arXiv subjects

Konrad P. Kording

Publications and source records attributed to Konrad P. Kording.

At least 19 recordsLinked to original sources

arXiv2026

Partially Observed Structural Causal Models

Here we introduce Partially Observed Structural Causal Models (POSCMs) as an extension of structural causal models (SCMs) to settings where upstream contexts co-determine both the interaction structure and downstream mechanisms on observed variables. POSCMs thus provide a self-contained causal modeling framework for endogenous graphs, allowing for an intervention hierarchy spanning node- and edge-level contexts and endogenous variable interventions. To define edge interventions, we separate node mechanisms into edge-local transmission channels that can be modified without changing the source node or the rest of the target mechanism. We provide an identifiability theory that clarifies which intervention families would suffice to disentangle structure formation from mechanisms. We then empirically validate these theoretical results in two external simulators: a biophysically detailed virtual human retina and a gene-regulatory analogue. The experiments reproduce non-identifiability under latent context, expose structure-mechanism confounding under latent edges, and recover pathway-level input-output relationships under targeted interventions, consistent with our positive Markov kernel identifiability results. Together, POSCMs provide an intervention-oriented framework for causal systems in which contexts, graph structure, mechanisms, and measurements are jointly generated and only partially observed.

cs.LG↗

arXiv2026

Formalizing the Binding Problem

Representations of the world, arguably, contain information about features (e.g. something is blue, something is a circle) but also information about which features are part of the same object (e.g. the circle is blue), which we call binding information. Any system with the ability to understand scenes with multiple objects must be able to solve the binding problem: it needs to know which features belong together. However, despite work showing that Vision Transformers (ViTs) know which patches belong together, it is not known whether current deep learning models learn to exhibit binding information, i.e., for features. We may believe that there is not much binding information, after all misattributing features to wrong objects is a common failure of ViT-based architectures, especially in scenes with objects sharing features. Here we formalize the binding problem with an information-theoretic approach, and introduce a probing method to measure binding information in model representations. We perform experiments on ViTs, measuring binding from different components of the architecture, such as the image summary token [CLS] or the spatial tokens. We use datasets with different binding challenges, such as feature sharing, occlusion, and natural features, while comparing the performance of several pre-trained ViTs. Overall, our research demonstrates binding as a key ingredient to strong visual recognition and reasoning.

cs.CV↗

arXiv2026

Estimating Implicit Regularization in Deep Learning

Deep learning systems are known to exhibit implicit regularization (alt. implicit bias), favoring simple solutions instead of merely minimizing the loss function. In some cases, we can analytically derive the implicit regularization -- connecting it to an equivalent penalty that augments the learning objective. However, modern deep learning systems are complex, carrying modifications to the training procedure and architecture (e.g. early stopping, minibatching, dropout) whose effects are not always directly interpretable. Although estimating the resulting implicit regularization could aid theorists in algorithm design and practitioners in interpreting their hyperparameter choices, this problem has received little direct attention. It is also tractable: regularization makes weight updates deviate from loss gradients, promising a signal for identifying implicit bias. Here we provide gradient matching methods that can be used to empirically estimate the implicit regularization. Our method works on networks with known regularization, recovering popular explicit penalties like $\ell_1$ and $\ell_2$. It also replicates known implicit effects, like the quadratic weight penalty induced by early stopping in gradient descent, demonstrating that it can be used to test theories of implicit regularization. Crucially, because our method is empirical, it can handle implicit regularization in arbitrary networks. We demonstrate this use by characterizing the effects of dropout in deep networks, showing implicit $\ell_2$ effects in this popular method. Our work shows that practitioners can use gradient matching to understand regularization in networks with implicit biases that are too complicated to derive analytically.

