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Article ; Online: SMEMO: Social Memory for Trajectory Forecasting.

Marchetti, Francesco / Becattini, Federico / Seidenari, Lorenzo / Bimbo, Alberto Del

IEEE transactions on pattern analysis and machine intelligence

2024 Volume PP

Abstract: Effective modeling of human interactions is of utmost importance when forecasting behaviors such as future trajectories. Each individual, with its motion, influences surrounding agents since everyone obeys to social non-written rules such as collision ... ...

Abstract	Effective modeling of human interactions is of utmost importance when forecasting behaviors such as future trajectories. Each individual, with its motion, influences surrounding agents since everyone obeys to social non-written rules such as collision avoidance or group following. In this paper we model such interactions, which constantly evolve through time, by looking at the problem from an algorithmic point of view, i.e. as a data manipulation task. We present a neural network based on an end-to-end trainable working memory, which acts as an external storage where information about each agent can be continuously written, updated and recalled. We show that our method is capable of learning explainable cause-effect relationships between motions of different agents, obtaining state-of-the-art results on multiple trajectory forecasting datasets.
Language	English
Publishing date	2024-01-22
Publishing country	United States
Document type	Journal Article
ISSN	1939-3539
ISSN (online)	1939-3539
DOI	10.1109/TPAMI.2024.3356755
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Article ; Online: Multiple Trajectory Prediction of Moving Agents With Memory Augmented Networks.

Marchetti, Francesco / Becattini, Federico / Seidenari, Lorenzo / Bimbo, Alberto Del

IEEE transactions on pattern analysis and machine intelligence

2023 Volume 45, Issue 6, Page(s) 6688–6702

Abstract: Pedestrians and drivers are expected to safely navigate complex urban environments along with several non cooperating agents. Autonomous vehicles will soon replicate this capability. Each agent acquires a representation of the world from an egocentric ... ...

Abstract	Pedestrians and drivers are expected to safely navigate complex urban environments along with several non cooperating agents. Autonomous vehicles will soon replicate this capability. Each agent acquires a representation of the world from an egocentric perspective and must make decisions ensuring safety for itself and others. This requires to predict motion patterns of observed agents for a far enough future. In this paper we propose MANTRA, a model that exploits memory augmented networks to effectively predict multiple trajectories of other agents, observed from an egocentric perspective. Our model stores observations in memory and uses trained controllers to write meaningful pattern encodings and read trajectories that are most likely to occur in future. We show that our method is able to natively perform multi-modal trajectory prediction obtaining state-of-the art results on four datasets. Moreover, thanks to the non-parametric nature of the memory module, we show how once trained our system can continuously improve by ingesting novel patterns.
Language	English
Publishing date	2023-05-05
Publishing country	United States
Document type	Journal Article
ISSN	1939-3539
ISSN (online)	1939-3539
DOI	10.1109/TPAMI.2020.3008558
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Article ; Online: The functional mutational landscape of the

Beal, Marc A / Meier, Matthew J / Dykes, Angela / Yauk, Carole L / Lambert, Iain B / Marchetti, Francesco

iScience

2023 Volume 26, Issue 12, Page(s) 108407

Abstract: ... ...

Abstract	The
Language	English
Publishing date	2023-11-07
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.108407
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Book ; Online: A comprehensive theoretical framework for the optimization of neural networks classification performance with respect to weighted metrics

Marchetti, Francesco / Guastavino, Sabrina / Campi, Cristina / Benvenuto, Federico / Piana, Michele

2023

Abstract: In many contexts, customized and weighted classification scores are designed in order to evaluate the goodness of the predictions carried out by neural networks. However, there exists a discrepancy between the maximization of such scores and the ... ...

Abstract	In many contexts, customized and weighted classification scores are designed in order to evaluate the goodness of the predictions carried out by neural networks. However, there exists a discrepancy between the maximization of such scores and the minimization of the loss function in the training phase. In this paper, we provide a complete theoretical setting that formalizes weighted classification metrics and then allows the construction of losses that drive the model to optimize these metrics of interest. After a detailed theoretical analysis, we show that our framework includes as particular instances well-established approaches such as classical cost-sensitive learning, weighted cross entropy loss functions and value-weighted skill scores.
Keywords	Computer Science - Machine Learning ; Mathematics - Numerical Analysis ; Statistics - Machine Learning
Publishing date	2023-05-22
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mechanisms of oocyte aneuploidy associated with advanced maternal age.

