Podcasts about umap

VIDEO - https://youtu.be/Gtw2cQuRJ0sEste análisis revela la verdadera naturaleza de las Unidades Militares de Ayuda a la Producción (UMAP), campos de concentración establecidos en Cuba entre 1965-1968. Basado en seis documentos históricos recientemente revelados por el periodista José Raúl Gallego, el video expone el carácter sistemático y planificado de estos campos de trabajo forzado donde fueron internados miles de cubanos considerados "desviados": homosexuales, religiosos, disidentes y otros catalogados como "lacra social".Los documentos desmienten la narrativa oficial que presentaba las UMAP como un "error histórico" de la Revolución Cubana. En cambio, muestran un sistema meticulosamente diseñado con planes específicos para la "reeducación" mediante trabajo forzado, tortura psicológica y física, y experimentos pseudocientíficos inspirados en teorías pavlovianas. Un documento detalla un "Centro Modelo de Reeducación" para homosexuales, clasificándolos según categorías y diseñando intervenciones para "corregir" su orientación.El material revela métodos brutales de tortura como "El Hoyo" (enterramiento), ahogamientos, y descargas eléctricas, todo justificado bajo el concepto de "higiene social" promovido por intelectuales afines al régimen como Samuel Feijóo. Los documentos también exponen la persecución sistemática contra grupos religiosos, principalmente católicos y bautistas, considerados contrarrevolucionarios.Este testimonio documental demuestra la institucionalización del mal en la Cuba revolucionaria, un sistema que no surgió por accidente sino como parte de un plan estructurado para eliminar cualquier elemento que no encajara en la visión del "hombre nuevo" socialista, un capítulo oscuro de la historia cubana que intentó ser borrado.**** Para más videos VISITA - www.ErnestoMiami.com

Special guest Shannon Russell   Giveaways https://startyoursecondact.com   In this empowering episode of Podcast Profits Unleashed, I had the absolute pleasure of chatting with career transition and business coach Shannon Russell—also the brilliant author of Start Your Second Act: How to Change Careers, Launch a Business, and Create Your Best Life. Shannon's story is one of courage, clarity, and conscious change. After 16 successful years in the television industry, she made the bold decision to pivot into entrepreneurship, launching a franchise that gave her more time with her family—and more personal fulfillment. We dove deep into the realities women face when trying to leave careers that no longer serve them, especially during midlife or motherhood. Shannon shares the most common fears her clients experience and how she helps them overcome analysis paralysis and self-doubt by aligning their passion, skills, and values using the UMAP career assessment. What stood out to me is Shannon's emphasis on research and realism. She reminds us that not every business idea is a good fit—especially if it conflicts with your lifestyle goals. I loved hearing her examples of how diving into the “day-to-day” of a business idea helps people avoid burnout before it begins. We also discussed the dangers of diving into entrepreneurship without a clear plan—a mistake she sees far too often, especially among expats and creatives looking for a quick escape from their current path. Shannon's structured, tailored approach to coaching is a breath of fresh air. She helps her clients build businesses around their lives—not the other way around. Her message is clear: you can start a second act filled with purpose, but success begins with strategy, self-awareness, and support.

VIDEO - https://youtu.be/NrjuSjawICsErnestoMiami revela la historia oculta de las Unidades Militares de Ayuda a la Producción (UMAP), campos de concentración y trabajo forzado que operaron en Cuba entre 1965 y 1968. A través de testimonios y documentación histórica, se expone cómo más de 30,000 jóvenes cubanos fueron secuestrados y enviados a estos campos en Camagüey por "delitos" como ser homosexual, practicar una religión, usar pelo largo o simplemente no encajar en el ideal del "hombre nuevo" revolucionario.ErnestoMiami analiza el fundamento ideológico detrás de las UMAP, influenciado por las teorías de Ernesto "Che" Guevara sobre el "hombre nuevo" y los conceptos de reeducación forzada.Los prisioneros enfrentaron condiciones inhumanas: cercas de alambre de púas, barracones insalubres, jornadas de trabajo extenuantes cortando caña de azúcar, alimentación deficiente y castigos brutales. Particularmente severo fue el trato hacia los Testigos de Jehová, quienes se negaban a participar en rituales revolucionarios.Este video incluye testimonios conmovedores y examina las secuelas psicológicas que sufrieron las víctimas, incluyendo el desarrollo de un síndrome similar al de Estocolmo.Este oscuro capítulo de la historia cubana fue minimizado por el régimen castrista y olvidado internacionalmente, a pesar de representar una violación sistemática de derechos humanos comparable a otros campos de concentración condenados históricamente.**** Para más videos VISITA - www.ErnestoMiami.com

We kick off Season 4 with a deep, layered look at resurrection, queer liberation, and spiritual unbinding. Host Peterson Toscano brings together three unique stories—tied together by one enduring biblical moment: Jesus calling Lazarus out of the tomb.

University of Washington の浜崎伸彦さん(@Nobu_Hamazaki)がゲスト。Human RA-Gastruloid論文、条件探索のコツ、ステージング問題、卵子形成論文、PI生活、今後目指す合成的発生生物学の方向性など (12/12収録) Show Notes (番組HP): 浜崎ラボHP 博士課程(の後半)での所属ラボ：中島欽一ラボ 日本での所属ラボ：林克彦ラボ (現在は阪大) 日本にいたときの卵子形成転写因子論文 かぐや論文 Parthenogenesisのレビュー 留学先の所属ラボ：Jay Shendureラボ 留学先でのHuman RA-Gastruloid論文 最初にあったマウスGastruloid論文 Matrigel おすすめの発生生物学の教科書ギルバート発生生物学、ウォルパート発生生物学とラングマン人体発生学とそのムービー JayのGestalt イベントのレコーディング シュペーマンのオーガナイザー (pdf) Turner Syndrome Wntアゴニストのカイロン 下流のBrachyury (T)という転写因子 最近出ていた脊索が現れる3D trunk organoid論文 bioRxivに最初に出た論文 とその数日後にアップロードされた競合論文 その１ ２ ３ ４ の出版論文としての結果 1 2 3 4 最近溜まっているEmbryonic single cell data 1 2 3 4 5 6 7 10x sci-RNA-seq3 Smart-seq3 Wei Yangさん（Jayラボメンバーページ） マーカージーンをGPTに入れると予測してくる Mappingする方法  UMAPのco-embedding Foundation modelを作っていく例 今村さん とやっていたgene regulation Zygotic genome activation 精子のヒストンがプロタミンに置き換わる機構 残ったヒストンがinter-generationalなepigenetic memoryに関与する？（pdf） 父が肥満だと子が肥満になりやすい、母だとそうでもない ダーウィン vs ルイセンコ iPSで精子作成している例 減数分裂？に関するプレプリント パキテンで止まっている 山中論文は24から4へ 卵子が大きくなるためにはアクアポリンが必要。

