
[{"content":"We have become very good at modeling chemical data, but a prediction only matters once it turns into a real molecule or material. Self-driving labs close that gap by pairing robots with models that decide what to try next. Automation also improves the data itself: cheaper, more consistent and easier to replicate. U of T has one of the densest clusters of SDLs anywhere. We expect the line between experimental and computational chemists to fade. The chemist of the future will program a robot to run experiments while modeling the chemistry behind them.\n","externalUrl":null,"permalink":"/research/topics/self-driving-labs/","section":"Research","summary":"","title":"Self-Driving Laboratories","type":"research"},{"content":"Whenever we care about how things relate, graphs are a natural language: objects become nodes and relationships become edges. Chemistry is full of relationships at every scale, from atoms bonding into molecules to enzymes, metabolic networks and even tequila production. How you set up the graph often decides whether a model succeeds, because it encodes the right priors. We study these choices and how to build them into graph neural networks and transformers alike.\n","externalUrl":null,"permalink":"/research/topics/graphs/","section":"Research","summary":"","title":"Graphs","type":"research"},{"content":"Modeling is rarely the hardest part anymore. More often the bottleneck is framing the right problem and finding the data to answer it. Data-centric AI starts from a simple observation: progress happens one dataset at a time. This matters more in chemistry than in images or text, because experimental data is scarce, expensive and scattered across labs. A large part of our work is curating, generating and releasing datasets and benchmarks that let the field measure real progress.\n","externalUrl":null,"permalink":"/research/topics/datacentric-ai/","section":"Research","summary":"","title":"Data-Centric AI","type":"research"},{"content":"Perfumes, shampoos, foods and fuels are all mixtures, yet most machine learning in chemistry still studies one molecule at a time. Mixtures decide how drugs dissolve, how fuels ignite and how electrolytes move ions. The space of possible blends explodes with each added component, so exhaustive experiments are out of reach. We study how to represent mixtures well: which symmetries to build in, whether one representation can serve many tasks, and when physics helps.\n","externalUrl":null,"permalink":"/research/topics/mixtures/","section":"Research","summary":"","title":"Mixtures","type":"research"},{"content":"Machine learning can see and hear, but it has barely started to smell. Olfaction is our guide to the chemical world, and digitizing it means understanding how small molecules become percepts. In 2019 we sketched a map of odor space, then spent three years testing it: with human panels smelling new molecules, in the search for mosquito repellents, and against metabolism. Much of what we call flavor is retronasal smell, so food is part of the story too.\n","externalUrl":null,"permalink":"/research/topics/olfaction/","section":"Research","summary":"","title":"Olfaction \u0026 Sensory AI","type":"research"},{"content":"Proteins and enzymes do the chemistry of life. Enzymes speed up reactions by many orders of magnitude and chain together into metabolic networks that build everything a cell needs. Many of nature\u0026rsquo;s most interesting molecules come from biosynthetic gene clusters, sets of genes that encode an entire assembly line. We model enzymes, their kinetics and the networks they form. We are lucky to sit just below the BioZone, a huge collaborative lab space for bioengineering.\n","externalUrl":null,"permalink":"/research/topics/proteins/","section":"Research","summary":"","title":"Proteins \u0026 Enzymes","type":"research"},{"content":"Small molecules are the workhorses of chemistry: drugs, dyes, fragrances, pesticides and the building blocks of materials. Estimates put the number of drug-like molecules around 10⁶⁰, far more than anyone could make or test. We build models that learn useful representations of molecules, including their quantum and stereoelectronic character, and use them to search this space with intent. The goal is to propose molecules worth making and to explain why the model chose them.\n","externalUrl":null,"permalink":"/research/topics/small-molecules/","section":"Research","summary":"","title":"Small Molecules","type":"research"},{"content":"Molecules are everywhere, so their effects show up across many systems and scales: solar cells, solutions, crystals, metal-organic frameworks and batteries. Materials add a layer that molecular models miss, since performance depends on composition, structure and processing history. We carry ideas from molecules and mixtures into this setting and pair them with automated platforms, so predictions become real candidates, such as new organic laser materials.