Recent views on pre-registration

A discussion on some recent perspectives on pre-registration, which has become a growing trend in the past few years. This is not just limited to neuroimaging, and it applies to most scientific fields. We will start with this overview editorial by Simmons et al. (2021): https://faculty.wharton.upenn.edu/wp-content/uploads/2016/11/34-Simmons-Nelson-Simonsohn-2021a.pdf, and also talk about a more critical perspective by Pham & Oh (2021): https://www.researchgate.net/profile/Michel-Pham/publication/349545600_Preregistration_Is_Neither_Sufficient_nor_Necessary_for_Good_Science/links/60fb311e2bf3553b29096aa7/Preregistration-Is-Neither-Sufficient-nor-Necessary-for-Good-Science.pdf. I would like us to discuss the pros and cons of pre-registration, and if we have time, I may do a demonstration of how to perform a pre-registration through the Open Science Framework.

Llama 3.1 Paper: The Llama Family of Models

Modern artificial intelligence (AI) systems are powered by foundation models. This paper presents a new set of foundation models, called Llama 3. It is a herd of language models that natively support multilinguality, coding, reasoning, and tool usage. Our largest model is a dense Transformer with 405B parameters and a context window of up to 128K tokens. This paper presents an extensive empirical evaluation of Llama 3. We find that Llama 3 delivers comparable quality to leading language models such as GPT-4 on a plethora of tasks. We publicly release Llama 3, including pre-trained and post-trained versions of the 405B parameter language model and our Llama Guard 3 model for input and output safety. The paper also presents the results of experiments in which we integrate image, video, and speech capabilities into Llama 3 via a compositional approach. We observe this approach performs competitively with the state-of-the-art on image, video, and speech recognition tasks. The resulting models are not yet being broadly released as they are still under development.

The quest for brain identification

In the 17th century, physician Marcello Malpighi observed the existence of distinctive patterns of ridges and sweat glands on fingertips. This was a major breakthrough, and originated a long and continuing quest for ways to uniquely identify individuals based on fingerprints, a technique massively used until today. It is only in the past few years that technologies and methodologies have achieved high-quality measures of an individual’s brain to the extent that personality traits and behavior can be characterized. The concept of “fingerprints of the brain” is very novel and has been boosted thanks to a seminal publication by Finn et al. in 2015. They were among the firsts to show that an individual’s functional brain connectivity profile is both unique and reliable, similarly to a fingerprint, and that it is possible to identify an individual among a large group of subjects solely on the basis of her or his connectivity profile. Yet, the discovery of brain fingerprints opened up a plethora of new questions. In particular, what exactly is the information encoded in brain connectivity patterns that ultimately leads to correctly differentiating someone’s connectome from anybody else’s? In other words, what makes our brains unique? In this talk I am going to partially address these open questions while keeping a personal viewpoint on the subject. I will outline the main findings, discuss potential issues, and propose future directions in the quest for identifiability of human brain networks.

Quasicriticality and the quest for a framework of neuronal dynamics

Critical phenomena abound in nature, from forest fires and earthquakes to avalanches in sand and neuronal activity. Since the 2003 publication by Beggs & Plenz on neuronal avalanches, a growing body of work suggests that the brain homeostatically regulates itself to operate near a critical point where information processing is optimal. At this critical point, incoming activity is neither amplified (supercritical) nor damped (subcritical), but approximately preserved as it passes through neural networks. Departures from the critical point have been associated with conditions of poor neurological health like epilepsy, Alzheimer's disease, and depression. One complication that arises from this picture is that the critical point assumes no external input. But, biological neural networks are constantly bombarded by external input. How is then the brain able to homeostatically adapt near the critical point? We’ll see that the theory of quasicriticality, an organizing principle for brain dynamics, can account for this paradoxical situation. As external stimuli drive the cortex, quasicriticality predicts a departure from criticality while maintaining optimal properties for information transmission. We’ll see that simulations and experimental data confirm these predictions and describe new ones that could be tested soon. More importantly, we will see how this organizing principle could help in the search for biomarkers that could soon be tested in clinical studies.

Autopoiesis and Enaction in the Game of Life

Enaction plays a central role in the broader fabric of so-called 4E (embodied, embedded, extended, enactive) cognition. Although the origin of the enactive approach is widely dated to the 1991 publication of the book "The Embodied Mind" by Varela, Thompson and Rosch, many of the central ideas trace to much earlier work. Over 40 years ago, the Chilean biologists Humberto Maturana and Francisco Varela put forward the notion of autopoiesis as a way to understand living systems and the phenomena that they generate, including cognition. Varela and others subsequently extended this framework to an enactive approach that places biological autonomy at the foundation of situated and embodied behavior and cognition. I will describe an attempt to place Maturana and Varela's original ideas on a firmer foundation by studying them within the context of a toy model universe, John Conway's Game of Life (GoL) cellular automata. This work has both pedagogical and theoretical goals. Simple concrete models provide an excellent vehicle for introducing some of the core concepts of autopoiesis and enaction and explaining how these concepts fit together into a broader whole. In addition, a careful analysis of such toy models can hone our intuitions about these concepts, probe their strengths and weaknesses, and move the entire enterprise in the direction of a more mathematically rigorous theory. In particular, I will identify the primitive processes that can occur in GoL, show how these can be linked together into mutually-supporting networks that underlie persistent bounded entities, map the responses of such entities to environmental perturbations, and investigate the paths of mutual perturbation that these entities and their environments can undergo.

