arXiv subjects

Kanaka Rajan

Publications and source records attributed to Kanaka Rajan.

At least 19 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↗

arXiv2026

Implications of hierarchical Markov models of behavior: on irreversibility, predictability, and dimensionality

The maturation of quantitative tools for studying the high-level structure of animal behavior, and especially tools which represent spontaneous behavior as a sequence of stereotyped and neurally well-defined 'syllables', demands that the field revisit a fundamental theoretical question: if the coarse structure of behavior can be accurately described by Markov models, what do these models really tell us about behavior? In this work, we explore the theoretical implications of these models and discuss how they allow us to quantitatively formulate questions about the sequence-like nature and effective dimensionality of behavior. One important insight is that the eigenvalues and eigenvectors of various model-associated matrices furnish interpretable time scales and modifications of behavior that occur on those time scales. We illustrate our points using both toy examples and Markov models fit to real data. By analyzing the consequences of Markov representations, we clarify the theoretical meaning of progress in quantifying behavior.

q-bio.NC↗

arXiv2026

A dimensional R2 regression metric

R2 score is the standard metric for evaluating regression tasks, offering a normalized magnitude-agnostic measure of accuracy that captures variance. However, R2 has three key limitations: it is limited to at most two dimensional inputs, it reduces the score to a single scalar that hides rich patterns of prediction accuracy, and it is sensitive to low-variance noise channels which can yield large, uninterpretable negative values. We introduce the Dimensional R2 score (Dim-R2), a simple extension of R2 that accepts data of arbitrary dimensionality, provides a multidimensional view of accuracy, and reduces sensitivity to noise. We demonstrate its advantages on both synthetic sinusoidal data and three multidimensional regression datasets. Dim-R2 offers an interpretable and flexible metric that highlights patterns in regression accuracy, guiding regression modeling.

cs.LG↗

arXiv2025

From Memories to Maps: Mechanisms of In-Context Reinforcement Learning in Transformers

Humans and animals show remarkable learning efficiency, adapting to new environments with minimal experience. This capability is not well captured by standard reinforcement learning algorithms that rely on incremental value updates. Rapid adaptation likely depends on episodic memory -- the ability to retrieve specific past experiences to guide decisions in novel contexts. Transformers provide a useful setting for studying these questions because of their ability to learn rapidly in-context and because their key-value architecture resembles episodic memory systems in the brain. We train a transformer to in-context reinforcement learn in a distribution of planning tasks inspired by rodent behavior. We then characterize the learning algorithms that emerge in the model. We first find that representation learning is supported by in-context structure learning and cross-context alignment, where representations are aligned across environments with different sensory stimuli. We next demonstrate that the reinforcement learning strategies developed by the model are not interpretable as standard model-free or model-based planning. Instead, we show that in-context reinforcement learning is supported by caching intermediate computations within the model's memory tokens, which are then accessed at decision time. Overall, we find that memory may serve as a computational resource, storing both raw experience and cached computations to support flexible behavior. Furthermore, the representations developed in the model resemble computations associated with the hippocampal-entorhinal system in the brain, suggesting that our findings may be relevant for natural cognition. Taken together, our work offers a mechanistic hypothesis for the rapid adaptation that underlies in-context learning in artificial and natural settings.

cs.AI↗

arXiv2025

Deep RL Needs Deep Behavior Analysis: Exploring Implicit Planning by Model-Free Agents in Open-Ended Environments

Understanding the behavior of deep reinforcement learning (DRL) agents -particularly as task and agent sophistication increase- requires more than simple comparison of reward curves, yet standard methods for behavioral analysis remain underdeveloped in DRL. We apply tools from neuroscience and ethology to study DRL agents in a novel, complex, partially observable environment, ForageWorld, designed to capture key aspects of real-world animal foraging- including sparse, depleting resource patches, predator threats, and spatially extended arenas. We use this environment as a platform for applying joint behavioral and neural analysis to agents, revealing detailed, quantitatively grounded insights into agent strategies, memory, and planning. Contrary to common assumptions, we find that model-free RNN-based DRL agents can exhibit structured, planning-like behavior purely through emergent dynamics- without requiring explicit memory modules or world models. Our results show that studying DRL agents like animals -analyzing them with neuroethology-inspired tools that reveal structure in both behavior and neural dynamics- uncovers rich structure in their learning dynamics that would otherwise remain invisible. We distill these tools into a general analysis framework linking core behavioral and representational features to diagnostic methods, which can be reused for a wide range of tasks and agents. As agents grow more complex and autonomous, bridging neuroscience, cognitive science, and AI will be essential- not just for understanding their behavior, but for ensuring safe alignment and maximizing desirable behaviors that are hard to measure via reward. We show how this can be done by drawing on lessons from how biological intelligence is studied.