\n","externalUrl":null,"permalink":"/research/topics/materials/","section":"Research","summary":"","title":"Materials","type":"research"},{"content":"","date":"1 December 2026","externalUrl":null,"permalink":"/tags/ai/","section":"Tags","summary":"","title":"Ai","type":"tags"},{"content":"","date":"1 December 2026","externalUrl":null,"permalink":"/authors/anna-t.-thomas/","section":"Authors","summary":"","title":"Anna T. Thomas","type":"authors"},{"content":"","date":"1 December 2026","externalUrl":null,"permalink":"/authors/","section":"Authors","summary":"","title":"Authors","type":"authors"},{"content":"","date":"1 December 2026","externalUrl":null,"permalink":"/authors/benjamin-sanchez-lengeling/","section":"Authors","summary":"","title":"Benjamin Sanchez-Lengeling","type":"authors"},{"content":"","date":"1 December 2026","externalUrl":null,"permalink":"/authors/caroline-cotto/","section":"Authors","summary":"","title":"Caroline Cotto","type":"authors"},{"content":"","date":"1 December 2026","externalUrl":null,"permalink":"/","section":"Chemical Cognition Lab","summary":"","title":"Chemical Cognition Lab","type":"page"},{"content":"","date":"1 December 2026","externalUrl":null,"permalink":"/publications/","section":"Publications","summary":"","title":"Publications","type":"publications"},{"content":"","date":"1 December 2026","externalUrl":null,"permalink":"/authors/sohum-patnaik/","section":"Authors","summary":"","title":"Sohum Patnaik","type":"authors"},{"content":"","date":"1 December 2026","externalUrl":null,"permalink":"/tags/","section":"Tags","summary":"","title":"Tags","type":"tags"},{"content":"Introduces TasteBench, a multimodal benchmark and competition for sensory prediction across 21K+ human evaluations on 215 plant-based foods and 15K flavor molecules, providing computational proxies to accelerate sustainable food discovery.\n","date":"1 December 2026","externalUrl":"https://openreview.net/forum?id=k3djmwrAXd","permalink":"/publications/thomas2026tastebench/","section":"Publications","summary":"","title":"TasteBench: Multimodal Benchmark for Sensory Prediction, from Molecules to Sustainable Foods","type":"publications"},{"content":"Couples deep learning turnover number predictions with stochastic simulated annealing to parameterize enzyme-constrained genome-scale models across 93 organisms, resolving long-standing biocatalytic data sparsity.\n","date":"6 October 2026","externalUrl":"https://doi.org/10.64898/2026.03.14.711833","permalink":"/publications/barghout2026kingems/","section":"Publications","summary":"","title":"kinGEMs: A scalable framework for resource-constrained models through stochastic tuning of deep learning-predicted kinetic parameters","type":"publications"},{"content":"","date":"6 October 2026","externalUrl":null,"permalink":"/authors/lya-chinas-serrano/","section":"Authors","summary":"","title":"Lya Chinas Serrano","type":"authors"},{"content":"","date":"6 October 2026","externalUrl":null,"permalink":"/authors/radhakrishnan-mahadevan/","section":"Authors","summary":"","title":"Radhakrishnan Mahadevan","type":"authors"},{"content":"","date":"6 October 2026","externalUrl":null,"permalink":"/authors/rana-a.-barghout/","section":"Authors","summary":"","title":"Rana A. Barghout","type":"authors"},{"content":"[WIP] This section is under active development.\nThis document specifies the visual identity, typography hierarchy, color palette, and design tokens for the lab website, slide decks, and digital communications. Institutional references follow the University of Toronto Brand Portal.\n1. Color System # Institutional Primary Anchor # UofT Navy Blue: #002A5C Lab Identity Tones # Lab Dark Pink (Rosa Mexicano): #E7298A Lab Dark Green (Cactus): #66A61E UofT Supporting Accents (Full Extended Set) # Cool Tones # UofT Light Blue: #0072CE UofT Teal: #00828A UofT Slate: #1A3B68 UofT Midnight Blue: #001C3D Warm Tones # UofT Gold: #FFC72C UofT Orange: #E87722 UofT Crimson: #DA291C UofT Burgundy: #7A003C Rich Tones # UofT Purple: #4F2D7F UI Canvas \u0026amp; Neutrals # Primary Text: #1E293B Light Canvas: #F8FAFC Dark Canvas: #1C1D1F Divider Gray: #E2E8F0 Interactive Visual Swatches # UofT Navy Blue #002A5C --color-uoft-blue Rosa Mexicano Pink #E7298A --color-lab-pink Cactus Green #66A61E --color-lab-green UofT Light Blue #0072CE --color-uoft-light-blue UofT Teal #00828A --color-uoft-teal UofT Slate #1A3B68 --color-uoft-slate UofT Midnight Blue #001C3D --color-uoft-midnight UofT Gold #FFC72C --color-uoft-gold UofT Orange #E87722 --color-uoft-orange UofT Crimson #DA291C --color-uoft-crimson UofT Burgundy #7A003C --color-uoft-burgundy UofT Purple #4F2D7F --color-uoft-purple Color Palette Tokens # Token Name Color Name Hex Code --color-uoft-blue UofT Navy Blue #002A5C --color-lab-pink Lab Dark Pink (Rosa Mexicano) #E7298A --color-lab-green Lab Dark Green (Cactus) #66A61E --color-uoft-light-blue UofT Light Blue #0072CE --color-uoft-teal UofT Teal #00828A --color-uoft-slate UofT Slate #1A3B68 --color-uoft-midnight UofT Midnight Blue #001C3D --color-uoft-gold UofT Gold #FFC72C --color-uoft-orange UofT Orange #E87722 --color-uoft-crimson UofT Crimson #DA291C --color-uoft-burgundy UofT Burgundy #7A003C --color-uoft-purple UofT Purple #4F2D7F --color-text-main Primary Text #1E293B --color-bg-light Light Canvas #F8FAFC --color-bg-dark Dark Canvas #1C1D1F --color-border Divider Gray #E2E8F0 2. Typography System # Font Families # Display \u0026amp; Titles: Spectral (Serif, weights: 400, 600) Body \u0026amp; UI: Fira Sans (Sans-Serif, weights: 300, 400, 500) Technical \u0026amp; Data: Fira Code (Monospace, weights: 400, 500) Display \u0026 Titles Spectral (Serif) Chemical Cognition Lab reasoning about molecular structures \u0026 chemical representations. Body \u0026 UI Fira Sans Clean, legible sans-serif for UI elements, article body text, cards, and lab documentation. Technical \u0026 Data Fira Code SMILES = \"CC(=O)OC1=CC=CC=C1C(=O)O\" loss = criterion(pred, target) 3. Structural Constraints # Header Titles (\u0026lt;h1\u0026gt; / Slide Titles): Maximum ~41 characters. Formatted as a declarative sentence. Subtitles (\u0026lt;p.lead\u0026gt; / Slide Subtitles): Maximum ~63 characters. Summarizes the core message. 4. Web CSS Tokens # :root { /* Typography */ --font-title: \u0026#39;Spectral\u0026#39;, Georgia, serif; --font-body: \u0026#39;Fira Sans\u0026#39;, -apple-system, BlinkMacSystemFont, sans-serif; --font-code: \u0026#39;Fira Code\u0026#39;, monospace; /* Institutional Primary \u0026amp; Lab Identity */ --color-uoft-blue: #002A5C; --color-lab-pink: #E7298A; --color-lab-green: #66A61E; /* UofT Cool Accents */ --color-uoft-light-blue: #0072CE; --color-uoft-teal: #00828A; --color-uoft-slate: #1A3B68; --color-uoft-midnight: #001C3D; /* UofT Warm Accents */ --color-uoft-gold: #FFC72C; --color-uoft-orange: #E87722; --color-uoft-crimson: #DA291C; --color-uoft-burgundy: #7A003C; /* UofT Rich Accents */ --color-uoft-purple: #4F2D7F; /* Canvas \u0026amp; Neutrals */ --color-text-main: #1E293B; --color-bg-light: #F8FAFC; --color-bg-dark: #1C1D1F; --color-border: #E2E8F0; } 5. Categorical 12-Color Tag \u0026amp; Topic Palette # For scientific topic tags, data graphics, and member research badges, the lab uses a curated 12-color categorical palette across three variations: Dark, Set (Normal), and Pastel.\nThe active UI standard for web badges and tags is the Pastel variation, paired with high-contrast text (#1E293B in light mode, #0F172A in dark mode):\nIndex Color Role Pastel (Active Badge) Dark Set Default Topic / Keyword 0 Teal #9AD7C8 #049D86 #60C2AC datacentric-ai, datasets, bgcs 1 Orange #FAB891 #D0670C #F79250 mixtures, chemical-mixtures 2 Blue #B4C1DD #5C78B6 #8CA0CB graphs 3 Pink #F5B2CC #E52A8F #EE88B3 olfaction 4 Green #C3E792 #75A30A #A6D854 proteins, enzymes 5 Yellow #FFE490 #D9B218 #FFD853 benchmarks 6 Tan #F0D8BA #A97420 #E7C395 reviews 7 Light Blue #A8CEDE #0E7DA0 #78B4CD self-driving-labs, sdls 8 Brick / Rust #D19287 #B55344 #B75748 materials 9 Purple #D0ADD7 #7C3589 #B881C2 small-molecules, molecules 10 Pale Green #CFF4EF #0D8178 #B3EEE6 Fallback / secondary tags 11 Gray #CECECE #666666 #B3B3B3 General keywords - White #FFFFFF #FFFFFF #FFFFFF #ai, molecular-ai (bordered badge) 6. Interaction Principles: Zero Hover Action # The website strictly adheres to a Zero Hover Action invariant:\nNo Physical Movement on Hover: Cards, member photos, buttons, and icons do not translate, elevate, scale, jump, or bounce when hovered (transform: none !important;). Subtle State Changes: Interactive affordances are communicated purely through color transitions, text underline or accent shifts, and subtle background opacity changes. Academic Serenity: This stillness prioritizes calm authority, readability, and accessibility over gamified web trends. 7. Website Architectural \u0026amp; Design Decisions Log # All visual and architectural decisions governing this website are recorded in the repository\u0026rsquo;s permanent log:\nLocation: docs/decisions.md Specification: docs/design_specification.md Whenever modifying layouts, styles, or schemas, contributors must verify compliance against these documents.\n","date":"8 August 2026","externalUrl":null,"permalink":"/culture/aesthetics/","section":"How We Work 🚧","summary":"","title":"Aesthetics [WIP]","type":"culture"},{"content":"[WIP] This handbook is under active development.\nWelcome to the How We Work guide for the Chemical Cognition Lab. This serves as a living handbook for onboarding, computing guidelines, research practices, scientific communication, and lab operations.\nSections \u0026amp; Guides # Aesthetics [WIP]: Visual identity, typography hierarchy, UofT brand palette, and design tokens. Getting Started [WIP]: Onboarding guide, accounts, first week setup. Research Practices [WIP]: Reproducibility, project management, and data management. Computing \u0026amp; Infrastructure [WIP]: GitHub guidelines, Python environments, and cluster execution (Balam, Killarney, Trillium). Communication [WIP]: Lab meetings, paper writing, and scientific presentations. Lab Operations [WIP]: Equipment purchasing, travel reimbursement, and lab procedures. ","date":"8 August 2026","externalUrl":null,"permalink":"/culture/","section":"How We Work 🚧","summary":"","title":"How We Work 🚧","type":"culture"},{"content":"Crowdsources predictive models across 26 international teams in the DREAM Olfactory Challenge, demonstrating that compact semantic representations of single odorants generalize to complex mixture perceptual spaces.