skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: Tracers in neuroscience: Causation, constraints, and connectivity
This paper examines tracer techniques in neuroscience, which are used to identify neural connections in the brain and nervous system. These connections capture a type of “structural connectivity” that is expected to inform our understanding of the functional nature of these tissues (Sporns in Scholarpedia, 2007). This is due to the fact that neural connectivity constrains the flow of signal propagation, which is a type of causal process in neurons. This work explores how tracers are used to identify causal information, what standards they are expected to meet, the forms of causal information they provide, and how an analysis of these techniques contributes to the philosophical literature, in particular, the literature on mark transmission and mechanistic accounts of causation.  more » « less
Award ID(s):
1945647
PAR ID:
10231003
Author(s) / Creator(s):
Date Published:
Journal Name:
Synthese
ISSN:
0039-7857
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. In this video article, accompanying the paper “An approach to learning the hierarchical organization of the frontal lobe”, we discuss a data driven approach to learning brain connectivity. Hierarchical models of brain connectivity are useful to understand how the brain can process sensory information, make decisions, and perform other high-level tasks. Despite extensive research, understanding the structure of the prefrontal cortex (PFC) remains a crucial challenge. In this work, we propose an approach to studying brain signals and uncovering characteristics of the underlying neural circuity, based on the mathematics of Gaussian processes and causal strengths. For discovering causations, we propose a metric referred to as double-averaged differential causal effect, which is a variant of the recently proposed differential causal effect, and it can be used as a principled measure of the causal strength between time series. We applied this methodology to study local field potential data from the frontal lobe, where the interest was in finding the causal relationship between the medial and lateral PFC areas of the brain. Our results suggest that the medial PFC causally influences the lateral PFC. 
    more » « less
  2. Abstract Neural networks have become increasingly prevalent within the geosciences, although a common limitation of their usage has been a lack of methods to interpret what the networks learn and how they make decisions. As such, neural networks have often been used within the geosciences to most accurately identify a desired output given a set of inputs, with the interpretation of what the network learns used as a secondary metric to ensure the network is making the right decision for the right reason. Neural network interpretation techniques have become more advanced in recent years, however, and we therefore propose that the ultimate objective of using a neural network can also be the interpretation of what the network has learned rather than the output itself. We show that the interpretation of neural networks can enable the discovery of scientifically meaningful connections within geoscientific data. In particular, we use two methods for neural network interpretation called backward optimization and layerwise relevance propagation, both of which project the decision pathways of a network back onto the original input dimensions. To the best of our knowledge, LRP has not yet been applied to geoscientific research, and we believe it has great potential in this area. We show how these interpretation techniques can be used to reliably infer scientifically meaningful information from neural networks by applying them to common climate patterns. These results suggest that combining interpretable neural networks with novel scientific hypotheses will open the door to many new avenues in neural network‐related geoscience research. 
    more » « less
  3. Abstract This paper examines constraints and their role in scientific explanation. Common views in the philosophical literature suggest that constraints are non-causal and that they provide non-causal explanations. While much of this work focuses on examples from physics, this paper explores constraints from other fields, including neuroscience, physiology, and the social sciences. I argue that these cases involve constraints that are causal and that provide a unique type of causal explanation. This paper clarifies what it means for a factor to be a constraint, when such constraints are causal, and how they figure in scientific explanation. 
    more » « less
  4. Abstract Neural circuit function is shaped both by the cell types that comprise the circuit and the connections between those cell types1. Neural cell types have previously been defined by morphology2, 3, electrophysiology4, 5, transcriptomic expression6–8, connectivity9–13, or even a combination of such modalities14–16. More recently, the Patch-seq technique has enabled the characterization of morphology (M), electrophysiology (E), and transcriptomic (T) properties from individual cells17–20. Using this technique, these properties were integrated to define 28, inhibitory multimodal, MET-types in mouse primary visual cortex21. It is unknown how these MET-types connect within the broader cortical circuitry however. Here we show that we can predict the MET-type identity of inhibitory cells within a large-scale electron microscopy (EM) dataset and these MET-types have distinct ultrastructural features and synapse connectivity patterns. We found that EM Martinotti cells, a well defined morphological cell type22, 23known to be Somatostatin positive (Sst+)24, 25, were successfully predicted to belong to Sst+ MET-types. Each identified MET-type had distinct axon myelination patterns and synapsed onto specific excitatory targets. Our results demonstrate that morphological features can be used to link cell type identities across imaging modalities, which enables further comparison of connectivity in relation to transcriptomic or electrophysiological properties. Furthermore, our results show that MET-types have distinct connectivity patterns, supporting the use of MET-types and connectivity to meaningfully define cell types. 
    more » « less
  5. Despite their successes, machine learning techniques are often stochastic, error-prone and blackbox. How could they then be used in fields such as theoretical physics and pure mathematics for which error-free results and deep understanding are a must? In this Perspective, we discuss techniques for obtaining zero-error results with machine learning, with a focus on theoretical physics and pure mathematics. Non-rigorous methods can enable rigorous results via conjecture generation or verification by reinforcement learning. We survey applications of these techniques-for-rigor ranging from string theory to the smooth 4D Poincaré conjecture in low-dimensional topology. We also discuss connections between machine learning theory and mathematics or theoretical physics such as a new approach to field theory motivated by neural network theory, and a theory of Riemannian metric flows induced by neural network gradient descent, which encompasses Perelman’s formulation of the Ricci flow that was used to solve the 3D Poincaré conjecture. 
    more » « less