, turned out to generate interesting results when compared to classic ACO. Even though it does not always find better solutions to the considered problems, it usually finds sub-optimal solutions. Moreover, instead of a trial-and-error...
Article
Full-text available
The wide range of applications of the Iterated prisoner's dilemma (IPD) game made it a popular subject of study for the research community. As a consequence, numerous experiments have been conducted by researchers along the last decades. However, topics related with scaling simulation leveraging existing HPC infrastructure in the field of IPD did n...
Article
Background: Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. Methods: Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and mu...
Article
Full-text available
To further our understanding of the complexity and genetic heterogeneity of rare diseases, it has become essential to shed light on how combinations of variants in different genes are responsible for a disease phenotype. With the appearance of a resource on digenic diseases, it has become possible to evaluate how digenic combinations differ in term...
Preprint
Full-text available
Background The advent of next-generation sequencing technologies has opened new avenues for clinical genomics research. In particular, as sequencing costs continue to decrease, an ever-growing number of clinical genomics institutes now rely on DNA sequencing studies at varying scales - genome, exome, mendeliome - for uncovering disease-associated v...
Article
Full-text available
Background Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. Methods Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and mur...
Article
Motivation: Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for...
Article
Full-text available
Agreements and commitments have provided a novel mechanism to promote cooperation in social dilemmas in both one-shot and repeated games. Individuals requesting others to commit to cooperate (proposers) incur a cost, while their co-players are not necessarily required to pay any, allowing them to free-ride on the proposal investment cost (acceptors...
Article
Full-text available
High-throughput sequencing methods are generating enormous amounts of genomic data, giving unprecedented insights into human genetic variation and its relation to disease. An individual human genome contains millions of Single Nucleotide Variants: to discriminate the deleterious from the benign ones, a variety of methods have been developed that pr...
Conference Paper
Full-text available
Inspired by psychological and evolutionary studies, we present here theoretical models wherein agents have the potential to express guilt with the ambition to study the role of this emotion in the promotion of pro-social behaviour. To achieve this goal, analytical and numerical methods from evolutionary game theory are employed to identify the cond...
Conference Paper
Full-text available
Before engaging in a group venture agents may seek to secure commitments from other members of the group, and based on the level of participation (i.e. how many group members commit) they can then decide whether it is worth- while joining the group effort [12, 1, 5]. Many group ventures can be launched only when the majority of the participants com...
Article
Full-text available
Before engaging in a group venture agents may require commitments from other members in the group, and based on the level of acceptance (participation) they can then decide whether it is worthwhile joining the group e ort. Here, we show in the context of Public Goods Games and using stochastic evolutionary game theory modelling, which implies imita...
Conference Paper
Full-text available
Evolutionary psychologists have argued that revenge, apology and forgiveness are moral sentiments that humans acquired to establish and maintain long-term mutually beneficial relationships, especially since misapprehensions, intentional or not, can always occur that could lead to worse outcomes. Their argument assumes an evolutionary advantage to s...
Conference Paper
Full-text available
Inspired by psychological and evolutionary studies, we present two theoretical models wherein agents have the potential to express guilt, with the ambition to study the role of this emotion in the promotion of pro-social behaviour. We show that the inclusion of the emotion of guilt, in the sense arising from actual harm done to others from inapprop...
Conference Paper
Full-text available
Before engaging in a group venture agents may seek commitments from other members in the group and, based on the level of participation (i.e. the number of actually committed participants), decide whether it is worth joining the venture. Alternatively, agents can delegate this costly process to a (beneficent or non- costly) third-party, who helps s...
Conference Paper
Full-text available
Various social situations entail a collective risk. A well-known example is climate change, wherein the risk of a future environmental disaster clashes with the immediate economic interest of developed and developing countries. The collective-risk game operationalizes this kind of situations. The decision process of the participants is determined b...
Conference Paper
Full-text available
Evolutionary game theory focuses on the fitness differences between simple discrete or probabilistic strategies to explain the evolution of particular decision-making behavior within strategic situations. Although this approach has provided substantial insights into the presence of fairness or generosity in gift-giving games, it does not fully reso...
Article
Full-text available
Before engaging in a group venture agents may seek commitments from other members in the group and, based on the level of participation (i.e. the number of actually committed participants), decide whether it is worth joining the venture. Alternatively, agents can delegate this costly process to a (beneficent or non-costly) third-party, who helps se...
Chapter
Src homology 2 (SH2) domains are key modulators in various signaling pathways allowing the recognition of phosphotyrosine sites of different proteins. Despite the fact that SH2 domains acquire their biological functions in a monomeric state, a multitude of reports have shown their tendency to dimerize. Here, we provide a technical description on ho...
Article
Full-text available
In the paper a modification of a Socio-cognitive Particle Swarm Optimization algorithm, recently proposed by the authors, is presented. This modification consists in devising a mechanism for dynamic adaptation of the population structure of the swarm. Besides the design and rationale for the approach, referring to the state-of-the-art PSO original...
Article
Blood of mammals is composed of a variety of cells suspended in a fluid medium known as plasma. Hematopoiesis is the biological process of birth, replication and differentiation of blood cells. Despite of being essentially a stochastic phenomenon followed by a huge number of discrete entities, blood formation has naturally an associated continuous...
Article
Full-text available
Methicillin-resistant Staphylococcus aureus (MRSA) is a difficult-to-treat infection that only in the European Union affects about 150,000 patients and causes extra costs of 380 million Euros annually to the health-care systems. Increasing efforts have been taken to mitigate the epidemics and to avoid potential outbreaks in low endemic settings. Un...
Preprint
Full-text available
Based on the clonal evolution theory of cancer formation, a single cell within a tissue gains a cancer-driving mutation and thus a growth advantage. From this expanded cellular mass, another cell gains a new mutation allowing this newly mutated cell to gain new competitive advantage and to expand in number (thus clonal expansion). Another clone the...
Article
Recently we proposed an application of Ant Colony Optimization (ACO) to simulate socio-cognitive features of a population, incorporating perspective-taking ability to generate differently acting ant colonies. Although our main goal was simulation, we took advantage of the fact that the quality of the constructed system was evaluated based on select...
Article
Full-text available
Src kinase activity is controlled by various mechanisms involving a coordinated movement of kinase and regulatory domains. Notwithstanding the extensive knowledge related to the backbone dynamics, little is known about the more subtle side-chain dynamics within the regulatory domains and their role in the activation process. Here, we show through e...
Article
Full-text available
To ensure cooperation in the Prisoner’s Dilemma, individuals may require prior commitments from others, subject to compensations when agreements to cooperate are violated. Alternatively, individuals may prefer to behave reactively, without arranging prior commitments, by simply punishing those who misbehave. These two mechanisms have been shown to...
Conference Paper
Full-text available
When interactions are repeated mistakes, whether intentionally or not, tend to occur. Researchers have argued that revenge, apology and forgiveness are mechanisms that humans have acquired to ensure that intentional mistakes are avoided and that mutually beneficial relationships can continue. We have shown in the context of the iterated prisoners d...

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