\n","date":"1 August 2026","externalUrl":"https://doi.org/10.1073/pnas.2611057123","permalink":"/publications/satarifard2026semantic/","section":"Publications","summary":"","title":"A semantic-based community model for high-fidelity tuning of olfactory mixture distances","type":"publications"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/achilleas-ghinis/","section":"Authors","summary":"","title":"Achilleas Ghinis","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/aharon-ravia/","section":"Authors","summary":"","title":"Aharon Ravia","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/cici-xingyu-zheng/","section":"Authors","summary":"","title":"CiCi Xingyu Zheng","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/gaia-andreoletti/","section":"Authors","summary":"","title":"Gaia Andreoletti","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/jake-albrecht/","section":"Authors","summary":"","title":"Jake Albrecht","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/jiacheng-chen/","section":"Authors","summary":"","title":"Jiacheng Chen","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/jianing-tang/","section":"Authors","summary":"","title":"Jianing Tang","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/jianming-tang/","section":"Authors","summary":"","title":"Jianming Tang","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/jiazhen-he/","section":"Authors","summary":"","title":"Jiazhen He","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/joel-d.-mainland/","section":"Authors","summary":"","title":"Joel D. Mainland","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/laura-sisson/","section":"Authors","summary":"","title":"Laura Sisson","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/liangzhen-pan/","section":"Authors","summary":"","title":"Liangzhen Pan","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/matej-hladi%C5%A1/","section":"Authors","summary":"","title":"Matej Hladiš","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/maxence-lalis/","section":"Authors","summary":"","title":"Maxence Lalis","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/menglong-dong/","section":"Authors","summary":"","title":"Menglong Dong","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/min-zhang/","section":"Authors","summary":"","title":"Min Zhang","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/pablo-meyer/","section":"Authors","summary":"","title":"Pablo Meyer","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/pedro-il%C3%ADdio/","section":"Authors","summary":"","title":"Pedro Ilídio","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/ping-li/","section":"Authors","summary":"","title":"Ping Li","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/qian-shen/","section":"Authors","summary":"","title":"Qian Shen","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/richard-c.-gerkin/","section":"Authors","summary":"","title":"Richard C. Gerkin","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/robbe-dh%CC%81ondt/","section":"Authors","summary":"","title":"Robbe Dh́ondt","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/robert-pellegrino/","section":"Authors","summary":"","title":"Robert Pellegrino","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/siyuan-chen/","section":"Authors","summary":"","title":"Siyuan Chen","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/stephen-yang/","section":"Authors","summary":"","title":"Stephen Yang","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/stijn-vranckx/","section":"Authors","summary":"","title":"Stijn Vranckx","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/tiffany-yang/","section":"Authors","summary":"","title":"Tiffany Yang","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/vahid-satarifard/","section":"Authors","summary":"","title":"Vahid Satarifard","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/wenjie-yin/","section":"Authors","summary":"","title":"Wenjie Yin","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/xuebo-song/","section":"Authors","summary":"","title":"Xuebo Song","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/yang-liu/","section":"Authors","summary":"","title":"Yang Liu","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/yikun-han/","section":"Authors","summary":"","title":"Yikun Han","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/yuan-yuan/","section":"Authors","summary":"","title":"Yuan Yuan","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/yue-hu/","section":"Authors","summary":"","title":"Yue Hu","type":"authors"},{"content":"","date":"1 August 2026","externalUrl":null,"permalink":"/authors/zehua-wang/","section":"Authors","summary":"","title":"Zehua Wang","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/anna-thomas/","section":"Authors","summary":"","title":"Anna Thomas","type":"authors"},{"content":"Comprehensive review articulating an AI-driven framework for sustainable food formulation, spanning perception modeling, multi-omics fermentation engineering, and consumer acceptance.