In this episode, In Plain English joins the discourse on the All of Us Genomics project and their use of UMAP, an algorithm that reduces complex data to 2 dimensions. Join guests Konrad Kording, William Lima, and Jake Walker to learn why this mathematical model made such a splash on Twitter, and how scientists can analyze and communicate large data sets more rigorously. See how UMAP works on randomly generated data: https://koerding.github.io/umap-web-app/ See the papers and other resources discussed in this article: https://inplainenglishpod.org/2024/12/10/season-4-episode-3-the-umap-algorithm-look-pretty-and-do-as-little-as-possible/ In Plain English now has a Discord server! Join ⁠⁠here ⁠⁠to chat with other listeners, past experts, and guests about science, suggest new episode topics, and more! Remember to follow In Plain English on ⁠⁠Facebook ⁠⁠, ⁠⁠Twitter⁠⁠, Bluesky, and ⁠⁠Instagram ⁠⁠to keep up with the latest announcements! If you are able, please consider ⁠⁠becoming a Patron⁠⁠ to help support In Plain English! And check out our ⁠⁠Where to Listen⁠⁠ page to subscribe to our podcast on your favorite platform! Intro/Outro music credit: Sam Brunwasser (⁠⁠https://soundcloud.com/visualsnowbeats⁠⁠) Logo credit: Biographics (Jessica Higginbotham, Tania Lintz, and Yolanda Campos Jurado)

In this episode of Learning from Machine Learning, we explore the intersection of pure mathematics and modern data science with Leland McInnes, the mind behind an ecosystem of tools for unsupervised learning including UMAP, HDBSCAN, PyNN Descent and DataMapPlot. As a researcher at the Tutte Institute for Mathematics and Computing, McInnes has fundamentally shaped how we approach and understand complex data.McInnes views data through a unique geometric lens, drawing from his background in algebraic topology to uncover hidden patterns and relationships within complex datasets. This perspective led to the creation of UMAP, a breakthrough in dimensionality reduction that preserves both local and global data structure to allow for incredible visualizations and clustering. Similarly, his clustering algorithm HDBSCAN tackles the messy reality of real-world data, handling varying densities and noise with remarkable effectiveness.But perhaps what's most striking about McInnes isn't just his technical achievements – it's his philosophy toward algorithm development. He champions the concept of "decomposing black box algorithms," advocating for transparency and understanding over blind implementation. By breaking down complex algorithms into their fundamental components, McInnes argues, we gain the power to adapt and innovate rather than simply consume.For those entering the field, McInnes offers poignant advice: resist the urge to chase the hype. Instead, find your unique angle, even if it seems unconventional. His own journey – applying concepts from algebraic topology and fuzzy simplicial sets to data science – demonstrates how breakthrough innovations often emerge from unexpected connections.Throughout our conversation, McInnes's passion for knowledge and commitment to understanding shine through. His approach reminds us that the most powerful advances in data science often come not from following the crowd, but from diving deep into fundamentals and drawing connections across disciplines.There's immense value in understanding the tools you use, questioning established approaches, and bringing your unique perspective to the field. As McInnes shows us, sometimes the most significant breakthroughs come from seeing familiar problems through a new lens.Resources for Leland McInnesLeland's GithubUMAPHDBSCANPyNN DescentDataMapPlotEVoCReferencesMaarten GrootendorstLearning from Machine Learning Episode 1Vincent Warmerdam - CalmcodeLearning from Machine Learning Episode 2Matt RocklinEmily Riehl - Category Theory in ContextLorena BarbaDavid Spivak - Fuzzy Simplicial SetsImproving Mapper's Robustness by Varying Resolution According to Lens-Space DensityLearning from Machine LearningYoutubehttps://mindfulmachines.substack.com/

Markus Stoll is the Co-Founder of Renumics and the developer behind the open-source interactive ML dataset exploration tool, Spotlight. He shares insights on: AI in Engineering and ManufacturingInteractive ML Data VisualizationML Data Exploration Follow Markus for hands-on articles about leveraging ML while keeping a strong focus on data. Visualize - Bringing Structure to Unstructured Data // MLOps Podcast #258 with Markus Stoll, CTO of Renumics. A huge thank you to SAS for their generous support! // Abstract This talk is about how data visualization and embeddings can support you in understanding your machine-learning data. We explore methods to structure and visualize unstructured data like text, images, and audio for applications ranging from classification and detection to Retrieval-Augmented Generation. By using tools and techniques like UMAP to reduce data dimensions and visualization tools like Renumics Spotlight, we aim to make data analysis for ML easier. Whether you're dealing with interpretable features, metadata, or embeddings, we'll show you how to use them all together to uncover hidden patterns in multimodal data, evaluate the model performance for data subgroups, and find failure modes of your ML models. // Bio Markus Stoll began his career in the industry at Siemens Healthineers, developing software for the Heavy Ion Therapy Center in Heidelberg. He learned about software quality while developing a treatment machine weighing over 600 tons. He earned a Ph.D., focusing on combining biomechanical models with statistical models, through which he learned how challenging it is to bridge the gap between research and practical application in the healthcare domain. Since co-founding Renumics, he has been active in the field of AI for Engineering, e.g., AI for Computer Aided Engineering (CAE), implementing projects, contributing to their open-source library for data exploration for ML datasets (Renumics Spotlight) and writing articles about data visualization. // MLOps Jobs board https://mlops.pallet.xyz/jobs // MLOps Swag/Merch https://mlops-community.myshopify.com/ // Related Links Website: https://renumics.com/ MLSecOps Community: https://community.mlsecops.com/ Blogs: https://towardsdatascience.com/visualize-your-rag-data-evaluate-your-retrieval-augmented-generation-system-with-ragas-fc2486308557 : https://medium.com/itnext/how-to-explore-and-visualize-ml-data-for-object-detection-in-images-88e074f46361 --------------- ✌️Connect With Us ✌️ ------------- Join our slack community: https://go.mlops.community/slack Follow us on Twitter: @mlopscommunity Sign up for the next meetup: https://go.mlops.community/register Catch all episodes, blogs, newsletters, and more: https://mlops.community/ Connect with Demetrios on LinkedIn: https://www.linkedin.com/in/dpbrinkm/ Connect with Markus on LinkedIn: https://www.linkedin.com/in/markus-stoll-b39a42138/

In this heartfelt episode, Avik Chakraborty dives into a deep and transformative conversation with Victoria Volk, an advanced certified grief recovery specialist, energy healer, and author. Victoria shares her personal journey of navigating grief from a young age and how it shaped her life and career. She discusses the profound impact of energy healing in overcoming the emotional turmoil of loss and introduces listeners to practical tools for moving from surviving to thriving. About the Guest: Victoria Volk is a beacon of hope in the realm of grief recovery. She is a self-published author, advanced certified grief recovery specialist, and the creator and host of the podcast "Grieving Voices." With certifications in Reiki, Biofield Tuning, and UMAP coaching, Victoria combines traditional grief recovery methods with energy healing, offering a unique path to resilience. Key Takeaways: Grief is cumulative and can manifest in various physical and emotional ways if not addressed. Energy healing can play a crucial role in processing and releasing deep-seated grief. Practical strategies for supporting yourself or others through the grieving process.