cs.AI↗

arXiv2025

A Variational Manifold Embedding Framework for Nonlinear Dimensionality Reduction

Dimensionality reduction algorithms like principal component analysis (PCA) are workhorses of machine learning and neuroscience, but each has well-known limitations. Variants of PCA are simple and interpretable, but not flexible enough to capture nonlinear data manifold structure. More flexible approaches have other problems: autoencoders are generally difficult to interpret, and graph-embedding-based methods can produce pathological distortions in manifold geometry. Motivated by these shortcomings, we propose a variational framework that casts dimensionality reduction algorithms as solutions to an optimal manifold embedding problem. By construction, this framework permits nonlinear embeddings, allowing its solutions to be more flexible than PCA. Moreover, the variational nature of the framework has useful consequences for interpretability: each solution satisfies a set of partial differential equations, and can be shown to reflect symmetries of the embedding objective. We discuss these features in detail and show that solutions can be analytically characterized in some cases. Interestingly, one special case exactly recovers PCA.

cs.LG↗

arXiv2025

Measuring and Controlling Solution Degeneracy across Task-Trained Recurrent Neural Networks

Task-trained recurrent neural networks (RNNs) are widely used in neuroscience and machine learning to model dynamical computations. To gain mechanistic insight into how neural systems solve tasks, prior work often reverse-engineers individual trained networks. However, different RNNs trained on the same task and achieving similar performance can exhibit strikingly different internal solutions, a phenomenon known as solution degeneracy. Here, we develop a unified framework to systematically quantify and control solution degeneracy across three levels: behavior, neural dynamics, and weight space. We apply this framework to 3,400 RNNs trained on four neuroscience-relevant tasks: flip-flop memory, sine wave generation, delayed discrimination, and path integration, while systematically varying task complexity, learning regime, network size, and regularization. We find that higher task complexity and stronger feature learning reduce degeneracy in neural dynamics but increase it in weight space, with mixed effects on behavior. In contrast, larger networks and structural regularization reduce degeneracy at all three levels. These findings empirically validate the Contravariance Principle and provide practical guidance for researchers seeking to tune the variability of RNN solutions, either to uncover shared neural mechanisms or to model the individual variability observed in biological systems. This work provides a principled framework for quantifying and controlling solution degeneracy in task-trained RNNs, offering new tools for building more interpretable and biologically grounded models of neural computation.

cs.LG↗

arXiv2025

Military AI Needs Technically-Informed Regulation to Safeguard AI Research and its Applications

Military weapon systems and command-and-control infrastructure augmented by artificial intelligence (AI) have seen rapid development and deployment in recent years. However, the sociotechnical impacts of AI on combat systems, military decision-making, and the norms of warfare have been understudied. We focus on a specific subset of lethal autonomous weapon systems (LAWS) that use AI for targeting or battlefield decisions. We refer to this subset as AI-powered lethal autonomous weapon systems (AI-LAWS) and argue that they introduce novel risks -- including unanticipated escalation, poor reliability in unfamiliar environments, and erosion of human oversight -- all of which threaten both military effectiveness and the openness of AI research. These risks cannot be addressed by high-level policy alone; effective regulation must be grounded in the technical behavior of AI models. We argue that AI researchers must be involved throughout the regulatory lifecycle. Thus, we propose a clear, behavior-based definition of AI-LAWS -- systems that introduce unique risks through their use of modern AI -- as a foundation for technically grounded regulation, given that existing frameworks do not distinguish them from conventional LAWS. Using this definition, we propose several technically-informed policy directions and invite greater participation from the AI research community in military AI policy discussions.

cs.CY↗

arXiv2025

InputDSA: Demixing then Comparing Recurrent and Externally Driven Dynamics

In control problems and basic scientific modeling, it is important to compare observations with dynamical simulations. For example, comparing two neural systems can shed light on the nature of emergent computations in the brain and deep neural networks. Recently, Ostrow et al. (2023) introduced Dynamical Similarity Analysis (DSA), a method to measure the similarity of two systems based on their recurrent dynamics rather than geometry or topology. However, DSA does not consider how inputs affect the dynamics, meaning that two similar systems, if driven differently, may be classified as different. Because real-world dynamical systems are rarely autonomous, it is important to account for the effects of input drive. To this end, we introduce a novel metric for comparing both intrinsic (recurrent) and input-driven dynamics, called InputDSA (iDSA). InputDSA extends the DSA framework by estimating and comparing both input and intrinsic dynamic operators using a variant of Dynamic Mode Decomposition with control (DMDc) based on subspace identification. We demonstrate that InputDSA can successfully compare partially observed, input-driven systems from noisy data. We show that when the true inputs are unknown, surrogate inputs can be substituted without a major deterioration in similarity estimates. We apply InputDSA on Recurrent Neural Networks (RNNs) trained with Deep Reinforcement Learning, identifying that high-performing networks are dynamically similar to one another, while low-performing networks are more diverse. Lastly, we apply InputDSA to neural data recorded from rats performing a cognitive task, demonstrating that it identifies a transition from input-driven evidence accumulation to intrinsically-driven decision-making. Our work demonstrates that InputDSA is a robust and efficient method for comparing intrinsic dynamics and the effect of external input on dynamical systems.