\n","date":"1 July 2026","externalUrl":"https://doi.org/10.1038/s43016-026-01380-7","permalink":"/publications/datta2026artificial/","section":"Publications","summary":"","title":"Artificial intelligence for food innovation","type":"publications"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/bianca-datta/","section":"Authors","summary":"","title":"Bianca Datta","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/dan-jurafsky/","section":"Authors","summary":"","title":"Dan Jurafsky","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/david-l.-kaplan/","section":"Authors","summary":"","title":"David L. Kaplan","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/ellen-kuhl/","section":"Authors","summary":"","title":"Ellen Kuhl","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/giorgia-del-missier/","section":"Authors","summary":"","title":"Giorgia Del Missier","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/ilias-tagkopoulos/","section":"Authors","summary":"","title":"Ilias Tagkopoulos","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/karim-pichara/","section":"Authors","summary":"","title":"Karim Pichara","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/kristina-gligori%C4%87/","section":"Authors","summary":"","title":"Kristina Gligorić","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/lisa-neidhardt/","section":"Authors","summary":"","title":"Lisa Neidhardt","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/markus-j.-buehler/","section":"Authors","summary":"","title":"Markus J. Buehler","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/matthew-watson/","section":"Authors","summary":"","title":"Matthew Watson","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/miek-schlangen/","section":"Authors","summary":"","title":"Miek Schlangen","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/tags/reviews/","section":"Tags","summary":"","title":"Reviews","type":"tags"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/rodrigo-ledesma-amaro/","section":"Authors","summary":"","title":"Rodrigo Ledesma-Amaro","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/skyler-r.-st.-pierre/","section":"Authors","summary":"","title":"Skyler R. St. Pierre","type":"authors"},{"content":"","date":"1 July 2026","externalUrl":null,"permalink":"/authors/yvonne-chow/","section":"Authors","summary":"","title":"Yvonne Chow","type":"authors"},{"content":"","date":"1 January 2026","externalUrl":null,"permalink":"/authors/abhiram-chalamalasetty/","section":"Authors","summary":"","title":"Abhiram Chalamalasetty","type":"authors"},{"content":"","date":"1 January 2026","externalUrl":null,"permalink":"/authors/adesh-rohan-mishra/","section":"Authors","summary":"","title":"Adesh Rohan Mishra","type":"authors"},{"content":"","date":"1 January 2026","externalUrl":null,"permalink":"/authors/adrian-jinich/","section":"Authors","summary":"","title":"Adrian Jinich","type":"authors"},{"content":"","date":"1 January 2026","externalUrl":null,"permalink":"/authors/eric-sivonxay/","section":"Authors","summary":"","title":"Eric Sivonxay","type":"authors"},{"content":"","date":"1 January 2026","externalUrl":null,"permalink":"/authors/evan-walter-clark-spotte-smith/","section":"Authors","summary":"","title":"Evan Walter Clark Spotte-Smith","type":"authors"},{"content":"","date":"1 January 2026","externalUrl":null,"permalink":"/authors/fleur-m.-ferguson/","section":"Authors","summary":"","title":"Fleur M. Ferguson","type":"authors"},{"content":"Develops differentiable heterogeneous graph neural network surrogates for kinetic Monte Carlo simulations of core-shell upconverting nanoparticles, achieving 6.5-fold experimental emission enhancement via gradient ascent.\n","date":"1 January 2026","externalUrl":"https://doi.org/10.1038/s43588-025-00917-3","permalink":"/publications/sivonxay2026gradient/","section":"Publications","summary":"","title":"Gradient-based optimization of complex nanoparticle heterostructures enabled by deep learning on heterogeneous graphs","type":"publications"},{"content":"","date":"1 January 2026","externalUrl":null,"permalink":"/authors/jos%C3%A9-manuel-barraza-chavez/","section":"Authors","summary":"","title":"José Manuel Barraza-Chavez","type":"authors"},{"content":"","date":"1 January 2026","externalUrl":null,"permalink":"/authors/lucas-attia/","section":"Authors","summary":"","title":"Lucas Attia","type":"authors"},{"content":"","date":"1 January 2026","externalUrl":null,"permalink":"/authors/robert-bardhan/","section":"Authors","summary":"","title":"Robert Bardhan","type":"authors"},{"content":"","date":"1 January 2026","externalUrl":null,"permalink":"/authors/samuel-m.-blau/","section":"Authors","summary":"","title":"Samuel M. Blau","type":"authors"},{"content":"Pairs a GINE molecular graph encoder with frozen ESM-C protein language model embeddings via cross-attention to predict covalent target engagement across pathogen proteomes with few-shot transfer.