¿Tienes unos minutos? Te contamos la actualidad de Cuba y del resto del mundo en 'Cuba a Diario', el podcast noticioso de Diario De Cuba. CINCO NOTICIAS DEL DÍA: —Ya está abierta la convocatoria para la lotería de visas de EEUU 2026 https://diariodecuba.com/cuba/1723569745_56567.html —Documentos filtrados de las UMAP revelan un plan del régimen cubano para 'borrar' la homosexualidad https://diariodecuba.com/cuba/1723561352_56562.html —La nueva generación de gallinas ponedoras de Cuba será yanqui https://diariodecuba.com/economia/1723571674_56568.html —El Oropouche llega a Islas Canarias procedente de Cuba https://diariodecuba.com/cuba/1723591289_56575.html —Las ayudas de la FAO para desarrollar la pesca en Cuba no detienen las quejas de los pescadores https://diariodecuba.com/cuba/1723583976_56573.html ESCÚCHANOS de lunes a viernes en: DDC Radio: https://diariodecuba.com/radio Soundcloud: https://is.gd/Da9TSp Apple Podcast: https://is.gd/3V010V Google Podcast: https://is.gd/kbaiIl Spotify: https://is.gd/J2Ifoy SÍGUENOS: • FB: www.facebook.com/DIARIODECUBA • TW: https://twitter.com/diariodecuba • IG: www.instagram.com/diariodecuba/ • YT: https://www.youtube.com/@DDCTV-DIARIODECUBA • Telegram: https://t.me/titularesDDC Lee hoy la Cuba de mañana: https://diariodecuba.com/

Buenos días desde La Habana, soy Yoani Sánchez y en el "cafecito informativo" de este martes 13 de agosto de 2024 tocaré estos temas: - Bielorrusia envía a Cuba los primeros 12 tractores que prometió - Documentos filtrados de las Umap revelan sus técnicas - Convocar a orar por Venezuela es una actividad delictiva en Cuba - Galería 'Máxima' presenta la exposición 'Germinal' Gracias por compartir este "cafecito informativo" y te espero para el programa de mañana. Puedes conocer más detalles de estas noticias en el diario https://www.14ymedio.com Los enlaces de hoy, para abrirlos desde la Isla se debe usar un proxy o un VPN para evadir la censura: Bielorrusia envía a Cuba los primeros 12 tractores que prometió a cambio de café y ron https://www.14ymedio.com/cuba/bielorrusia-envia-cuba-primeros-12_1_1105238.html Documentos filtrados de las Umap revelan técnicas para "borrar" comportamientos homosexuales https://www.14ymedio.com/cuba/documentos-filtrados-umap-revelan-tecnicas_1_1105234.html “Convocar a orar en parques es una actividad predelictiva”, según las autoridades cubanas https://www.14ymedio.com/cuba/convocar-orar-parques-actividad-predelictiva_1_1105236.html Maduro asegura que no va a "entregar el poder político a esta oligarquía fascista" https://www.14ymedio.com/internacional/maduro-asegura-no-entregar-politico_1_1105241.html En Caibarién, solo los pescadores privados tienen prohibido capturar peces grandes https://www.14ymedio.com/cuba/caibarien-pescadores-privados-prohibido-capturar_1_1105144.html México aumentó sus envíos de petróleo a Cuba en previsión de la crisis venezolana https://www.14ymedio.com/internacional/mexico-aumento-envios-petroleo-cuba_1_1105157.html Muere en Nueva York el actor Ángel Salazar, que huyó de Cuba nadando en Guantánamo https://www.14ymedio.com/cultura/muere-nueva-york-actor-angel_1_1105250.html Malas noticias para Cuba: el boxeo queda fuera de los Juegos Olímpicos de Los Ángeles 2028 https://www.14ymedio.com/deportes/malas-noticias-cuba-boxeo-queda_1_1105244.html Como ocurrió con el 11J en Cuba, la Policía detiene a menores en Venezuela https://www.14ymedio.com/internacional/ocurrio-11j-cuba-policia-detiene_1_1105253.html Entre los libros de julio, uno de Chomsky que se atreve a presentar a Cuba como modelo de país socialista https://www.14ymedio.com/cultura/libros-julio-chomsky-atreve-presentar_1_1104922.html Galería 'Máxima' presenta la exposición 'Germinal' en La Habana https://www.14ymedio.com/cartelera/galeria-maxima-presenta-exposicion-germinal_1_1105072.html

Noticiero de Martí Noticias presenta un resumen de las noticias más importantes de Cuba y el mundo. Titulares: | Amenazan con prisión a joven cubano por canciones contra el gobierno | Documentos sobre campamentos de la UMAP confirman homofobia y discriminación | Varados en Brasil cubanos beneficiarios de parole humanitario con permiso de viaje activo | Afirma Maduro que no entregará el poder a la oposición venezolana | Migrantes utilizan rutas alternativas ante cierre del Darién, alerta Panamá, entre otras noticias

Do you feel stuck in your career and wonder if there's something more fulfilling out there for you? What if you could pivot to a new career that aligns with your passions and life goals while maintaining a balanced lifestyle?In the latest episode of Daring to Leap, Shannon Russell, a career transition coach, certified UMAP coach, writer, speaker, and host of the Second Act Success Career Podcast, joins our host, Loree Philip, to discuss how you can achieve a balanced and fulfilling second act in your career.This conversation breaks down practical strategies and empowering insights that will help you navigate career pivots and embrace new opportunities without losing sight of what matters most.By listening to this episode you'll:Learn the importance of career identity and how to transfer your skills to new opportunities.Gain insights into overcoming societal pressure and self-doubt during a career change.Find out how to set priorities and non-negotiables for a fulfilling career transition.Explore the value of support systems and incremental steps in career pivots. Get practical tips on researching and testing new career paths. By the end of this episode, you'll be inspired and equipped with actionable steps to confidently embark on a successful career change, ensuring a seamless alignment with your personal and professional goals. So why wait? Hit play and start planning your fulfilling second act today!Connect with Shannon:https://secondactsuccess.co/Connect with Loree:Instagram - @loreephilipLinkedIn - @loree-philip

Leland McInnes is known for a lot of packages. There's UMAP, but also PyNNDescent and HDBScan. Recently he's also been working on tools to help visualise clusters of data and he's also cooking up something new that's related to nearest neighbor algorithms. This interview touches all of these topics.If you're interested in learning more about the MoMA exhibition, it was by Refik Anadol: https://refikanadol.com/ and this was the work at MoMA: https://refikanadol.com/works/unsupervised/.The other artist was Kyle McDonald: https://kylemcdonald.net/ and the piece we mentioned was this one: https://www.youtube.com/watch?v=04DqdT0-NtI.