stat.ML↗

arXiv2026

Compiling molecular ultrastructure into neural dynamics

High-resolution brain imaging can now capture not just synapse locations but their molecular composition, with the cost of such mapping falling exponentially. Yet such ultrastructural data has so far told us little about local neuronal physiology - specifically, the parameters (e.g., synaptic efficacies, local conductances) that govern neural dynamics. We propose to translate molecularly annotated ultrastructure into physiology, introducing the concept of an ultrastructure-to-dynamics compiler: a learned mapping from molecularly annotated ultrastructure to simulator-ready, uncertainty-aware physiological parameters. The requirement is paired training data, with jointly acquired ultrastructure from imaging, and dynamical responses to perturbations from physiological experiments. With this data we can train models that predict local physiology directly from structure. Such a compiler would support biophysical simulations by turning anatomical maps into models of circuit dynamics, shifting structure-to-function from a descriptive program to a predictive one and opening routes to understanding neural computation and forecasting intervention effects.

q-bio.NC↗

arXiv2026

Does Object Binding Naturally Emerge in Large Pretrained Vision Transformers?

Object binding, the brain's ability to bind the many features that collectively represent an object into a coherent whole, is central to human cognition. It groups low-level perceptual features into high-level object representations, stores those objects efficiently and compositionally in memory, and supports human reasoning about individual object instances. While prior work often imposes object-centric attention (e.g., Slot Attention) explicitly to probe these benefits, it remains unclear whether this ability naturally emerges in pre-trained Vision Transformers (ViTs). Intuitively, they could: recognizing which patches belong to the same object should be useful for downstream prediction and thus guide attention. Motivated by the quadratic nature of self-attention, we hypothesize that ViTs represent whether two patches belong to the same object, a property we term IsSameObject. We decode IsSameObject from patch embeddings across ViT layers using a quadratic similarity probe, which reaches over 90% accuracy. Crucially, this object-binding capability emerges reliably in DINO, CLIP, and ImageNet-supervised ViTs, but is markedly weaker in MAE, suggesting that binding is not a trivial architectural artifact, but an ability acquired through specific pretraining objectives. We further discover that IsSameObject is encoded in a low-dimensional subspace on top of object features, and that this signal actively guides attention. Ablating IsSameObject from model activations degrades downstream performance and works against the learning objective, implying that emergent object binding naturally serves the pretraining objective. Our findings challenge the view that ViTs lack object binding and highlight how symbolic knowledge of "which parts belong together" emerges naturally in a connectionist system.

cs.CV↗

arXiv2025

A Scalable, Causal, and Energy Efficient Framework for Neural Decoding with Spiking Neural Networks

Brain-computer interfaces (BCIs) promise to enable vital functions, such as speech and prosthetic control, for individuals with neuromotor impairments. Central to their success are neural decoders, models that map neural activity to intended behavior. Current learning-based decoding approaches fall into two classes: simple, causal models that lack generalization, or complex, non-causal models that generalize and scale offline but struggle in real-time settings. Both face a common challenge, their reliance on power-hungry artificial neural network backbones, which makes integration into real-world, resource-limited systems difficult. Spiking neural networks (SNNs) offer a promising alternative. Because they operate causally these models are suitable for real-time use, and their low energy demands make them ideal for battery-constrained environments. To this end, we introduce Spikachu: a scalable, causal, and energy-efficient neural decoding framework based on SNNs. Our approach processes binned spikes directly by projecting them into a shared latent space, where spiking modules, adapted to the timing of the input, extract relevant features; these latent representations are then integrated and decoded to generate behavioral predictions. We evaluate our approach on 113 recording sessions from 6 non-human primates, totaling 43 hours of recordings. Our method outperforms causal baselines when trained on single sessions using between 2.26 and 418.81 times less energy. Furthermore, we demonstrate that scaling up training to multiple sessions and subjects improves performance and enables few-shot transfer to unseen sessions, subjects, and tasks. Overall, Spikachu introduces a scalable, online-compatible neural decoding framework based on SNNs, whose performance is competitive relative to state-of-the-art models while consuming orders of magnitude less energy.