q-bio.NC↗

arXiv2025

Gradient Descent as Loss Landscape Navigation: a Normative Framework for Deriving Learning Rules

Learning rules -- prescriptions for updating model parameters to improve performance -- are typically assumed rather than derived. Why do some learning rules work better than others, and under what assumptions can a given rule be considered optimal? We propose a theoretical framework that casts learning rules as policies for navigating (partially observable) loss landscapes, and identifies optimal rules as solutions to an associated optimal control problem. A range of well-known rules emerge naturally within this framework under different assumptions: gradient descent from short-horizon optimization, momentum from longer-horizon planning, natural gradients from accounting for parameter space geometry, non-gradient rules from partial controllability, and adaptive optimizers like Adam from online Bayesian inference of loss landscape shape. We further show that continual learning strategies like weight resetting can be understood as optimal responses to task uncertainty. By unifying these phenomena under a single objective, our framework clarifies the computational structure of learning and offers a principled foundation for designing adaptive algorithms.

cs.LG↗

arXiv2025

POCO: Scalable Neural Forecasting through Population Conditioning

Predicting future neural activity is a core challenge in modeling brain dynamics, with applications ranging from scientific investigation to closed-loop neurotechnology. While recent models of population activity emphasize interpretability and behavioral decoding, neural forecasting-particularly across multi-session, spontaneous recordings-remains underexplored. We introduce POCO, a unified forecasting model that combines a lightweight univariate forecaster with a population-level encoder to capture both neuron-specific and brain-wide dynamics. Trained across five calcium imaging datasets spanning zebrafish, mice, and C. elegans, POCO achieves state-of-the-art accuracy at cellular resolution in spontaneous behaviors. After pre-training, POCO rapidly adapts to new recordings with minimal fine-tuning. Notably, POCO's learned unit embeddings recover biologically meaningful structure-such as brain region clustering-without any anatomical labels. Our comprehensive analysis reveals several key factors influencing performance, including context length, session diversity, and preprocessing. Together, these results position POCO as a scalable and adaptable approach for cross-session neural forecasting and offer actionable insights for future model design. By enabling accurate, generalizable forecasting models of neural dynamics across individuals and species, POCO lays the groundwork for adaptive neurotechnologies and large-scale efforts for neural foundation models. Code is available at https://github.com/yuvenduan/POCO.

q-bio.NC↗

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

The time is ripe to reverse engineer an entire nervous system: simulating behavior from neural interactions

Just like electrical engineers understand how microprocessors execute programs in terms of how transistor currents are affected by their inputs, neuroscientists want to understand behavior production in terms of how neuronal outputs are affected by their inputs and internal states. This dependency of neuronal outputs on inputs can be described by a state-dependent input-output (IO)-function. However, to reliably identify these IO-functions, we need to perturb each input and combinations of inputs while observing all the outputs. Here, we argue that such completeness is possible in C. elegans; a complete description that goes all the way from the activity of every neuron to predict behavior. The established and growing toolkit of optophysiology can non-invasively capture and control every neuron's activity and scale to countless experiments. The information from many such experiments can be pooled while capturing the inter-individual variability because neuronal identity and function are largely conserved across individuals. Just like electrical engineers use transistor IO-functions to simulate program execution, we argue that neuronal IO-functions could be used to simulate the impressive breadth of brain states and behaviors of C. elegans.

q-bio.NC↗

arXiv2024

AI-Powered Autonomous Weapons Risk Geopolitical Instability and Threaten AI Research

The recent embrace of machine learning (ML) in the development of autonomous weapons systems (AWS) creates serious risks to geopolitical stability and the free exchange of ideas in AI research. This topic has received comparatively little attention of late compared to risks stemming from superintelligent artificial general intelligence (AGI), but requires fewer assumptions about the course of technological development and is thus a nearer-future issue. ML is already enabling the substitution of AWS for human soldiers in many battlefield roles, reducing the upfront human cost, and thus political cost, of waging offensive war. In the case of peer adversaries, this increases the likelihood of "low intensity" conflicts which risk escalation to broader warfare. In the case of non-peer adversaries, it reduces the domestic blowback to wars of aggression. This effect can occur regardless of other ethical issues around the use of military AI such as the risk of civilian casualties, and does not require any superhuman AI capabilities. Further, the military value of AWS raises the specter of an AI-powered arms race and the misguided imposition of national security restrictions on AI research. Our goal in this paper is to raise awareness among the public and ML researchers on the near-future risks posed by full or near-full autonomy in military technology, and we provide regulatory suggestions to mitigate these risks. We call upon AI policy experts and the defense AI community in particular to embrace transparency and caution in their development and deployment of AWS to avoid the negative effects on global stability and AI research that we highlight here.