In this podcast episode, Ben and Cynthia discuss the YouMap assessment, which helps identify teenagers' strengths, values, preferred skills, burnout skills, and interests. They emphasize the importance of understanding oneself and using this knowledge to make informed decisions. Things we discuss:Importance of self-awareness and understanding one's strengths and values.How the Umap assessment helps identify teenagers' strengths and interests.The significance of using the assessment results for scholarship and college applications.Exploring the application of the assessment in improving relationships between parents and teens.The potential benefits of taking action based on the insights gained from the YouMap assessment.Cynthia is offering a special 50% discount for listeners using the promo code "BenPugh" on her website, betterregulatethannever.comTake the free Parent Trap quiz If you have a teen you should take this Parent Trap Quiz .It will help you uncover specific parenting patterns that might be hindering your relationship with your teen. By identifying your Parent Trap, you gain the tools to have better communication, resolve conflicts, and build greater confidence in your parenting decisions. This self-awareness ultimately strengthens your relationship with your teen, which leads to a more open and harmonious connection. This quiz is your gateway to becoming the parent of your dreams and paving the way for a happier and healthier family life.TAKE THE QUIZ

Buckle up for a thrilling discourse as we journey alongside Deb Schell, an indomitable spirit who charted her course from journalism to corporate sales, and now thrives as a location-independent travel writer. Together, we'll be unraveling the intricacies of building thriving online communities, like her own Find Calm Here, delving into the importance of genuine connections and the overwhelming power of support. The conversation illuminates how Deb leveraged her transformative experiences to assist other budding entrepreneurs in launching their courses and consulting services.As we navigate the vast virtual landscape, we'll dissect the unique elements of Facebook groups and online communities, outlining the triumphs and trials that come with each. Guiding you through a thoughtful consideration of which platform dovetails with your aspirations, we highlight the importance of authenticity, the role of patience in member conversion, and the power of a message that truly resonates. We'll also touch on Deb's evolution from a consultant to a coach, spotlighting how structured programs like UMAP can be instrumental in matching your values, strengths, and preferred skills for a successful professional transition.Having walked the talk, Deb lends us her invaluable insights on structuring a vibrant online community. She shares her wisdom on picking the right platform, transitioning into coaching, and how UMAP can help align your values with your professional intentions. As we chronicle her journey from a corporate job to a multi-potential life, we understand how she employed these learnings to guide others on their entrepreneurial path. So, tune in and equip yourself with the essential toolkit to chase your passion and build your own community. Prepare to be inspired, enlightened, and empowered.Learn more about Deb: https://find-calm-here.ck.page/summerWe're happy you're here! Like the pod? Follow us on all socials at @amplifywithanika and @yourbrandamplified Leave a review on Apple Podcasts Visit our website Connect with us at anika@yourbrandamplified.com Join me on PodMatch to start your own journey as a podcast guest!

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.06.547914v1?rss=1 Authors: Brunner, M., Lopez-Rodriguez, D., Messina, A., Thorens, B., Santoni, F., Langlet, F. Abstract: The ependyma lining the third ventricle (3V) in the mediobasal hypothalamus is recognized as a critical player in controlling energy balance and glucose homeostasis. Its molecularly distinct cell types, including diverse tanycyte subpopulations and typical ependymal cells, confer a high functional heterogeneity. The study of gene expression profiles and dynamics of ependymal cells has the potential to uncover fundamental mechanisms and pathways involved in metabolic regulation. Here, we cataloged 5481 hypothalamic ependymocytes using FACS-assisted single-cell RNA sequencing from fed, 12h-fasted, and 24h-fasted adult male mice. First, standard clustering analysis revealed the limitation of the current characterization regarding the different ependymal cell subpopulations along the 3V. Indeed, while typical ependymal cells and {beta}2-tanycytes are sharply defined at the molecular level, other subpopulations (i.e., {beta}1-, 2-, and 1 tanycytes) display fuzzy boundaries and very few specific markers. Moreover, we observed that 12h- and 24h-fasting dynamically modulate gene expression, increasing tanycyte subgroup heterogeneity. Secondly, pseudospatial trajectory analysis based on peculiar UMAP neuroanatomical distribution improved the identification of tanycyte markers, distinguishing specific versus overlapping features and better segregating tanycyte specific versus standard functions. Intriguingly, we discovered numerous functions related to tanycyte-neuron and tanycyte-synapse interactions with modulation by energy balance. Finally, combining pseudospatial analysis and gene regulatory network inference, we observed that fasting dynamically shifts patterns in gene expression and transcription activity along the 3v, creating a metabolic and functional switch for some subpopulations. Altogether, this data provides a mechanism through which energy status leads to distinct cell type-specific responses along the 3V and gives new insights into molecular diversity underlying tanycyte classification. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.12.536531v1?rss=1 Authors: Kwon, J., Kim, S., Kim, D.-K., Joo, J., Kim, S., Cha, M., Lee, C. J. Abstract: While huge strides have recently been made in language-based machine learning, the ability of artificial systems to comprehend the sequences that comprise animal behavior has been lagging behind. In contrast, humans instinctively recognize behaviors by finding similarities in behavioral sequences. Here, we develop an unsupervised behavior-mapping framework, SUBTLE (spectrogram-UMAP-based temporal-link embedding), to capture comparable behavioral repertoires from 3D action skeletons. To find the best embedding method, we devise a temporal proximity index as a metric to gauge temporal representation in the behavioral embedding space. The method achieves the best performance compared to current embedding strategies. Its spectrogram-based UMAP clustering not only identifies subtle inter-group differences but also matches human-annotated labels. SUBTLE framework automates the tasks of both identifying behavioral repertoires like walking, grooming, standing, and rearing, and profiling individual behavior signatures like subtle inter-group differences by age. SUBTLE highlights the importance of temporal representation in the behavioral embedding space for human-like behavioral categorization. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Buenos días, soy Yoani Sánchez y en el "cafecito informativo" de este miércoles 15 de marzo de 2023 tocaré estos temas: - ¿Es Cuba "una dictadura bloqueada"? - La tasa de ocupación hotelera es de apenas 15,6% - La prensa oficial retira el discurso de Castro que dio origen a las Umap - Presentación de "Mi diario personal de Luis Manuel Otero Alcántara" Gracias por compartir este "cafecito informativo" y te espero para el programa de mañana. Puedes conocer más detalles de estas noticias en el diario https://www.14ymedio.com Los enlaces de hoy: 'Cubadebate' exhuma el discurso de Castro que dio origen a las Umap y lo retira horas después https://enterate.link/cuba/Cubadebate-discurso-Castro-Umap-despues_0_3495250446.html El atleta cubano Pichardo y el marfileño Évora polemizan sobre sus pasaportes portugueses https://enterate.link/deportes/Pichardo-Evora-polemizan-pasaportes-portugueses_0_3495850384.html Un ex agente de la CIA cuestiona descartar la mano extranjera en el síndrome de La Habana https://enterate.link/internacional/CIA-cuestiona-descartar-extranjera-Habana_0_3495850382.html EE UU devuelve 37 migrantes a Cuba y ya suman 2.761 desde varios países https://enterate.link/cuba/EE-UU-devuelve-migrantes-Cuba_0_3495850381.html Disfrazada de médica, una cubana de Sancti Spíritus cambiaba billetes falsos de 100 dólares https://enterate.link/cuba/Disfrazada-Sancti-Spiritus-cambiaba-billetes_0_3495250449.html "Abajo la dictadura, los Castros asesinos", escriben a plena luz en La Habana https://enterate.link/cuba/Abajo-dictadura-Castros-asesinos-Habana_0_3495250451.html Los titulares de la tarjeta rusa Mir ya pueden sacar dinero en los cajeros cubanos https://enterate.link/cuba/titulares-tarjeta-Mir-cajeros-cubanos_0_3495250450.html Un diario para Luis Manuel Otero https://enterate.link/eventos_culturales/libros/diario-Luis-Manuel-Otero_13_3495380428.html