Mikwar, Myy / MacFarlane, Amanda J / Marchetti, Francesco

Mutation research. Reviews in mutation research

2020 Volume 785, Page(s) 108320

Abstract: It is well established that maternal age is associated with a rapid decline in the production of healthy and high-quality oocytes resulting in reduced fertility in women older than 35 years of age. In particular, chromosome segregation errors during ... ...

Abstract	It is well established that maternal age is associated with a rapid decline in the production of healthy and high-quality oocytes resulting in reduced fertility in women older than 35 years of age. In particular, chromosome segregation errors during meiotic divisions are increasingly common and lead to the production of oocytes with an incorrect number of chromosomes, a condition known as aneuploidy. When an aneuploid oocyte is fertilized by a sperm it gives rise to an aneuploid embryo that, except in rare situations, will result in a spontaneous abortion. As females advance in age, they are at higher risk of infertility, miscarriage, or having a pregnancy affected by congenital birth defects such as Down syndrome (trisomy 21), Edwards syndrome (trisomy 18), and Turner syndrome (monosomy X). Here, we review the potential molecular mechanisms associated with increased chromosome segregation errors during meiosis as a function of maternal age. Our review shows that multiple exogenous and endogenous factors contribute to the age-related increase in oocyte aneuploidy. Specifically, the weight of evidence indicates that recombination failure, cohesin deterioration, spindle assembly checkpoint (SAC) disregulation, abnormalities in post-translational modification of histones and tubulin, and mitochondrial dysfunction are the leading causes of oocyte aneuploidy associated with maternal aging. There is also growing evidence that dietary and other bioactive interventions may mitigate the effect of maternal aging on oocyte quality and oocyte aneuploidy, thereby improving fertility outcomes. Maternal age is a major concern for aneuploidy and genetic disorders in the offspring in the context of an increasing proportion of mothers having children at increasingly older ages. A better understanding of the mechanisms associated with maternal aging leading to aneuploidy and of intervention strategies that may mitigate these detrimental effects and reduce its occurrence are essential for preventing abnormal reproductive outcomes in the human population.
MeSH term(s)	Aneuploidy ; Cell Cycle Proteins/genetics ; Chromosomal Proteins, Non-Histone/genetics ; Chromosome Segregation/genetics ; Congenital Abnormalities/genetics ; Congenital Abnormalities/prevention & control ; Female ; Humans ; M Phase Cell Cycle Checkpoints/genetics ; Maternal Age ; Meiosis/genetics ; Mitochondria/physiology ; Oocytes/physiology ; Cohesins
Chemical Substances	Cell Cycle Proteins ; Chromosomal Proteins, Non-Histone
Language	English
Publishing date	2020-07-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2727833-5
ISSN	1388-2139 ; 1383-5742
ISSN (online)	1388-2139
ISSN	1383-5742
DOI	10.1016/j.mrrev.2020.108320
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Article ; Online: Asciminib Mitigates DNA Damage Stress Signaling Induced by Cyclophosphamide in the Ovary.

Mattiello, Luca / Pucci, Giulia / Marchetti, Francesco / Diederich, Marc / Gonfloni, Stefania

International journal of molecular sciences

2021 Volume 22, Issue 3

Abstract: Cancer treatments can often adversely affect the quality of life of young women. One of the most relevant negative impacts is the loss of fertility. Cyclophosphamide is one of the most detrimental chemotherapeutic drugs for the ovary. Cyclophosphamide ... ...