\n","date":"1 January 2026","externalUrl":"https://www.biorxiv.org/content/10.64898/2026.01.04.697588v1","permalink":"/publications/chalamalasetty2026tubercuprobe/","section":"Publications","summary":"","title":"TubercuProbe: A cross-attention graph-sequence model for cross-species chemoproteomic discovery in Mycobacterium tuberculosis","type":"publications"},{"content":"","date":"1 January 2026","externalUrl":null,"permalink":"/authors/xiaojing-xia/","section":"Authors","summary":"","title":"Xiaojing Xia","type":"authors"},{"content":"Establishes the first unified open-source benchmark suite spanning 11 diverse chemical mixture domains with standardized splitting protocols and deep learning baseline models.\n","date":"1 December 2025","externalUrl":"https://arxiv.org/abs/2506.12231","permalink":"/publications/rajaonson2025chemixhub/","section":"Publications","summary":"","title":"CheMixHub: Datasets and benchmarks for chemical mixture property prediction","type":"publications"},{"content":"","date":"1 December 2025","externalUrl":null,"permalink":"/authors/ella-miray-rajaonson/","section":"Authors","summary":"","title":"Ella Miray Rajaonson","type":"authors"},{"content":"","date":"1 December 2025","externalUrl":null,"permalink":"/authors/luis-martin-mej%C3%ADa-mendoza/","section":"Authors","summary":"","title":"Luis Martin Mejía Mendoza","type":"authors"},{"content":"","date":"1 December 2025","externalUrl":null,"permalink":"/authors/mahyar-rajabi-kochi/","section":"Authors","summary":"","title":"Mahyar Rajabi Kochi","type":"authors"},{"content":"","date":"1 December 2025","externalUrl":null,"permalink":"/authors/seyed-mohamad-moosavi/","section":"Authors","summary":"","title":"Seyed Mohamad Moosavi","type":"authors"},{"content":"A foundational pedagogical text and monograph introducing structural, geometric, and kinetic graph neural networks for molecules, macromolecular proteins, and complex biological pathways.\n","date":"1 September 2025","externalUrl":"https://doi.org/10.1021/acsinfocus.7e9017","permalink":"/publications/barrazachavez2025graph/","section":"Publications","summary":"","title":"Graph Data Modeling: Molecules, Proteins, \u0026 Chemical Processes","type":"publications"},{"content":"","date":"1 September 2025","externalUrl":null,"permalink":"/authors/ricardo-almada-monter/","section":"Authors","summary":"","title":"Ricardo Almada-Monter","type":"authors"},{"content":"","date":"1 August 2025","externalUrl":null,"permalink":"/authors/al%C3%A1n-aspuru-guzik/","section":"Authors","summary":"","title":"Alán Aspuru-Guzik","type":"authors"},{"content":"","date":"1 August 2025","externalUrl":null,"permalink":"/authors/brian-k.-lee/","section":"Authors","summary":"","title":"Brian K. Lee","type":"authors"},{"content":"","date":"1 August 2025","externalUrl":null,"permalink":"/authors/cher-tian-ser/","section":"Authors","summary":"","title":"Cher Tian Ser","type":"authors"},{"content":"Introduces POMMix, incorporating inductive perceptual pooling operations on molecular graphs to predict the non-linear emergent sensory properties of multi-component odorant mixtures.\n","date":"1 August 2025","externalUrl":"https://doi.org/10.1088/2632-2153/adfffc","permalink":"/publications/tom2025olfactory/","section":"Publications","summary":"","title":"Does this smell the same? Learning representations of olfactory mixtures using inductive biases","type":"publications"},{"content":"","date":"1 August 2025","externalUrl":null,"permalink":"/authors/gary-tom/","section":"Authors","summary":"","title":"Gary Tom","type":"authors"},{"content":"","date":"1 August 2025","externalUrl":null,"permalink":"/authors/hyun-suk-park/","section":"Authors","summary":"","title":"Hyun Suk Park","type":"authors"},{"content":"Demonstrates that pairwise ranking surrogates systematically outperform point regression models in Bayesian optimization for molecular property design, mitigating miscalibration and heteroskedastic noise.\n","date":"1 August 2025","externalUrl":"https://doi.org/10.1063/5.0272663","permalink":"/publications/tom2025ranking/","section":"Publications","summary":"","title":"Ranking over regression for Bayesian optimization and molecule selection","type":"publications"},{"content":"","date":"1 August 2025","externalUrl":null,"permalink":"/authors/samantha-corapi/","section":"Authors","summary":"","title":"Samantha Corapi","type":"authors"},{"content":"","date":"1 August 2025","externalUrl":null,"permalink":"/authors/stanley-lo/","section":"Authors","summary":"","title":"Stanley Lo","type":"authors"},{"content":"Leverages graph neural representations from the Principal Odor Map (POM) to discover potent, novel repellent chemotypes validated experimentally against multiple mosquito disease vectors.\n","date":"1 July 2025","externalUrl":"https://doi.org/10.1093/chemse/bjaf021","permalink":"/publications/chemsenses2025repellents/","section":"Publications","summary":"","title":"A deep learning and digital archaeology approach for mosquito repellent discovery","type":"publications"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/alexander-b.-wiltschko/","section":"Authors","summary":"","title":"Alexander B. Wiltschko","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/carlos-ruiz/","section":"Authors","summary":"","title":"Carlos Ruiz","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/d.