Sequence modeling and design from molecular to genome scale with Evo.

The genome is a sequence that encodes the DNA, RNA, and proteins that orchestrate an organism's function. We present Evo, a long-context genomic foundation model with a frontier architecture trained on millions of prokaryotic and phage genomes, and report scaling laws on DNA to complement observations in language and vision. Evo generalizes across DNA, RNA, and proteins, enabling zero-shot function prediction competitive with domain-specific language models and the generation of functional CRISPR-Cas and transposon systems, representing the first examples of protein-RNA and protein-DNA codesign with a language model.

Benchmarking explanation methods for mental state decoding with deep learning models.

Deep learning (DL) models find increasing application in mental state decoding, where researchers seek to understand the mapping between mental states (e.g., experiencing anger or joy) and brain activity by identifying those spatial and temporal features of brain activity that allow to accurately identify (i.

Interpreting mental state decoding with deep learning models.

In mental state decoding, researchers aim to identify the set of mental states (e.g., experiencing happiness or fear) that can be reliably identified from the activity patterns of a brain region (or network).

Gaze-dependent evidence accumulation predicts multi-alternative risky choice behaviour.

Choices are influenced by gaze allocation during deliberation, so that fixating an alternative longer leads to increased probability of choosing it. Gaze-dependent evidence accumulation provides a parsimonious account of choices, response times and gaze-behaviour in many simple decision scenarios. Here, we test whether this framework can also predict more complex context-dependent patterns of choice in a three-alternative risky choice task, where choices and eye movements were subject to attraction and compromise effects.

Uncovering the computational mechanisms underlying many-alternative choice.

How do we choose when confronted with many alternatives? There is surprisingly little decision modelling work with large choice sets, despite their prevalence in everyday life. Even further, there is an apparent disconnect between research in small choice sets, supporting a process of gaze-driven evidence accumulation, and research in larger choice sets, arguing for models of optimal choice, satisficing, and hybrids of the two. Here, we bridge this divide by developing and comparing different versions of these models in a many-alternative value-based choice experiment with 9, 16, 25, or 36 alternatives.

Analyzing Neuroimaging Data Through Recurrent Deep Learning Models.

The application of deep learning (DL) models to neuroimaging data poses several challenges, due to the high dimensionality, low sample size, and complex temporo-spatial dependency structure of these data. Even further, DL models often act as , impeding insight into the association of cognitive state and brain activity. To approach these challenges, we introduce the DeepLight framework, which utilizes long short-term memory (LSTM) based DL models to analyze functional Magnetic Resonance Imaging (fMRI) data.

GLAMbox: A Python toolbox for investigating the association between gaze allocation and decision behaviour.

Recent empirical findings have indicated that gaze allocation plays a crucial role in simple decision behaviour. Many of these findings point towards an influence of gaze allocation onto the speed of evidence accumulation in an accumulation-to-bound decision process (resulting in generally higher choice probabilities for items that have been looked at longer). Further, researchers have shown that the strength of the association between gaze and choice behaviour is highly variable between individuals, encouraging future work to study this association on the individual level.

Gaze bias differences capture individual choice behaviour.

How do we make simple choices such as deciding between an apple and an orange? Recent empirical evidence suggests that choice behaviour and gaze allocation are closely linked at the group level, whereby items looked at longer during the decision-making process are more likely to be chosen. However, it is unclear how variable this gaze bias effect is between individuals. Here we investigate this question across four different simple choice experiments and using a computational model that can be easily applied to individuals.