Abstract	Cancer treatments can often adversely affect the quality of life of young women. One of the most relevant negative impacts is the loss of fertility. Cyclophosphamide is one of the most detrimental chemotherapeutic drugs for the ovary. Cyclophosphamide may induce the destruction of dormant follicles while promoting follicle activation and growth. Herein, we demonstrate the in vivo protective effect of the allosteric Bcr-Abl tyrosine kinase inhibitor Asciminib on signaling pathways activated by cyclophosphamide in mouse ovaries. We also provide evidence that Asciminib does not interfere with the cytotoxic effect of cyclophosphamide in Michigan Cancer Foundation (MCF)7 breast cancer cells. Our data indicate that concomitant administration of Asciminib mitigates the cyclophosphamide-induced ovarian reserve loss without affecting the anticancer potential of cyclophosphamide. Taken together, these observations are relevant for the development of effective ferto-protective adjuvants to preserve the ovarian reserve from the damaging effects of cancer therapies.
MeSH term(s)	Animals ; Antineoplastic Agents, Alkylating/administration & dosage ; Antineoplastic Agents, Alkylating/adverse effects ; Apoptosis/drug effects ; Cyclophosphamide/administration & dosage ; Cyclophosphamide/adverse effects ; DNA Damage/drug effects ; Disease Models, Animal ; Female ; Fertility/drug effects ; Fertility Preservation/methods ; Humans ; MCF-7 Cells ; Mice ; Neoplasms/drug therapy ; Niacinamide/administration & dosage ; Niacinamide/analogs & derivatives ; Ovarian Follicle/drug effects ; Ovarian Follicle/pathology ; Ovarian Reserve/drug effects ; Pyrazoles/administration & dosage ; Signal Transduction/drug effects ; Signal Transduction/genetics
Chemical Substances	Antineoplastic Agents, Alkylating ; Pyrazoles ; asciminib ; Niacinamide (25X51I8RD4) ; Cyclophosphamide (8N3DW7272P)
Language	English
Publishing date	2021-01-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22031395
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Article ; Online: A Case Study on Integrating a New Key Event Into an Existing Adverse Outcome Pathway on Oxidative DNA Damage: Challenges and Approaches in a Data-Rich Area.

Huliganga, Elizabeth / Marchetti, Francesco / O'Brien, Jason M / Chauhan, Vinita / Yauk, Carole L

Frontiers in toxicology

2022 Volume 4, Page(s) 827328

Abstract: Adverse outcome pathways (AOPs) synthesize toxicological information to convey and weigh evidence in an accessible format. AOPs are constructed in modules that include key events (KEs) and key event relationships (KERs). This modular structure ... ...

Abstract	Adverse outcome pathways (AOPs) synthesize toxicological information to convey and weigh evidence in an accessible format. AOPs are constructed in modules that include key events (KEs) and key event relationships (KERs). This modular structure facilitates AOP expansion and network development. AOP development requires finding relevant information to evaluate the weight of evidence supporting each KER. To do this, the use of transparent/reproducible search methods, such as systematic review (SR), have been proposed. Applying SR to AOP development in a data-rich area is difficult as SR requires screening each article returned from a search. Here we describe a case study to integrate a single new KE into an existing AOP. We explored the use of SR concepts and software to conduct a transparent and documented literature search to identify empirical data supporting the incorporation of a new KE, increase in cellular reactive oxygen species (ROS), upstream of an existing AOP: "Oxidative DNA Damage Leading to Chromosomal Aberrations and Mutations". Connecting this KE to the AOP is supported by the development of five new KERs, the most important being the first adjacent KER (increase in ROS leading to oxidative DNA damage). We initially searched for evidence of all five KERs and screened 100 papers to develop a preliminary evidence map. After removing papers not containing relevant data based on our Population, Exposure, Comparator and Outcome statement, 39 articles supported one or more KERs; these primarily addressed temporal or dose concordance of the non-adjacent KERs with limited evidence supporting the first adjacent KER. We thus conducted a second focused set of searches using search terms for specific methodologies to measure these first two KEs. After screening, 12 articles were identified that contained quantitative evidence supporting the first adjacent KER. Given that integrating a new KE into an existing AOP requires the development of multiple KERs, this approach of building a preliminary evidence map, focusing evidence gathering on the first adjacent KER, and applying reproducible search strategies using specific methodologies for the first adjacent KER, enabled us to prioritize studies to support expansion of this data-rich AOP.
Language	English
Publishing date	2022-04-28
Publishing country	Switzerland
Document type	Journal Article
ISSN	2673-3080
ISSN (online)	2673-3080
DOI	10.3389/ftox.2022.827328
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Article ; Online: A Return to the Origin of the EMGS: Rejuvenating the Quest for Human Germ Cell Mutagens and Determining the Risk to Future Generations.

Marchetti, Francesco / Douglas, George R / Yauk, Carole L

Environmental and molecular mutagenesis

2019 Volume 61, Issue 1, Page(s) 42–54

Abstract: Fifty years ago, the Environmental Mutagen Society (now Environmental Mutagenesis and Genomics Society) was founded with a laser-focus on germ cell mutagenesis and the protection of "our most vital assets"-the sperm and egg genomes. Yet, five decades on, ...