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.01.10.523448v1?rss=1 Authors: Chen, A. A., Clark, K., Dewey, B., DuVal, A., Pellegrini, N., Nair, G., Jalkh, Y., Khalil, S., Zurawski, J., Calabresi, P., Reich, D., Bakshi, R., Shou, H., Shinohara, R. T. Abstract: Dimension reduction tools preserving similarity and graph structure such as t-SNE and UMAP can capture complex biological patterns in high-dimensional data. However, these tools typically are not designed to separate effects of interest from unwanted effects due to confounders. We introduce the partial embedding (PARE) framework, which enables removal of confounders from any distance-based dimension reduction method. We then develop partial t-SNE and partial UMAP and apply these methods to genomic and neuroimaging data. Our results show that the PARE framework can remove batch effects in single-cell sequencing data as well as separate clinical and technical variability in neuroimaging measures. We demonstrate that the PARE framework extends dimension reduction methods to highlight biological patterns of interest while effectively removing confounding effects. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.25.517966v1?rss=1 Authors: Hermansen, E., Klindt, D. A., Dunn, B. A. Abstract: Neuroscience is pushing toward studying the brain during naturalistic behaviors with open-ended tasks. Grid cells are a classic example, where free behavior was key to observing their characteristic spatial representations in two-dimensional environments. In contrast, it has been difficult to identify grid cells and study their computations in more restrictive experiments, such as head-fixed wheel running. Here, we challenge this view by showing that shifting the focus from single neurons to the population level changes the minimal experimental complexity required to study grid cell representations. Specifically, we combine the manifold approximation in UMAP with persistent homology to study the topology of the population activity. With these methods, we show that the population activity of grid cells covers a similar two-dimensional toroidal state space during wheel running as in open field foraging, with and without a virtual reality setup. Trajectories on the torus correspond to single trial runs in virtual reality and changes in experimental conditions are reflected in the internal representation, while the toroidal representation undergoes occasional shifts in its alignment to the environment. These findings show that our method can uncover latent topologies that go beyond the complexity of the task, allowing us to investigate internal dynamics in simple experimental settings in which the analysis of grid cells has so far remained elusive. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Reconstructing and Classifying SDSS DR16 Galaxy Spectra with Machine-Learning and Dimensionality Reduction Algorithms by Felix Pat et al. on Wednesday 23 November Optical spectra of galaxies and quasars from large cosmological surveys are used to measure redshifts and infer distances. They are also rich with information on the intrinsic properties of these astronomical objects. However, their physical interpretation can be challenging due to the substantial number of degrees of freedom, various sources of noise, and degeneracies between physical parameters that cause similar spectral characteristics. To gain deeper insights into these degeneracies, we apply two unsupervised machine learning frameworks to a sample from the Sloan Digital Sky Survey data release 16 (SDSS DR16). The first framework is a Probabilistic Auto-Encoder (PAE), a two-stage deep learning framework consisting of a data compression stage from 1000 elements to 10 parameters and a density estimation stage. The second framework is a Uniform Manifold Approximation and Projection (UMAP), which we apply to both the uncompressed and compressed data. Exploring across regions on the compressed data UMAP, we construct sequences of stacked spectra which show a gradual transition from star-forming galaxies with narrow emission lines and blue spectra to passive galaxies with absorption lines and red spectra. Focusing on galaxies with broad emission lines produced by quasars, we find a sequence with varying levels of obscuration caused by cosmic dust. The experiments we present here inform future applications of neural networks and dimensionality reduction algorithms for large astronomical spectroscopic surveys. arXiv: http://arxiv.org/abs/http://arxiv.org/abs/2211.11783v1

Reconstructing and Classifying SDSS DR16 Galaxy Spectra with Machine-Learning and Dimensionality Reduction Algorithms by Felix Pat et al. on Tuesday 22 November Optical spectra of galaxies and quasars from large cosmological surveys are used to measure redshifts and infer distances. They are also rich with information on the intrinsic properties of these astronomical objects. However, their physical interpretation can be challenging due to the substantial number of degrees of freedom, various sources of noise, and degeneracies between physical parameters that cause similar spectral characteristics. To gain deeper insights into these degeneracies, we apply two unsupervised machine learning frameworks to a sample from the Sloan Digital Sky Survey data release 16 (SDSS DR16). The first framework is a Probabilistic Auto-Encoder (PAE), a two-stage deep learning framework consisting of a data compression stage from 1000 elements to 10 parameters and a density estimation stage. The second framework is a Uniform Manifold Approximation and Projection (UMAP), which we apply to both the uncompressed and compressed data. Exploring across regions on the compressed data UMAP, we construct sequences of stacked spectra which show a gradual transition from star-forming galaxies with narrow emission lines and blue spectra to passive galaxies with absorption lines and red spectra. Focusing on galaxies with broad emission lines produced by quasars, we find a sequence with varying levels of obscuration caused by cosmic dust. The experiments we present here inform future applications of neural networks and dimensionality reduction algorithms for large astronomical spectroscopic surveys. arXiv: http://arxiv.org/abs/http://arxiv.org/abs/2211.11783v1

En un intento por satisfacer la producción agrícola de la isla, entre 1965 y 1968 el régimen de Fidel Castro creó la Unidad Militar de Ayuda a la Producción (UMAP). Se trataba de una especie de campos de trabajo forzado donde, además de aprovechar la mano de obra sin paga, el Gobierno cubano trataba de "lavarle el cerebro" y "cambiar la ideología" a las personas no gratas como los homosexuales, los religiosos y los opositores, entre otros.Para conocer sobre cómo CNN protege la privacidad de su audiencia, visite CNN.com/privacidad

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.08.23.505030v1?rss=1 Authors: Dhinagar, N. J., Thomopoulos, S. I., Rajagopalan, P., Stripelis, D., Ambite, J. L., Steeg, G. V., Thompson, P. M. Abstract: Deep neural networks show great promise for classifying brain diseases and making prognostic assessments based on neuroimaging data, but large, labeled training datasets are often required to achieve high predictive accuracy. Here we evaluated a range of transfer learning or pre-training strategies to create useful MRI representations for downstream tasks that lack large amounts of training data, such as Alzheimer's disease (AD) classification. To test our models, we analyzed 4,098 3D T1-weighted brain MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort and independently validated our proposed methods for detecting AD with an out-of-distribution test set of 600 scans from the Open Access Series of Imaging Studies (OASIS3) cohort. First, we trained 3D and 2D convolutional neural network (CNN) architectures. We tested combinations of multiple pre-training strategies based on (1) supervised, (2) contrastive learning, and (3) self-supervised learning - using pre-training data within versus outside the MRI domain. In our experiments, the 3D CNN pre-trained with contrastive learning provided the best overall results - when fine-tuned on T1-weighted scans for AD classification - outperformed the baseline by 2.8% when trained with all of the training data from ADNI. We also show test performance as a function of the training dataset size and the chosen pre-training method. Transfer learning offered significant benefits in low data regimes, with a performance boost of 7.7%. When the pre-trained model was used for AD classification, we were able to visualize an improved clustering of test subjects' diagnostic groups, as illustrated via a uniform manifold approximation (UMAP) projection of the high-dimensional model embedding space. Further, saliency maps indicate the additional activation regions in the brain scan using pre-training, that then maximally contributed towards the final prediction score. Copy rights belong to original authors. Visit the link for more info Podcast created by PaperPlayer

