From 59462729e178f53a0e477ce1902fd82a24e083e9 Mon Sep 17 00:00:00 2001 From: csaben Date: Sat, 24 Feb 2024 17:05:41 -0500 Subject: [PATCH] cleaning up posts --- .../2023-19-23-structure-function-papers.md | 69 ------------------- .../2023-8-23-meta-is-the-new-santa.md | 13 ---- src/posts/tests/2023-03-10-example-post-1.md | 9 --- 3 files changed, 91 deletions(-) delete mode 100644 src/posts/archive/2023-19-23-structure-function-papers.md delete mode 100644 src/posts/archive/2023-8-23-meta-is-the-new-santa.md delete mode 100644 src/posts/tests/2023-03-10-example-post-1.md diff --git a/src/posts/archive/2023-19-23-structure-function-papers.md b/src/posts/archive/2023-19-23-structure-function-papers.md deleted file mode 100644 index 5494c8e..0000000 --- a/src/posts/archive/2023-19-23-structure-function-papers.md +++ /dev/null @@ -1,69 +0,0 @@ ---- -title: "Structure Function Papers" -date: 2023-03-19 -description: "Annotating structure function papers" - ---- -This isn't much of a blog post but rather a starting point for myself to reference (on the fly, from anywhere) papers that I'm actively reading or have marked to read next. I hope others that find this post will be able to more quickly narrow down there search for a specific topic by using some of the annotations I've done. - -As I consider reading and diving deeper into the literature as my current [march 2023] priority, that will be reflected in this style of notes. I.e. I will be making an attempt to tabulate referenced papers. In papers that require mathematics (appendices, toy problems, etc), I will switch, but for papers that are mostly word dense I will omit much as the best source is the primary linked one. I will also try to code out aspects of papers if it is ever meaningful and makes sense to do so. - -**Note:** -* this is a living post that will be updated with future annotations -* any [0-9] refers to the citations listed within a given paper and you need to look in the paper to find out more about said reference - -## Table of Contents ---- -[[toc]] - -## from the connectome to brain function ---- -[`Cornelia I Bargmann & Eve Marder`]("https://d1wqtxts1xzle7.cloudfront.net/48812919/From_the_connectome_to_brain_function20160913-29300-1fosjpb-libre.pdf?1473811373=&response-content-disposition=inline%3B+filename%3DFrom_the_connectome_to_brain_function.pdf&Expires=1679198836&Signature=CZEwAYZT2Kg7O4qeLuD-jpVrn3uYoWzaDw6FrBpZm1E6CBXAu4MfMCHjMV4pbpnkBZzIAEVTBsvol52ApIQALKdMMLJr2WLTcdsW3jR7wxb2LTDyCVnOV7sK6YEF2o5fRON5amNmzsUqo4-RHdIoe4S6I-IHxkviuxC5SrNAps5g-zkQXvNFn4hmpT-yeNR5G8kTbciiDhaLAhkbj1LfkK7kdXDcUcNg~ZI~wJNGpomL4LBJ5OKI~dwIwxbzXB-1N9A73ZKlyl1LiC2ozNPQGGwZbt5Z2PGouhVgkpqjK3cU33sT~e9WnMiaXA59b2xIyryIXphvWS-LLoyfK53AXw__&Key-Pair-Id=APKAJLOHF5GGSLRBV4ZA") @ 2013 - - - -[`first pass`](https://web.stanford.edu/class/ee384m/Handouts/HowtoReadPaper.pdf) of the aforementioned paper. This is in an effort to get as many [`hours`](https://www.youtube.com/watch?v=cdiD-9MMpb0) in as possible prior to diving into my independent summer research. - -### abstract -*Purpose:* -What additional info is needed beyond connectivity diagrams to understand circuit function, informed by invertebrate circuits whose connectivity is known (in this case the C. elegans' nervous system is used as the anatomical connectome was established over 25 years ago i.e. 1980 [14]) - -*Key References:* -[5-7] identified nueronal components of circuits that generate behaviors by using systematic electrophysiological recording (19602, 1970s) -[14] "heroic electron microscopy reconstruction of the full nervous system of C. elegans" (1980's) -[4,15-18] "Recent advances in electron microscopy and image analysis have made it possible to scale up this ultrastructural approach: to serially section and reconstruct pieces of both vertebrate and invertebrate nervous systems, with the stated purpose of using detailed connectomes to reveal how these circuits work" - -### What do functional and anatomical maps reveal? -Summary: Connectivity is complicated [^complicated] - -Key