{"id":15216,"date":"2024-01-26T14:08:52","date_gmt":"2024-01-26T13:08:52","guid":{"rendered":"https:\/\/sano.science\/?post_type=people&p=15216"},"modified":"2026-07-21T16:16:57","modified_gmt":"2026-07-21T14:16:57","slug":"jakub-klimczak","status":"publish","type":"people","link":"https:\/\/sano.science\/people\/jakub-klimczak\/","title":{"rendered":"Jakub Klimczak"},"excerpt":{"rendered":"

Master’s Student in Extreme-scale Data Computing<\/p>\n","protected":false},"featured_media":15217,"template":"","people_teams":[24],"class_list":["post-15216","people","type-people","status-publish","has-post-thumbnail","hentry","people_teams-alumni"],"yoast_head":"\nJakub Klimczak - Centre for Computational Personalized Medicine<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sano.science\/people\/jakub-klimczak\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Jakub Klimczak\" \/>\n<meta property=\"og:description\" content=\"Master's Student in Extreme-scale Data Computing\" \/>\n<meta property=\"og:url\" content=\"https:\/\/sano.science\/people\/jakub-klimczak\/\" \/>\n<meta property=\"og:site_name\" content=\"Centre for Computational Personalized Medicine\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/sano.science\/\" \/>\n<meta property=\"article:modified_time\" content=\"2026-07-21T14:16:57+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/sano.science\/wp-content\/uploads\/2024\/01\/jakub_klimczak.png\" \/>\n\t<meta property=\"og:image:width\" content=\"350\" \/>\n\t<meta property=\"og:image:height\" content=\"350\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@sanoscience\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/sano.science\\\/people\\\/jakub-klimczak\\\/\",\"url\":\"https:\\\/\\\/sano.science\\\/people\\\/jakub-klimczak\\\/\",\"name\":\"Jakub Klimczak - 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He joined Sano, working with Dr. Ahmed’s team to contribute to his master’s thesis. His interests span various areas of computer science, including software development and the fields of AI, ML, and data analysis. Outside of academia, he is passionate about traveling, history, and mountain hiking.<\/p>\n","email":"","position_with_team":{"text_before_link":"Master's Student in","link_text":"Extreme-scale Data Computing","text_after_link":"","link":"https:\/\/sano.science\/research-teams\/extreme-scale-data-and-computing\/"},"social_media":false,"tabs":false,"quote":"","publications":[{"ID":32176,"post_author":"8","post_date":"2026-07-21 16:15:23","post_date_gmt":"2026-07-21 14:15:23","post_content":"<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-XIhDT7\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Interpreting machine learning models trained on molecular data remains challenging, particularly at the level of individual atoms. Although many attribution methods can indicate which atoms influence a prediction, the field still lacks standardized benchmarks for determining whether these explanations are chemically and structurally meaningful.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-w7fPSA\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">To address this gap, this work introduces a controlled benchmark based on rule-derived pharmacophore annotations. Predefined geometric constraints describe the spatial arrangement of functional features within a molecule and provide reference atom sets against which model explanations can be evaluated.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-pY3VG2\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">The benchmark is accompanied by PharmacoScore, a metric that quantifies how closely atom-level attributions align with these pharmacophore-derived references. The framework was used to compare explanation methods across several model families, ranging from fragment-based approaches to distance-aware transformers that explicitly encode interatomic geometry.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-IljwbN\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">Distance-aware transformers consistently achieved higher PharmacoScore values, indicating that the atoms emphasized by their explanations more closely reflected the expected spatial relationships. Together, the benchmark and PharmacoScore provide a unified framework for systematically evaluating and comparing atom-level explainability methods in molecular machine learning.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-2gqUdL\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-gJa0es\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\"><strong>Autors<\/strong>: Adam Su\u0142ek, Jakub Klimczak, Jakub Jo\u0144czyk, Tomasz Kosciolek, Tomasz Danel, Barbara Pucelik<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-RtIONs\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:acf\/button {\"id\":\"block_6a5f7e6dca8e9\",\"name\":\"acf\/button\",\"data\":{\"title\":\"Read the article\",\"_title\":\"field_61d40397c2f0a\",\"button_type\":\"link\",\"_button_type\":\"field_63bbde3b8f0d0\",\"url\":\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S187775032600164X\",\"_url\":\"field_61d4039bc2f0b\",\"button_style\":\"primary\",\"_button_style\":\"field_63872d045d0f0\",\"target\":\"_self\",\"_target\":\"field_63872c705d0ef\",\"button_extra_classes\":\"\",\"_button_extra_classes\":\"field_642beab6a97de\"},\"align\":\"\",\"mode\":\"edit\"} \/-->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-RtIONs\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:image {\"id\":32193,\"sizeSlug\":\"large\",\"linkDestination\":\"none\",\"epAnimationGeneratedClass\":\"edplus_anim-eHjexA\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<figure class=\"wp-block-image size-large eplus-wrapper\"><img src=\"https:\/\/sano.science\/wp-content\/uploads\/2026\/07\/FIRST-TEAM-FENG-FNP-Foundation-for-Polish-Science-1024x88.png\" alt=\"\" class=\"wp-image-32193\"\/><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:spacer {\"height\":\"30px\",\"epAnimationGeneratedClass\":\"edplus_anim-RtIONs\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer eplus-wrapper\"><\/div>\n<!-- \/wp:spacer -->\n\n<!-- wp:paragraph {\"epAnimationGeneratedClass\":\"edplus_anim-BZNiNt\",\"epGeneratedClass\":\"eplus-wrapper\"} -->\n<p class=\" eplus-wrapper\">This publication is one of the outcomes of the FIRST TEAM FENG project\u00a0<a href=\"https:\/\/www.linkedin.com\/company\/foundation-for-polish-science\/\" target=\"_blank\" rel=\"noreferrer noopener\">FNP Foundation for Polish Science<\/a>, under which\u00a0<a href=\"https:\/\/www.linkedin.com\/company\/lukasiewicz-krakow-institute-of-technology\/\" target=\"_blank\" rel=\"noreferrer noopener\">\u0141ukasiewicz \u2013 Krakow Institute of Technology<\/a>\u00a0is developing\u00a0new approaches\u00a0to the identification and evaluation of therapeutic candidates in hormone-dependent breast cancer.\u00a0<\/p>\n<!-- \/wp:paragraph -->","post_title":"Benchmarking\u00a0atom-level\u00a0explainability\u00a0against\u00a0pharmacophore-computed\u00a0labels\u00a0in\u00a0molecular\u00a0machine\u00a0learning","post_excerpt":"In: Journal of Computational Science, 2026","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"benchmarking-atom-level-explainability-against-pharmacophore-computed-labels-in-molecular-machine-learning","to_ping":"","pinged":"","post_modified":"2026-07-22 11:36:50","post_modified_gmt":"2026-07-22 09:36:50","post_content_filtered":"","post_parent":0,"guid":"https:\/\/sano.science\/?post_type=research&p=32176","menu_order":0,"post_type":"research","post_mime_type":"","comment_count":"0","filter":"raw"}]},"_links":{"self":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/15216","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people"}],"about":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/types\/people"}],"version-history":[{"count":6,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/15216\/revisions"}],"predecessor-version":[{"id":32188,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people\/15216\/revisions\/32188"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media\/15217"}],"wp:attachment":[{"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/media?parent=15216"}],"wp:term":[{"taxonomy":"people_teams","embeddable":true,"href":"https:\/\/sano.science\/index.php\/wp-json\/wp\/v2\/people_teams?post=15216"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}