Fidelity and Replication: Modelling the Impact of Protocol Deviations on Effect Size

Cognitive science and cognitive neuroscience researchers have agreed that the replication of findings is important for establishing which ideas (or theories) are integral to the study of cognition across the lifespan. Recently, high-profile papers have called into question findings that were once thought to be unassailable. Much attention has been paid to how p-hacking, publication bias, and sample size are responsible for failed replications. However, much less attention has been paid to the fidelity by which researchers enact study protocols. Researchers conducting education or clinical trials are aware of the importance in fidelity – or the extent to which the protocols are delivered in the same way across participants. Nevertheless, this idea has not been applied to cognitive contexts. This seminar discusses factors that impact the replicability of findings alongside recent models suggesting that even small fidelity deviations have real impacts on the data collected.

Brain and Mind: Who is the Puppet and who the Puppeteer?

If the mind controls the brain, then there is free will and its corollaries, dignity and responsibility. You are king in your skull-sized kingdom and the architect of your destiny. If, on the other hand, the brain controls the mind, an incendiary conclusion follows: There can be no free will, no praise, no punishment and no purgatory. In this webinar, Professor George Paxinos will discuss his highly respected work on the construction of human and experimental animal brain atlases. He has discovered 94 brain regions, 64 homologies and published 58 books. His first book, The Rat Brain in Stereotaxic Coordinates, is the most cited publication in neuroscience and, for three decades, the third most cited book in science. Professor Paxinos will also present his recently published novel, A River Divided, which was 21 years in the making. Neuroscience principles were used in the formation of charters, such as those related to the mind, soul, free will and consciousness. Environmental issues are at the heart of the novel, including the question of whether the brain is the right ‘size’ for survival. Professor Paxinos studied at Berkeley, McGill and Yale and is now Scientia Professor of Medical Sciences at Neuroscience Research Australia and The University of New South Wales in Sydney.

The logopenic variant of primary progressive aphasia (lvPPA): language, cognitive, neuroradiological issues

Monash Biomedical Imaging highlights from 2021 and looking ahead to 2022

Despite the challenges COVID-19 has continued to present, Monash Biomedical Imaging (MBI) has had another outstanding year in terms of publications and scientific output. In this webinar, Professor Gary Egan, Director of MBI, will present an overview of MBI’s achievements during 2021 and outline the biomedical imaging research programs and partnerships in 2022. His presentation will cover: • MBI operational and research achievements during 2021 • Biomedical imaging technology developments and research outcomes during 2021 • Linked laboratories and research teams at MBI • Progress on the development of a cyclotron and precision radiopharmaceutical facility at Clayton • Emerging research opportunities at the Monash Heart Hospital in cardiology and cardiovascular disease. Professor Gary Egan is Director of Monash Biomedical Imaging, Director of the ARC Centre of Excellence for Integrative Brain Function and a Distinguished Professor at the Turner Institute for Brain and Mental Health, Monash University. He is also lead investigator of the Victorian Biomedical Imaging Capability, and Deputy Director of the Australian National Imaging Facility. His substantive body of published work has made a significant impact on the neuroimaging and neuroscience fields. He has sustained success in obtaining significant grants to support his own research and the development of facilities to advance biomedical imaging.

Redressing imbalances in the kind of research that gets done and who gets credit for it

If we want good work to get done, we should credit those who do it. In science, researchers are credited predominantly via authorship on publications. But many contributions to modern research are not recognized with authorship, due in part to the high bar imposed by the authorship criteria of many journals. “Contributorship” is a more inclusive framework for indicating who did what in the work described by a paper, and many scientific journals have recently implemented versions of it. I will consider the motivation for and specifics of this change, describe the tenzing tool we created to facilitate it, and how we might want to support and shape the shift toward contributorship

Communicating (Neuro)Science

In recent years, communicating one’s research to audiences outside of academia has grown in importance and time commitment for many researchers. Science Slams or University Open Days reliably draw large crowds, and the potential of social media to amplify any message has made it possible to reach interested recipients without the traditional press as a middleman. In this presentation, I will provide insights into science communication from my perspective as a neuroscience researcher, who enjoys spreading the word about how amazing insect brains are. We will have a look at the What?, Why? and How? of science communication. What do we generally mean by the term, and what forms can it take? Why should – or must – we engage in it? And how can we best achieve our aims with it? I will provide an overview of the current communication landscape, some food for (critical) thought, and many practical tips that help me when preparing to share my science with a wider audience.