Abstract	Fifty years ago, the Environmental Mutagen Society (now Environmental Mutagenesis and Genomics Society) was founded with a laser-focus on germ cell mutagenesis and the protection of "our most vital assets"-the sperm and egg genomes. Yet, five decades on, despite the fact that many agents have been demonstrated to induce inherited changes in the offspring of exposed laboratory rodents, there is no consensus on whether human germ cell mutagens exist. We argue that it is time to reevaluate the available data and conclude that we already have evidence for the existence of environmental exposures that impact human germ cells. What is missing are definite data to demonstrate a significant increase in de novo mutations in the offspring of exposed parents. We believe that with over two decades of research advancing knowledge and technologies in genomics, we are at the cusp of generating data to conclusively show that environmental exposures cause heritable de novo changes in the human offspring. We call on the research community to harness our technologies, synergize our efforts, and return to our Founders' original focus. The next 50 years must involve collaborative work between clinicians, epidemiologists, genetic toxicologists, genomics experts and bioinformaticians to precisely define how environmental exposures impact germ cell genomes. It is time for the research and regulatory communities to prepare to interpret the coming outpouring of data and develop a framework for managing, communicating and mitigating the risk of exposure to human germ cell mutagens. Environ. Mol. Mutagen. 61:42-54, 2020. © 2019 Her Majesty the Queen in Right of Canada.
MeSH term(s)	Animals ; Environmental Exposure/adverse effects ; Female ; Germ Cells/drug effects ; Germ Cells/metabolism ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Mutagenesis/drug effects ; Mutagenicity Tests/methods ; Mutagens/toxicity ; Risk Assessment ; Rodentia ; Transgenes
Chemical Substances	Mutagens
Language	English
Publishing date	2019-10-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639145-x
ISSN	1098-2280 ; 0893-6692
ISSN (online)	1098-2280
ISSN	0893-6692
DOI	10.1002/em.22327
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Zs.B 2404: Show issues

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Book ; Online: Score-oriented loss (SOL) functions

Marchetti, Francesco / Guastavino, Sabrina / Piana, Michele / Campi, Cristina

2021

Abstract: Loss functions engineering and the assessment of forecasting performances are two crucial and intertwined aspects of supervised machine learning. This paper focuses on binary classification to introduce a class of loss functions that are defined on ... ...

Abstract	Loss functions engineering and the assessment of forecasting performances are two crucial and intertwined aspects of supervised machine learning. This paper focuses on binary classification to introduce a class of loss functions that are defined on probabilistic confusion matrices and that allow an automatic and a priori maximization of the skill scores. The performances of these loss functions are validated during the training phase of two experimental forecasting problems, thus showing that the probability distribution function associated with the confusion matrices significantly impacts the outcome of the score maximization process.
Keywords	Computer Science - Machine Learning ; Mathematics - Numerical Analysis
Publishing date	2021-03-29
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: AI-FLARES

Piana, Michele / Benvenuto, Federico / Massone, Anna Maria / Campi, Cristina / Guastavino, Sabrina / Marchetti, Francesco / Massa, Paolo / Perracchione, Emma / Volpara, Anna

Artificial Intelligence for the Analysis of Solar Flares Data

2024

Abstract: AI-FLARES (Artificial Intelligence for the Analysis of Solar Flares Data) is a research project funded by the Agenzia Spaziale Italiana and by the Istituto Nazionale di Astrofisica within the framework of the ``Attivit\`a di Studio per la Comunit\`a ... ...

Abstract	AI-FLARES (Artificial Intelligence for the Analysis of Solar Flares Data) is a research project funded by the Agenzia Spaziale Italiana and by the Istituto Nazionale di Astrofisica within the framework of the ``Attivit\`a di Studio per la Comunit\`a Scientifica Nazionale Sole, Sistema Solare ed Esopianeti'' program. The topic addressed by this project was the development and use of computational methods for the analysis of remote sensing space data associated to solar flare emission. This paper overviews the main results obtained by the project, with specific focus on solar flare forecasting, reconstruction of morphologies of the flaring sources, and interpretation of acceleration mechanisms triggered by solar flares.
Keywords	Astrophysics - Solar and Stellar Astrophysics ; Computer Science - Artificial Intelligence ; 85-04 ; 68T01
Publishing date	2024-01-02
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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