takeaways: -* 60% of C. elegans neuron types have defined functions in one or more behaviors -* For C. elegans, although we know what most of the neurons do, we do not know what most of the connections do, we do not know which chemical connections are excitatory or inhibitory, and we cannot easily predict which connections will be important from the wiring diagram -* The wiring diagram could generate hypotheses to test, but solving a circuit by anatomical inspection alone was not successful. We believe that anatomical inspection fails because each wiring diagram encodes many possible circuit outcomes - -Key References -[21] "The complexity of this connection map poses the essential question: are all synapses important, or are some only important under certain conditions (as appears to be the case)" - -Reader notes: -* if you are skimming this I highly recommend taking a look at figures (1a) and (1b) to get a better idea of the difference between a connectivity diagram (1a) and a connectome (1b) -* connectome is organized in a signal flow view which reflects dominant information flow, from sensory neurons (top) -> interneurons (middle) -> motor neurons (bottom) - -[^complicated]: Additional connections are created by the widespread electrical synapses, mediated by direct cytoplasmic communication through gap junctions, through which current flows depending on the voltages of the coupled neurons. In the STG circuit, there are many instances of neurons that are connected by electrical synapses as well as by chemical inhibitory synapses - - - - - -## Reading List -* [A Modeling Framework for Deriving the Structure and Functional Architecture of a Short-Term Memory Microcircuit](https://drive.google.com/file/d/12peP0cvA6yXOCmo3HW1bdRqmGVuAAtg1/view?usp=share_link) -* [The space of interactions in neural network models](https://drive.google.com/file/d/1Fidly7Opqvq_lmegd3AD-AIYnxegTHgY/view?usp=share_link) -* [From connectome to brain function](https://drive.google.com/file/d/1lPd1AgE5EdPJYL5xKQulVKEEWymx5sGP/view?usp=share_link) -* [Geometrical and Statistical Properties of Systems of Linear Inequalities with Applications in Pattern Recognition](https://drive.google.com/file/d/1adQffIG-KziNR5JoiTB8QV7xNXzdKd_T/view?usp=share_link) -* [Sparse Coding with an Overcomplete Basis Set: A Strategy Employed by V1?](https://drive.google.com/file/d/1qFIHzCDTyFi6WiZCgGliVb10LMOix_Ep/view?usp=share_link) -* [Structural Properties of the Caenorhabditis elegans Neuronal Network](https://drive.google.com/file/d/1ETIxlWeSBeCc08WlUrZc8lISLPUWYsfC/view?usp=share_link) - -## Citations -* Bargmann, C., Marder, E. From the connectome to brain function. Nat Methods 10, 483–490 (2013). https://doi.org/10.1038/nmeth.2451 - - diff --git a/src/posts/archive/2023-8-23-meta-is-the-new-santa.md b/src/posts/archive/2023-8-23-meta-is-the-new-santa.md deleted file mode 100644 index 0090330..0000000 --- a/src/posts/archive/2023-8-23-meta-is-the-new-santa.md +++ /dev/null @@ -1,13 +0,0 @@ ---- -title: "Meta is the new santa" -date: 2023-08-23 -description: "Meta just keeps releasing open source models and I am here for it" ---- - - -**“Thanks Meta”** - -This is a short post but as I don’t post much aside from code online, but I just wanted to say, “Thanks Meta”. - - -For a research project, I was just about to finetune llama2 on python code and literally today Meta drops Code Llama. I realize that the model isn’t just for me but epic! Now we can just finetune code llama for codex related tasks (if that’s even necessary, evaluation of the model on my end still needs to be done). diff --git a/src/posts/tests/2023-03-10-example-post-1.md b/src/posts/tests/2023-03-10-example-post-1.md deleted file mode 100644 index fa64325..0000000 --- a/src/posts/tests/2023-03-10-example-post-1.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -title: This is my first post -date: 2023-03-10 -description: Fizzbuzz, foobar, insert description here. ---- - -Dross is a cool guy. He can be cryptic at times, but thats kind of his charm. - -This is a test post.