The recent history of the replication crisis in psychology & how Open Science can be part of the solution

In recent years, more and more evidence has accumulated showing that many studies in psychological research cannot be replicated, effects are often overestimated, and little is publicly known about unsuccessful studies. What are the mechanisms behind this crisis? In this talk, I will explain how we got there and why it is still difficult to break free from the current system. I will further explain which role Open Science plays within the replication crisis and how it can help to improve science. This might sound like a pessimistic, negative talk, but I will end it on a positive note, I promise!

Reproducible EEG from raw data to publication figures

In this talk I will present recent developments in data sharing, organization, and analyses that allow to build fully reproducible workflows. First, I will present the Brain Imaging Data structure and discuss how this allows to build workflows, showing some new tools to read/import/create studies from EEG data structured that way. Second, I will present several newly developed tools for reproducible pre-processing and statistical analyses. Although it does take some extra effort, I will argue that it largely feasible to make most EEG data analysis fully reproducible.

The early impact of COVID-19 on mental health and community physical health services and their patients’ mortality in Cambridgeshire and Peterborough, UK

COVID -19 has affected social interaction and healthcare worldwide. This talk will focus on the impact of the pandemic and “lockdown” on mental health services, community physical health services, and patient mortality in Cambridgeshire and Peterborough, based on the analysis of de-identified data from the primary NHS provider of secondary care mental health services to this population (~0.86 million)

Population studies and ageing brains, in a time of COVID

This presentation will include a brief resume of research in older populations led from Cambridge that have informed current clinical understanding and policy regarding services and prevention for and of dementia. These population studies have more recently been ‘re-purposed’ with enthusiasm from participants into a trial platform, and this also has enabled ongoing follow-up by telephone during the COVID pandemic. Although there are no formal outputs from these latter developments general impressions will be shared.

Cerebro Parental: La biología aun invisible del desarrollo infantil

Desde la investigación en antropología evolutiva, las neurociencias del comportamiento parental y los estudios de cohortes de orfelinatos, los nuevos conocimientos confluyen en la mayor importancia critica del periodo postnatal inmediato para el desarrollo social humano. Surge la explicación biológica de la interdependencia de los cambios comportamentales en los adultos que crían y el recién nacido: Nature of Nurture. Del concepto unidireccional clásico de la necesidad de estimular un cerebro inmaduro, se comienza a comprender la naturaleza de la interacción en red entre el cerebro neonatal y el cerebro parental que también debe ser estimulado. Concebir, engendra y criar son etapas sucesivas de la reproducción pero no indispensablemente continuas. La función parental es primariamente dependiente de la disponibilidad para cuidar al recién nacido.

How to assess and manage spastic gait in rare diseases?

Semantic variant of primary progressive aphasia, clinical manifestation and underlying neuropathology

Can machine learning learn new physics, or do we need to put it in by hand?"\

There has been a surge of publications on using machine learning (ML) on experimental data from physical systems: social, biological, statistical, and quantum. However, can these methods discover fundamentally new physics? It can be that their biggest impact is in better data preprocessing, while inferring new physics is unrealistic without specifically adapting the learning machine to find what we are looking for — that is, without the “intuition” — and hence without having a good a priori guess about what we will find. Is machine learning a useful tool for physics discovery? Which minimal knowledge should we endow the machines with to make them useful in such tasks? How do we do this? Eight speakers below will anchor the workshop, exploring these questions in contexts of diverse systems (from quantum to biological), and from general theoretical advances to specific applications. Each speaker will deliver a 10 min talk with another 10 minutes set aside for moderated questions/discussion. We expect the talks to be broad, bold, and provocative, discussing where the field is heading, and what is needed to get us there.

Open Neuroscience: Challenging scientific barriers with Open Source & Open Science tools

The Open Science movement advocates for more transparent, equitable and reliable science. It focusses on improving existing infrastructures and spans all aspects of the scientific process, from implementing systems that reward pre-registering studies and guarantee their publication, all the way to making research data citable and freely available. In this context, open source tools (and the development ethos supporting them) are becoming more and more present in academic labs, as researchers are realizing that they can improve the quality of their work, while cutting costs. In this talk an overview of OS tools for neuroscience will be given, with a focus on software and hardware, and how their use can bring scientific independence and make research evolve faster.

"Neuroscience? Isn't that for clever people": Bringing neuroscience to new audiences through public outreach and education

FENS Forum 2024

Scientific and public outreach of cell type taxonomy tools

FENS Forum 2024