This episode features an interview with Sophie Watson, Technical Product Marketing Manager at NVIDIA. Previously, Sophie served as a software engineer and principal data scientist at RedHat where she used machine learning to solve business problems in the hybrid cloud. Sophie has a PhD in Bayesian statistics and frequently speaks about machine learning workflows on Kubernetes, recommendation engines, and machine learning for search. In this episode, Sam and Sophie discuss Principal Component Analysis, computational acceleration, and MLOps.-------------------“We all start when we get hold of a data set by visualizing it to try to understand it. So that usually for me involves starting with a simple technique, something like PCA, Principal Component Analysis. It's been around since the eighties, probably longer, maybe the sixties. Don't quote me on that. With Principal Component Analysis, we can map our high dimensional data down to a smaller number of dimensions. Let's map it down to two so that we can visualize it. So we can go ahead and visualize it. But Principal Component Analysis is quite a simple technique in what it's doing and it's just mapping onto key components of our data. We might not be able to see, perhaps, separation of classes if we're working with data that's from a set of classes. Maybe we're looking at transactions, are they fraudulent or are they legitimate? And we might not be able to see that distinction. So that makes us think, "Is there something interesting in my data? Am I going to be able to train a machine learning model?" I don't know. Back in the day, I think the next step would've been, “Oh, let's train a model in C”, but now with accelerated compute within a really reasonable amount of time, we can go ahead and use a more sophisticated technique so we can use something like UMAP that's leaning on differential manifolds to do that projection to lower dimensions. And because this technique is slightly more sophisticated, what we find in general is that within the same amount of time, we're able to get more insight into the data. We're able to see the distinction in classes between our data sets. It keeps you in that loop. It keeps you in that productivity state.” – Sophie Watson-------------------Episode Timestamps:(01:22): What open source data means to Sophie(02:47): How Sophie is spending her time (07:52): What excites Sophia about the data science community(10:13): What Sophie is most excited about in data visibility(16:29): Data on servers versus data in the cloud(18:09): Accelerated computation on machine learning(22:27): Sophie breaks down probabilistic programming(24:21): What problem was Sophie trying to solve in her career(32:12): Sophie's dream job of working for Taylor Swift(34:48): Sophie's advice for those interested in open source-------------------Links:LinkedIn - Connect with SophieTwitter - Follow SophieTwitter - Follow NVIDIANVIDIA

come through with your pride and your flags swinging, this episode gets juicy as we take you through history into cuban queerness from how it started to how it's going.opening up season 4, we explore the queer in cubanity from figures to popular media and revolutions. check out @cubanecuir on instagram for more learnings on this topic. watch ana's story on the NYTimes: https://www.nytimes.com/video/opinion/100000003334885/anas-story-transgender-in-cuba.html **NOTE: we have two corrections: 1) an earlier version of this episode stated Jose Marti was in New York in the 1900s. As of June 22, 2022, at 10:30 am ET, we have revised to include a correction to state we meant to say the 1800s. 2) an earlier version of this episode stated that 250 people were confined in UMAP camps. As of June 22, 2022, at 8:30 pm ET, we have revised to include a correction to state we meant to say 30,000 people were confined. buy our merch: www.teikirisipod.com/shop follow us on social media @teikirisipod join us on patreon: https://www.patreon.com/teikirisipod episode transcript: https://bit.ly/3zNPCEb

come through with your pride and your flags swinging, this episode gets juicy as we take you through history into cuban queerness from how it started to how it's going.opening up season 4, we explore the queer in cubanity from figures to popular media and revolutions. check out @cubanecuir on instagram for more learnings on this topic. watch ana's story on the NYTimes: https://www.nytimes.com/video/opinion/100000003334885/anas-story-transgender-in-cuba.html**NOTE: we have two corrections: 1) an earlier version of this episode stated Jose Marti was in New York in the 1900s. As of June 22, 2022, at 10:30 am ET, we have revised to include a correction to state we meant to say the 1800s. 2) an earlier version of this episode stated that 250 people were confined in UMAP camps. As of June 22, 2022, at 8:30 pm ET, we have revised to include a correction to state we meant to say 30,000 people were confined.   buy our merch: www.teikirisipod.com/shopfollow us on social media @teikirisipodjoin us on patreon: https://www.patreon.com/teikirisipodepisode transcript: https://bit.ly/3zNPCEb

Silvio Rodriguez, concedió una entrevista al periodista Daniel Ramírez, publicada en el medio EL ESPAÑOL, que la publicó en la Internet el 22 de mayo de 2022, en la que el cantautor cubano, lejos de criticar la penosa situación política, económica y social por la que atraviesa Cuba, de la autoría de una tiranía de más de 60 años, justificó el panorama y sus razones, y fue conciliatorio con la dictadura. En este programa de EL ATICO DE PEPE, su conductor PEPE FORTE castiga fuertemente la pose del cantante que, entre otras cosas, dijo esto de las UMAP: "El Gobierno Revolucionario tuvo que cargar con todos los prejuicios que arrastraba nuestra sociedad desde tiempos de la colonia; entre ellos un machismo patriarcal y homofóbico. Sin embargo, conocí a miembros del Ejército Rebelde que eran homosexuales. Por supuesto, esto era de total conocimiento de la Dirección de la Revolución. Las Unidades Militares de Ayuda a la Producción fueron creadas para castigar indisciplinas de miembros del Ejército Rebelde. Después, algunos inconscientes pensaron que podían ser usadas para castigar a quienes no trabajaban, 'gente de la dulce vida', se les decía. Dentro de los estúpidos prejuicios que había con los homosexuales, estaba el de que no trabajaban, o que vivían una vida fácil. Fue un error espantoso y cuando lo que estaba pasando llegó a la jefatura revolucionaria, mandaron a cerrar aquellas unidades. Esto sucedió a fines de 1966 o principios de 1967. Conocí oficiales que tuvieron que ver con la clausura de aquellas prácticas".Para que conozcas otros detalles de la entrevista, y la respuesta de este programa, debe ver este episodio de EL ATICO DE PEPE. #SilvioRodriguez #ElAticoDePepe #pepeforte 

