arXiv subjects

Sonja Johnson-Yu

Publications and source records attributed to Sonja Johnson-Yu.

4 recordsLinked to original sources

arXiv2026

Active Electrosensing and Communication in MARL-trained Weakly Electric Fish Collectives

How complex collective behavior emerges from individual interactions is a fundamental scientific question, but experimental cost and difficulty of simultaneous multi-brain recordings limit direct study in animals. Here we introduce a novel computational framework modeling weakly electric fish-like agents with biophysically inspired electrosensing and actuation, trained to forage collectively via multi-agent reinforcement learning (MARL). Trained agents reproduce hallmarks of real fish, including curvilinear homing trajectories and heavy-tailed electric organ discharge (EOD) interval statistics, while exhibiting emergent active sensing, social foraging, dominance-like asymmetries, and aggression. We perform in silico interventions including sensor ablations, EOD silencing, and food distribution changes to identify causal drivers of social foraging. Analyses of recurrent neural dynamics further show robust encoding of task-relevant variables and social context. Our work has broad implications for the neuroethology of weakly electric fish and other social animals where extensive multi-individual neural recordings, and thus traditional data-driven modeling, remain challenging.

cs.NE↗

arXiv2025

Dissecting Larval Zebrafish Hunting using Deep Reinforcement Learning Trained RNN Agents

Larval zebrafish hunting provides a tractable setting to study how ecological and energetic constraints shape adaptive behavior in both biological brains and artificial agents. Here we develop a minimal agent-based model, training recurrent policies with deep reinforcement learning in a bout-based zebrafish simulator. Despite its simplicity, the model reproduces hallmark hunting behaviors -- including eye vergence-linked pursuit, speed modulation, and stereotyped approach trajectories -- that closely match real larval zebrafish. Quantitative trajectory analyses show that pursuit bouts systematically reduce prey angle by roughly half before strike, consistent with measurements. Virtual experiments and parameter sweeps vary ecological and energetic constraints, bout kinematics (coupled vs. uncoupled turns and forward motion), and environmental factors such as food density, food speed, and vergence limits. These manipulations reveal how constraints and environments shape pursuit dynamics, strike success, and abort rates, yielding falsifiable predictions for neuroscience experiments. These sweeps identify a compact set of constraints -- binocular sensing, the coupling of forward speed and turning in bout kinematics, and modest energetic costs on locomotion and vergence -- that are sufficient for zebrafish-like hunting to emerge. Strikingly, these behaviors arise in minimal agents without detailed biomechanics, fluid dynamics, circuit realism, or imitation learning from real zebrafish data. Taken together, this work provides a normative account of zebrafish hunting as the optimal balance between energetic cost and sensory benefit, highlighting the trade-offs that structure vergence and trajectory dynamics. We establish a virtual lab that narrows the experimental search space and generates falsifiable predictions about behavior and neural coding.

q-bio.NC↗

arXiv2024

SimGrade: Using Code Similarity Measures for More Accurate Human Grading

While the use of programming problems on exams is a common form of summative assessment in CS courses, grading such exam problems can be a difficult and inconsistent process. Through an analysis of historical grading patterns we show that inaccurate and inconsistent grading of free-response programming problems is widespread in CS1 courses. These inconsistencies necessitate the development of methods to ensure more fairer and more accurate grading. In subsequent analysis of this historical exam data we demonstrate that graders are able to more accurately assign a score to a student submission when they have previously seen another submission similar to it. As a result, we hypothesize that we can improve exam grading accuracy by ensuring that each submission that a grader sees is similar to at least one submission they have previously seen. We propose several algorithms for (1) assigning student submissions to graders, and (2) ordering submissions to maximize the probability that a grader has previously seen a similar solution, leveraging distributed representations of student code in order to measure similarity between submissions. Finally, we demonstrate in simulation that these algorithms achieve higher grading accuracy than the current standard random assignment process used for grading.

cs.CY↗

arXiv2020

ForestNet: Classifying Drivers of Deforestation in Indonesia using Deep Learning on Satellite Imagery

Characterizing the processes leading to deforestation is critical to the development and implementation of targeted forest conservation and management policies. In this work, we develop a deep learning model called ForestNet to classify the drivers of primary forest loss in Indonesia, a country with one of the highest deforestation rates in the world. Using satellite imagery, ForestNet identifies the direct drivers of deforestation in forest loss patches of any size. We curate a dataset of Landsat 8 satellite images of known forest loss events paired with driver annotations from expert interpreters. We use the dataset to train and validate the models and demonstrate that ForestNet substantially outperforms other standard driver classification approaches. In order to support future research on automated approaches to deforestation driver classification, the dataset curated in this study is publicly available at https://stanfordmlgroup.github.io/projects/forestnet .

cs.CV↗