-michael-ando/","section":"Authors","summary":"","title":"D. Michael Ando","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/jacob-n.-sanders/","section":"Authors","summary":"","title":"Jacob N. Sanders","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/jeffrey-a.-riffell/","section":"Authors","summary":"","title":"Jeffrey A. Riffell","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/jennifer-n.-wei/","section":"Authors","summary":"","title":"Jennifer N. Wei","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/koen-j.-dechering/","section":"Authors","summary":"","title":"Koen J. Dechering","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/kurt-m.-groetsch/","section":"Authors","summary":"","title":"Kurt M. Groetsch","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/luuk-berning/","section":"Authors","summary":"","title":"Luuk Berning","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/marnix-vlot/","section":"Authors","summary":"","title":"Marnix Vlot","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/martijn-w.-vos/","section":"Authors","summary":"","title":"Martijn W. Vos","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/rob-w.-m.-henderson/","section":"Authors","summary":"","title":"Rob W. M. Henderson","type":"authors"},{"content":"","date":"1 July 2025","externalUrl":null,"permalink":"/authors/wesley-w.-qian/","section":"Authors","summary":"","title":"Wesley W. Qian","type":"authors"},{"content":"Introduces Stereoelectronics-Infused Molecular Graphs (SIMGs) and neural surrogate estimators that encode Natural Bond Orbital interactions into molecular graphs in seconds, boosting property prediction accuracy.\n","date":"1 January 2025","externalUrl":"https://doi.org/10.1038/s42256-025-01031-9","permalink":"/publications/reschuetzegger2025stereoelectronics/","section":"Publications","summary":"","title":"Advancing molecular machine learning representations with stereoelectronics-infused molecular graphs","type":"publications"},{"content":"","date":"1 January 2025","externalUrl":null,"permalink":"/authors/daniil-a.-boiko/","section":"Authors","summary":"","title":"Daniil A. 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Burke","type":"authors"},{"content":"","date":"1 May 2024","externalUrl":null,"permalink":"/authors/martin-seifrid/","section":"Authors","summary":"","title":"Martin Seifrid","type":"authors"},{"content":"","date":"1 May 2024","externalUrl":null,"permalink":"/authors/masashi-mamada/","section":"Authors","summary":"","title":"Masashi Mamada","type":"authors"},{"content":"","date":"1 May 2024","externalUrl":null,"permalink":"/authors/mason-guy/","section":"Authors","summary":"","title":"Mason Guy","type":"authors"},{"content":"","date":"1 May 2024","externalUrl":null,"permalink":"/authors/mohammad-haddadnia/","section":"Authors","summary":"","title":"Mohammad Haddadnia","type":"authors"},{"content":"","date":"1 May 2024","externalUrl":null,"permalink":"/authors/n.-m.-anoop-krishnan/","section":"Authors","summary":"","title":"N. M. Anoop Krishnan","type":"authors"},{"content":"","date":"1 May 2024","externalUrl":null,"permalink":"/authors/nicholas-h.-angello/","section":"Authors","summary":"","title":"Nicholas H. Angello","type":"authors"},{"content":"","date":"1 May 2024","externalUrl":null,"permalink":"/authors/oscar-guti%C3%A9rrez-espinoza/","section":"Authors","summary":"","title":"Oscar Gutiérrez-Espinoza","type":"authors"},{"content":"Synthesizes key outcomes from the AI4Mat workshop at NeurIPS 2023, charting trajectories for self-driving laboratories, simulation-to-materials workflows, and language models for physical science.\n","date":"1 May 2024","externalUrl":"https://doi.org/10.1039/d4dd90010c","permalink":"/publications/miret2024perspective/","section":"Publications","summary":"","title":"Perspective on AI for accelerated materials design at the AI4Mat-2023 workshop at NeurIPS 2023","type":"publications"},{"content":"","date":"1 May 2024","externalUrl":null,"permalink":"/authors/rafal-roszak/","section":"Authors","summary":"","title":"Rafal Roszak","type":"authors"},{"content":"","date":"1 May 2024","externalUrl":null,"permalink":"/authors/riley-j.-hickman/","section":"Authors","summary":"","title":"Riley J. 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Present progress, literature reviews, or project proposals. Scientific Writing: Draft manuscripts using clear language and reproducible figures. ","externalUrl":null,"permalink":"/culture/communication/","section":"How We Work 🚧","summary":"","title":"Communication [WIP]","type":"culture"},{"content":"[WIP] This section is under active development.\nComputing \u0026amp; Infrastructure # Our lab utilizes local workstations and HPC clusters for machine learning and robotic workflows.\nEnvironment Management # Always manage dependencies via Mamba/Conda. Standard commands must execute within the dedicated environment.\nCluster Guidelines # Refer to cluster execution skills (balam-cluster, killarney-cluster, trillium-cluster) for Slurm job submit templates.