cs.CY↗

arXiv2022

Efficient and robust multi-task learning in the brain with modular latent primitives

Biological agents do not have infinite resources to learn new things. For this reason, a central aspect of human learning is the ability to recycle previously acquired knowledge in a way that allows for faster, less resource-intensive acquisition of new skills. In spite of that, how neural networks in the brain leverage existing knowledge to learn new computations is not well understood. In this work, we study this question in artificial recurrent neural networks (RNNs) trained on a corpus of commonly used neuroscience tasks. Combining brain-inspired inductive biases we call functional and structural, we propose a system that learns new tasks by building on top of pre-trained latent dynamics organised into separate recurrent modules. These modules, acting as prior knowledge acquired previously through evolution or development, are pre-trained on the statistics of the full corpus of tasks so as to be independent and maximally informative. The resulting model, we call a Modular Latent Primitives (MoLaP) network, allows for learning multiple tasks while keeping parameter counts, and updates, low. We also show that the skills acquired with our approach are more robust to a broad range of perturbations compared to those acquired with other multi-task learning strategies, and that generalisation to new tasks is facilitated. This work offers a new perspective on achieving efficient multi-task learning in the brain, illustrating the benefits of leveraging pre-trained latent dynamical primitives.

cs.AI↗

arXiv2021

A brain basis of dynamical intelligence for AI and computational neuroscience

The deep neural nets of modern artificial intelligence (AI) have not achieved defining features of biological intelligence, including abstraction, causal learning, and energy-efficiency. While scaling to larger models has delivered performance improvements for current applications, more brain-like capacities may demand new theories, models, and methods for designing artificial learning systems. Here, we argue that this opportunity to reassess insights from the brain should stimulate cooperation between AI research and theory-driven computational neuroscience (CN). To motivate a brain basis of neural computation, we present a dynamical view of intelligence from which we elaborate concepts of sparsity in network structure, temporal dynamics, and interactive learning. In particular, we suggest that temporal dynamics, as expressed through neural synchrony, nested oscillations, and flexible sequences, provide a rich computational layer for reading and updating hierarchical models distributed in long-term memory networks. Moreover, embracing agent-centered paradigms in AI and CN will accelerate our understanding of the complex dynamics and behaviors that build useful world models. A convergence of AI/CN theories and objectives will reveal dynamical principles of intelligence for brains and engineered learning systems. This article was inspired by our symposium on dynamical neuroscience and machine learning at the 6th Annual US/NIH BRAIN Initiative Investigators Meeting.

q-bio.NC↗

arXiv2017

full-FORCE: A Target-Based Method for Training Recurrent Networks

Trained recurrent networks are powerful tools for modeling dynamic neural computations. We present a target-based method for modifying the full connectivity matrix of a recurrent network to train it to perform tasks involving temporally complex input/output transformations. The method introduces a second network during training to provide suitable "target" dynamics useful for performing the task. Because it exploits the full recurrent connectivity, the method produces networks that perform tasks with fewer neurons and greater noise robustness than traditional least-squares (FORCE) approaches. In addition, we show how introducing additional input signals into the target-generating network, which act as task hints, greatly extends the range of tasks that can be learned and provides control over the complexity and nature of the dynamics of the trained, task-performing network.

cs.NE↗

arXiv2016

Recurrent Network Models Of Sequence Generation And Memory

Sequential activation of neurons is a common feature of network activity during a variety of behaviors, including working memory and decision making. Previous network models for sequences and memory emphasized specialized architectures in which a principled mechanism is pre-wired into their connectivity. Here we demonstrate that, starting from random connectivity and modifying a small fraction of connections, a largely disordered recur- rent network can produce sequences and implement working memory efficiently. We use this process, called Partial In-Network Training (PINning), to model and match cellular resolution imaging data from the posterior parietal cortex during a virtual memory- guided two-alternative forced-choice task. Analysis of the connectivity reveals that sequences propagate by the cooperation between recurrent synaptic interactions and external inputs, rather than through feedforward or asymmetric connections. Together our results suggest that neural sequences may emerge through learning from largely unstructured network architectures.

q-bio.NC↗