Welcome to The Nonlinear Library, where we use Text-to-Speech software to convert the best writing from the Rationalist and EA communities into audio. This is: A descriptive, not prescriptive, overview of current AI Alignment Research, published by Jan Hendrik Kirchner on June 6, 2022 on The AI Alignment Forum. TL;DR: In this project, we collected and cataloged AI alignment research literature and analyzed the resulting dataset in an unbiased way to identify major research directions. We found that the field is growing quickly, with several subfields emerging in parallel. We looked at the subfields and identified the prominent researchers, recurring topics, and different modes of communication in each. Furthermore, we found that a classifier trained on AI alignment research articles can detect relevant articles that we did not originally include in the dataset. Dataset Announcement In the context of the 6th AISC, we collected a dataset of alignment research articles from a variety of different sources. This dataset is now available for download here and the code for reproducing the scrape is on GitHub here. When using the dataset, please cite our manuscript as described in the footnote. Here follows an abbreviated version of the full manuscript, which contains additional analysis and discussion. Rapid growth of AI Alignment research from 2012 to 2022 across two platforms After collecting the dataset, we analyzed the two largest non-redundant sources of articles, Alignment Forum (AF) and arXiv. We found rapid growth in publications on the AF (Fig. 1a) and a long-tailed distribution of articles per researcher (Fig. 1b) and researchers per article (Fig. 1c). We were surprised to find a decrease in publications on the arXiv in recent years, but identified the cause for the decrease as spurious and fixed the issue in the published dataset (details in Fig. 4). Unsupervised decomposition of AI Alignment research into distinct clusters Given access to this unique dataset, we were curious to see if we could identify distinct clusters of research. We mapped the title + abstract of each article into vector form using the Allen Institute for AI's SPECTER model and reduced the dimensionality of the embedding with UMAP (Fig. 2a). The resulting manifold shows a continuum of AF posts and arXiv articles (Fig. 2b) and a temporal gradient from the top right to the bottom left (Fig. 2c). Using k-means and the elbow method, we obtain five clusters of research articles that map onto distinct regions of the UMAP projection (Fig. 2d). We were curious to see if the five clusters identified by k-means map onto existing distinctions in the field. When identifying the most prolific authors in each cluster, we noticed strong differences (consistent with previous work that suggests that author identity is an important indicator of research direction). By skimming articles in each cluster and given the typical research published by the authors, we suggest the following putative descriptions of each cluster: cluster one: Agent alignment is concerned with the problem of aligning agentic systems, i.e. those where an AI performs actions in an environment and is typically trained via reinforcement learning. cluster two: Alignment foundations research is concerned with deconfusion research, i.e. the task of establishing formal and robust conceptual foundations for current and future AI Alignment research. cluster three: Tool alignment is concerned with the problem of aligning non-agentic (tool) systems, i.e. those where an AI transforms a given input into an output. The current, prototypical example of tool AIs is the "large language model". cluster four: AI governance is concerned with how humanity can best navigate the transition to advanced AI systems. This includes focusing on the political, economic, military, governance, and ethical dimensions. cluster five: Value alignment is concerned with understanding and extracting human preferences and designing me...

Humberto Rodríguez nos habla del UMAP,Unidad Militar de Ayuda a la Producción. Campo de concentración donde reunieron a unas 3000 personas en Camagüei, Cuba.

America's Heroes Group Roundtable with Clean Energy Infrastructure Partner Zodiac Solutions, LLC Partner:Rob Howard, US Navy Veteran and President/CEO of Zodiac Solutions, LLC Panelist: Elizabeth Murray-Belcaster, EMB Consultants, Inc specializes in development of Military Training to placement efforts with Military leadership, industry, labor, academia, and regulatory agencies and stakeholders across the country

In episode three I am joined by Olivier Jeunen, who is a postdoctoral scientist at Amazon. Olivier obtained his PhD from University of Antwerp with his work "Offline Approaches to Recommendation with Online Success". His work concentrates on Bandits, Reinforcement Learning and Causal Inference for Recommender Systems.We talk about methods for evaluating online performance of recommender systems in an offline fashion and based on rich logging data. These methods stem from fields like bandit theory and reinforcement learning. They heavily rely on simulators whose benefits, requirements and limitations we discuss in greater detail. We further discuss the differences between organic and bandit feedback as well as what sets recommenders apart from advertising. We also talk about the right target for optimization and receive some advice to continue livelong learning as a researcher, be it in academia or industry.Olivier has published multiple papers at RecSys, NeurIPS, WSDM, UMAP, and WWW. He also won the RecoGym challenge with his team from University of Antwerp. With research internships at Criteo, Facebook and Spotify Research he brings significant experience to the table. Enjoy this enriching episode of RECSPERTS - Recommender Systems Experts.Links from this Episode: Olivier's Website Olivier Jeunen on LinkedIn and Twitter Simulators: RecoGym RecSim RecSimNG Open Bandit Pipeline Blogpost: Lessons Learned from Winning the RecoGym Challenge RecSys 2020 REVEAL Workshop on Bandit and Reinforcement Learning from User Interactions RecSys 2021 Tutorial on Counterfactual Learning and Evaluation for Recommender Systems NeurIPS 2021 Workshop on Causal Inference and Machine Learning Thesis and Papers: Dissertation: Offline Approaches to Recommendation with Online Success Chen et al. (2018): Top-K Off-Policy Correction for a REINFORCE Recommender System Jeunen et al. (2021): Disentangling Causal Effects from Sets of Interventions in the Presence of Unobserved Confounders Jeunen et al. (2021): Top-

In this episode of ACM ByteCast, Rashmi Mohan hosts Mounia Lalmas, Director of Research and Head of Tech Research in Personalization at Spotify, leading a team of researchers in content personalization and discovery. Prior to that, she was Director of Research at Yahoo London. She also holds an Honorary Professorship at University College London. Mounia's work focuses on studying user engagement in areas such as native advertising, digital media, social media, and search, and now audio (music and talk). She is a frequent conference speaker, author, and organizer whose research has appeared at many ACM (and other) conferences, including CIKM, RecSys, SIGIR, SIGKDD, UMAP, WSDM, WWW, and more. Mounia relates her beginnings in computing as a young student growing up in Algeria, her love for mathematical abstraction, and passion for evaluation and user engagement. She also traces her interest in the field of information retrieval and highlights some of the challenges in building robust recommender systems for music lovers. Mounia and Rashmi also discuss the differences between academic and industrial research, the important role conferences and networking play in computing research, and what excites her most in the fields of personalization research and information retrieval.

La frase no es mía, quizás mi amiga no quiso decir lo que yo entendí. UMAP, vuelos de la libertad, Mariel, Zafra de los 10 millones, Angola, el Quinquenio Gris, los balseros, la rectificación de errores y tendencias negativas, los fusilados, Ochoa... pobre pueblo obligado a llenar de silencios los espacios.