\n","externalUrl":null,"permalink":"/culture/computing/","section":"How We Work 🚧","summary":"","title":"Computing \u0026 Infrastructure [WIP]","type":"culture"},{"content":"","externalUrl":null,"permalink":"/people/dumebi-nasa-okolie/","section":"People","summary":"","title":"Dumebi Nasa-Okolie","type":"people"},{"content":"TODO\n","externalUrl":null,"permalink":"/people/edward-lombo/","section":"People","summary":"","title":"Edward Lombo","type":"people"},{"content":"TODO\n","externalUrl":null,"permalink":"/people/elizabeth-reynolds/","section":"People","summary":"","title":"Elizabeth Reynolds","type":"people"},{"content":"","externalUrl":null,"permalink":"/people/ella-rajaonson/","section":"People","summary":"","title":"Ella M. Rajaonson","type":"people"},{"content":"[WIP] This section is under active development.\nGetting Started # Welcome to the lab! Follow these steps during your first week:\nSet up communication channels: Join our lab Slack and mailing list. Access computing clusters: Request accounts on our compute clusters (Balam, Killarney). Configure local environment: Install Conda/Mamba and set up Python standard environments. ","externalUrl":null,"permalink":"/culture/getting-started/","section":"How We Work 🚧","summary":"","title":"Getting Started [WIP]","type":"culture"},{"content":"","externalUrl":null,"permalink":"/people/jessica-anirisaihan/","section":"People","summary":"","title":"Jessica Anirisaihan","type":"people"},{"content":" We are recruiting grad students (MSc and PhD) and postdocs, as well as undergrad and master's students for research projects. Who we\u0026rsquo;re looking for # We want people who care about what we\u0026rsquo;re trying to do here. Our work mixes three things:\nScience: Chemistry, biochemistry, or problems that touch people\u0026rsquo;s lives. Small molecules, proteins, DNA, and sometimes no molecules at all. AI: Be able to think about data in a mathy/statistical way. Engineering mindset: Solving problems, writing good code, and working well with people. It\u0026rsquo;s rare to find someone who has all three. Be good at one or two and want to get better at the rest.\nNon-traditional paths are welcome # My path wasn\u0026rsquo;t a straight line. I grew up in Guanajuato, Mexico, went to public school, and started university studying math because I wanted to make video games. I played in two electroacoustic bands, worked as a barista for a year, and was the oldest PhD student in my cohort. Along the way I modelled placentas, did quantum chemistry, spent five years at Google teaching computers to predict smell, and then started this lab.\nDon\u0026rsquo;t hide the things that got you here: a different field, time in industry, a career change, a gap, or a school nobody has heard of. It\u0026rsquo;s all part of your story, and I\u0026rsquo;d like to hear it.\nHow to reach out # Email me at ben.sanchez@utoronto.ca with [Prospective] in the subject line, including:\nWhich paper, project, or idea caught your eye, and why. Which part of the lab handbook you find interesting. Why you want to work on these problems. Any external funding (scholarships or fellowships). Your CV, plus links to code or projects you\u0026rsquo;re proud of. Write it yourself # I want to hear how you think. No AI-written emails.\nSadly, email sometimes gets overwhelming, so it is hard to respond always. If you haven\u0026rsquo;t heard back in two weeks, please send a nudge.\n","externalUrl":null,"permalink":"/contact/","section":"Chemical Cognition Lab","summary":"","title":"Join the Chemical Cognition Lab","type":"page"},{"content":"TODO\n","externalUrl":null,"permalink":"/people/jose-manuel-barraza/","section":"People","summary":"","title":"Jose Manuel Barraza","type":"people"},{"content":"TODO\n","externalUrl":null,"permalink":"/people/kevin-zhu/","section":"People","summary":"","title":"Kevin Zhu","type":"people"},{"content":"[WIP] This section is under active development.\nLab Operations # Find procedures for equipment purchases, conference travel grants, and administrative inquiries.\n","externalUrl":null,"permalink":"/culture/lab-operations/","section":"How We Work 🚧","summary":"","title":"Lab Operations [WIP]","type":"culture"},{"content":"TODO\n","externalUrl":null,"permalink":"/people/paola-driza/","section":"People","summary":"","title":"Paola Driza","type":"people"},{"content":"","externalUrl":null,"permalink":"/people/","section":"People","summary":"","title":"People","type":"people"},{"content":"","externalUrl":null,"permalink":"/people/rana-barghout/","section":"People","summary":"","title":"Rana A. Barghout","type":"people"},{"content":"","externalUrl":null,"permalink":"/research/","section":"Research","summary":"","title":"Research","type":"research"},{"content":"[WIP] This section is under active development.\nResearch Practices # We prioritize rigorous, reproducible scientific software development.\nData DAG: Raw data (data/raw/) is strictly read-only. Code Standards: Follow the ChemCognition coding philosophy skill guidelines. Publication Data: Publish code and datasets alongside preprints. 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