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Correlation is not causation. As simple as this widely agreed-upon statement may seem, scientifically defining causality and using it to drive our modern biomedical research is immensely challenging. In this perspective, we attempt to…

Molecular Networks · Quantitative Biology 2024-01-19 Sebastian Lobentanzer , Pablo Rodriguez-Mier , Stefan Bauer , Julio Saez-Rodriguez

Recent progress of deep generative models in the vision and language domain has stimulated significant interest in more structured data generation such as molecules. However, beyond generating new random molecules, efficient exploration and…

Machine Learning · Computer Science 2024-11-08 Guanghao Wei , Yining Huang , Chenru Duan , Yue Song , Yuanqi Du

A recent Science paper (Bushdid et al, 2014)[1] proposed that humans can discriminate between at least a trillion olfactory stimuli. Here we show that this claim is the result of a fragile estimation framework capable of producing nearly…

Neurons and Cognition · Quantitative Biology 2015-02-19 Richard C. Gerkin , Jason B. Castro

The limited extrapolative power of structure-based machine learning (ML) models is a critical bottleneck in chemical discovery, particularly for industrial R&D, where navigating uncharted chemical space to find next-generation materials or…

Machine learning-based design has gained traction in the sciences, most notably in the design of small molecules, materials, and proteins, with societal implications spanning drug development and manufacturing, plastic degradation, and…

Machine Learning · Computer Science 2025-04-04 Clara Fannjiang , Jennifer Listgarten

We investigate the extent to which modern, neural language models are susceptible to structural priming, the phenomenon whereby the structure of a sentence makes the same structure more probable in a follow-up sentence. We explore how…

Computation and Language · Computer Science 2022-06-30 Arabella Sinclair , Jaap Jumelet , Willem Zuidema , Raquel Fernández

Olfactory cues can enhance immersion in interactive media, yet smell remains rare because it is difficult to author and synchronize with dynamic video. Prior olfactory interfaces rely on designer triggers and fixed event-to-odor mappings…

Human-Computer Interaction · Computer Science 2026-01-28 Kaicheng Wang , Kevin Zhongyang Shao , Ruiqi Chen , Sep Makhsous , Denise Wilson

Glass formation is one of the most interesting phenomena in the condensed matter field. Considerable effort has gone into understanding and predicting the glass formability. However, the previous prediction requires the glass first made…

Materials Science · Physics 2019-02-12 R. Dai , R. Ashcraft , A. K. Gangopadhyay , K. F. Kelton

Designing new chemical compounds with desired pharmaceutical properties is a challenging task and takes years of development and testing. Still, a majority of new drugs fail to prove efficient. Recent success of deep generative modeling…

Machine Learning · Computer Science 2021-09-15 Karina Zadorozhny , Lada Nuzhna

Distributional models are derived from co-occurrences in a corpus, where only a small proportion of all possible plausible co-occurrences will be observed. This results in a very sparse vector space, requiring a mechanism for inferring…

Computation and Language · Computer Science 2016-08-25 Thomas Kober , Julie Weeds , Jeremy Reffin , David Weir

Reliable predictions of the behaviour of chemical systems are essential across many industries, from nanoscale engineering over validation of advanced materials to nanotoxicity assessment in health and medicine. For the future we therefore…

Chemical Physics · Physics 2021-03-05 Judith B. Rommel

Public olfaction datasets are small and fragmented across single molecules and mixtures, limiting learning of generalizable odor representations. Recent works either learn single-molecule embeddings or address mixtures via similarity or…

Machine Learning · Computer Science 2026-01-28 Dayoung Kang , JongWon Kim , Jiho Park , Keonseock Lee , Ji-Woong Choi , Jinhyun So

Recent advances in large language models (LLMs) have accelerated their adoption in software engineering contexts. However, concerns persist about the structural quality of the code they produce. In particular, LLMs often replicate poor…

Software Engineering · Computer Science 2026-01-19 Alejandro Velasco , Daniel Rodriguez-Cardenas , Dipin Khati , David N. Palacio , Luftar Rahman Alif , Denys Poshyvanyk

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations…

Machine Learning · Computer Science 2025-05-26 Jinho Chang , Jong Chul Ye

Providing explainable molecular property predictions is critical for many scientific domains, such as drug discovery and material science. Though transformer-based language models have shown great potential in accurate molecular property…

Machine Learning · Computer Science 2026-01-14 Zhenzhong Wang , Zehui Lin , Wanyu Lin , Ming Yang , Minggang Zeng , Kay Chen Tan

Discovery of atomistic systems with desirable properties is a major challenge in chemistry and material science. Here we introduce a novel, autoregressive, convolutional deep neural network architecture that generates molecular equilibrium…

Machine Learning · Statistics 2018-10-29 Niklas W. A. Gebauer , Michael Gastegger , Kristof T. Schütt

Traditional language models treat language as a finite state automaton on a probability space over words. This is a very strong assumption when modeling something inherently complex such as language. In this paper, we challenge this by…

Computation and Language · Computer Science 2016-04-04 Kushal Arora , Anand Rangarajan

Animal behavior and neural recordings show that the brain is able to measure both the intensity of an odor and the timing of odor encounters. However, whether intensity or timing of odor detections is more informative for olfactory-driven…

Quantitative Methods · Quantitative Biology 2021-06-17 Nicola Rigolli , Nicodemo Magnoli , Lorenzo Rosasco , Agnese Seminara

'Capsule' models try to explicitly represent the poses of objects, enforcing a linear relationship between an object's pose and that of its constituent parts. This modelling assumption should lead to robustness to viewpoint changes since…

Machine Learning · Computer Science 2021-01-07 Lewis Smith , Lisa Schut , Yarin Gal , Mark van der Wilk

Generating a novel and optimized molecule with desired chemical properties is an essential part of the drug discovery process. Failure to meet one of the required properties can frequently lead to failure in a clinical test which is costly.…

Machine Learning · Computer Science 2020-10-28 Bonggun Shin , Sungsoo Park , JinYeong Bak , Joyce C. Ho
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