論文紹介#1。"グリッド細胞の集合的な活動がドーナツ型になる" ことを示したプレプリントについて話しています。 Show notes グリッド細胞...内側嗅内皮質（MEC）にあるニューロンで、動物がいる場所に反応して活動する。一つの細胞が反応する場所は規則的に並んでおり、平行四辺形の格子（グリッド）の格子点に一致するのが特徴。 トーラス...ドーナツ（の表面）の形。 アトラクター・ネットワーク...時間に依存して状態を変化させるシステム（例：相互に結合するニューロンの活動）のうち、あるいくつかの特定の状態に落ち着く性質を持つもの。 コンティニュアス・アトラクター・ネットワーク...アトラクター・ネットワークの一種で、収束した状態を取るが、ある収束した状態から、それに近い別の収束状態へと遷移していく性質を持つもの。 Neuropixels...生きた動物の脳から神経細胞の電気的な活動（細胞外電位）を記録できる電極。1000, あるいは5000以上という大量の記録部位を持つ。 次元削減...大量の神経細胞の活動の時系列データは即ち "（神経細胞の個数）次元のデータ"だが、３次元以上のデータがもつ特徴を人間が直観的に認識するのは難しい。次元削減は、高次元のデータを、その特徴を保ったまま低次元データに置き換える手法。 Toroidal topology of population activity in grid cells...今回話題にした論文 本年度のノーベル生理学・医学賞の解説...場所細胞・グリッド細胞の解説 海馬体-嗅内皮質における空間認知システム...グリッド細胞の日本語レビュー Path integration and the neural basis of the 'cognitive map'...空間を表現する Continuous Attractive Network がトーラスになる理由など The entorhinal grid map is discretized...グリッド細胞のモジュール性を報告した論文 Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings...最新版Neuropixelsに関するプレプリント UMAP Uniform Manifold Approximation and Projection for Dimension Reduction | SciPy 2018 |...著者によるUMAPの解説 「柔らかいトポロジーの穴から眺める世界」...トポロジーの専門家、平岡裕章先生によるトポロジー講義 Editorial notes いきなりややマニアックな内容でしたが、圧倒的な論文で楽しかったです。宮脇さんがかなりちゃんと準備してきてくれたので今後の論文紹介回のハードルが...僕はここから徐々に下げていきます。ジェンダーニュートラルな表現を心がけてはいるのですが、「元妻」という響きはなんとなくエグいので「元奥さん」と言っていますが特に他意はないです。 萩原 マサチューセッツ州のドーナツ市場はダンキンドーナツ一強です。フレンチクルーラーやポンデリングも食べたいです。宮脇

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.17.385864v1?rss=1 Authors: Chevalier, A., Yang, S., Yajima, M., Campbell, J. D. Abstract: Mutational signatures are patterns of somatic alterations in the genome that cause carcinogenic exposures or aberrant cellular processes. We created the musicatk package to provide a comprehensive workflow for preprocessing, analysis, and visualization of mutational signatures. The musicatk package enables users to select different schemas for counting mutation types and easily combine count tables from different schemas. Several methods can be used to discover new signatures or infer the exposures for given a pre-existing set of signatures. Several visualizations are provided to facilitate exploratory analysis of signatures and exposures. These include comparison of discovered signatures to those in the COSMIC database, using UMAP to embed tumors in two dimensions, and plotting of exposure distributions across user-defined annotations. Overall, musicatk can be used to gain novel insights into the patterns of mutational signature observed in cancer. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.31.363580v1?rss=1 Authors: Weinstein, J. N., Rohrdanz, M. N., Stucky, M. T., Melott, J. M., Jun, M., Mohanty, V., Manyam, G. C., Wakefield, C., Chen, K., Navin, N., Ryan, M. C., Akbani, R., Broom, B. M. Abstract: OmicPioneer-sc is an open-source data visualization/analysis package that integrates dimensionality-reduction plots (DRPs) such as t-SNE and UMAP with Next-Generation Clustered Heat Maps (NGCHMs) and Pathway Visualization Modules (PVMs) in a seamless, highly interactive exploratory environment. It includes fluent zooming and navigation, a statistical toolkit, dozens of link-outs to external public bioinformatic resources, high-resolution graphics that meet the requirements of all major journals, and the ability to store all metadata needed to reproduce the visualizations at a later time. A user-friendly, multi-panel graphical interface enables non-informaticians to interact with the system without programming, asking and answering questions that require navigation among the three types of modules or extension from them to the Gene Ontology or information on therapies. The visual integration can be useful for detective work to identify and annotate cell-types for color-coding of the DRPs, and multiple NGCHMs can be layered on top of each other (with toggling among them) as an aid to multi-omic analysis. The tools are available in containerized form with APIs to facilitate incorporation as a plug-in to other bioinformatic environments. The capabilities of OmicPioneer-sc are illustrated here through application to a single-cell RNA-seq airway dataset pertinent to the biology of both cancer and COVID-19 Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.25.285619v1?rss=1 Authors: Zhang, W., Claesen, M., Moerman, T., Groseclose, M. R., Waelkens, E., De Moor, B., Verbeeck, N. Abstract: Computational analysis is crucial to capitalize on the wealth of spatio-molecular information generated by mass spectrometry imaging (MSI) experiments. Currently, the spatial information available in MSI data is often under-utilized, due to the challenges of in-depth spatial pattern extraction. The advent of deep learning has greatly facilitated such complex spatial analysis. In this work, we use a pre-trained neural network to extract high-level features from ion images in MSI data, and test whether this improves downstream data analysis. The resulting neural network interpretation of ion images, coined neural ion images, are used to cluster ion images based on spatial expressions. We evaluate the impact of neural ion images on two ion image clustering pipelines, namely DBSCAN clustering, combined with UMAP-based dimensionality reduction, and k-means clustering. In both pipelines, we compare regular and neural ion images from two different MSI datasets. All tested pipelines could extract underlying spatial patterns, but the neural network-based pipelines provided better assignment of ion images, with more fine-grained clusters, and greater consistency in the spatial structures assigned to individual clusters. Additionally, we introduce the Relative Isotope Ratio metric to quantitatively evaluate clustering quality. The resulting scores show that isotopical m/z values are more often clustered together in the neural network-based pipeline, indicating improved clustering outcomes. The usefulness of neural ion images extends beyond clustering towards a generic framework to incorporate spatial information into any MSI-focused machine learning pipeline, both supervised and unsupervised. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.25.267021v1?rss=1 Authors: Kurtenbach, S., Dollar, J. J., Durante, M. A., Harbour, J. W. Abstract: Single cell RNA sequencing (scRNA-seq) has been a transformative technology in many research fields. Dimensional reduction techniques such as UMAP and tSNE are used to visualize scRNA-seq data in two or three dimensions in order for cells to be clustered in biologically meaningful ways. Subsequently, gene expression is frequently mapped onto these plots to show the distribution of expression across cell types. However, plotting each cell with only one color leads to repetitive and unintuitive representations. Here, we present Pie Party, which allows scRNA-seq data to be plotted such that every cell is represented as a pie chart, where every slice in the pie charts correspond to the gene expression of individual genes, which allows for the simultaneous visualization of the expression of multiple genes and gene networks. The resulting figures are information dense, space efficient and highly intuitive. PieParty is publicly available on GitHub at https://github.com/harbourlab/PieParty. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.248278v1?rss=1 Authors: Kern, A. D., Coffing, G. C., Battey, C. J. Abstract: Dimensionality reduction is a common tool for visualization and inference of population structure from genotypes, but popular methods either return too many dimensions for easy plotting (PCA) or fail to preserve global geometry (t-SNE and UMAP). Here we explore the utility of variational autoencoders (VAEs) -- generative machine learning models in which a pair of neural networks seek to first compress and then recreate the input data -- for visualizing population genetic variation. VAEs incorporate non-linear relationships, allow users to define the dimensionality of the latent space, and in our tests preserve global geometry better than t-SNE and UMAP. Our implementation, which we call popvae, is available as a command-line python program at github.com/kr-colab/popvae. The approach yields latent embeddings that capture subtle aspects of population structure in humans and Anopheles mosquitoes, and can generate artificial genotypes characteristic of a given sample or population. Copy rights belong to original authors. Visit the link for more info