cs.LG↗

arXiv2025

Grounding Intelligence in Movement

Recent advances in machine learning have dramatically improved our ability to model language, vision, and other high-dimensional data, yet they continue to struggle with one of the most fundamental aspects of biological systems: movement. Across neuroscience, medicine, robotics, and ethology, movement is essential for interpreting behavior, predicting intent, and enabling interaction. Despite its core significance in our intelligence, movement is often treated as an afterthought rather than as a rich and structured modality in its own right. This reflects a deeper fragmentation in how movement data is collected and modeled, often constrained by task-specific goals and domain-specific assumptions. But movement is not domain-bound. It reflects shared physical constraints, conserved morphological structures, and purposeful dynamics that cut across species and settings. We argue that movement should be treated as a primary modeling target for AI. It is inherently structured and grounded in embodiment and physics. This structure, often allowing for compact, lower-dimensional representations (e.g., pose), makes it more interpretable and computationally tractable to model than raw, high-dimensional sensory inputs. Developing models that can learn from and generalize across diverse movement data will not only advance core capabilities in generative modeling and control, but also create a shared foundation for understanding behavior across biological and artificial systems. Movement is not just an outcome, it is a window into how intelligent systems engage with the world.

cs.AI↗

arXiv2025

Who Does What in Deep Learning? Multidimensional Game-Theoretic Attribution of Function of Neural Units

Neural networks now generate text, images, and speech with billions of parameters, producing a need to know how each neural unit contributes to these high-dimensional outputs. Existing explainable-AI methods, such as SHAP, attribute importance to inputs, but cannot quantify the contributions of neural units across thousands of output pixels, tokens, or logits. Here we close that gap with Multiperturbation Shapley-value Analysis (MSA), a model-agnostic game-theoretic framework. By systematically lesioning combinations of units, MSA yields Shapley Modes, unit-wise contribution maps that share the exact dimensionality of the model's output. We apply MSA across scales, from multi-layer perceptrons to the 56-billion-parameter Mixtral-8x7B and Generative Adversarial Networks (GAN). The approach demonstrates how regularisation concentrates computation in a few hubs, exposes language-specific experts inside the LLM, and reveals an inverted pixel-generation hierarchy in GANs. Together, these results showcase MSA as a powerful approach for interpreting, editing, and compressing deep neural networks.

cs.LG↗

arXiv2025

The Landscape of Causal Discovery Data: Grounding Causal Discovery in Real-World Applications

Causal discovery aims to automatically uncover causal relationships from data, a capability with significant potential across many scientific disciplines. However, its real-world applications remain limited. Current methods often rely on unrealistic assumptions and are evaluated only on simple synthetic toy datasets, often with inadequate evaluation metrics. In this paper, we substantiate these claims by performing a systematic review of the recent causal discovery literature. We present applications in biology, neuroscience, and Earth sciences - fields where causal discovery holds promise for addressing key challenges. We highlight available simulated and real-world datasets from these domains and discuss common assumption violations that have spurred the development of new methods. Our goal is to encourage the community to adopt better evaluation practices by utilizing realistic datasets and more adequate metrics.

cs.LG↗

arXiv2025

Causality in the human niche: lessons for machine learning

Humans interpret the world around them in terms of cause and effect and communicate their understanding of the world to each other in causal terms. These causal aspects of human cognition are thought to underlie humans' ability to generalize and learn efficiently in new domains, an area where current machine learning systems are weak. Building human-like causal competency into machine learning systems may facilitate the construction of effective and interpretable AI. Indeed, the machine learning community has been importing ideas on causality formalized by the Structural Causal Model (SCM) framework, which provides a rigorous formal language for many aspects of causality and has led to significant advances. However, the SCM framework fails to capture some salient aspects of human causal cognition and has likewise not yet led to advances in machine learning in certain critical areas where humans excel. We contend that the problem of causality in the ``human niche'' -- for a social, autonomous, and goal-driven agent sensing and acting in the world in which humans live -- is quite different from the kind of causality captured by SCMs. For example, everyday objects come in similar types that have similar causal properties, and so humans readily generalize knowledge of one type of object (cups) to another related type (bowls) by drawing causal analogies between objects with similar properties, but such analogies are at best awkward to express in SCMs. We explore how such causal capabilities are adaptive in, and motivated by, the human niche. By better appreciating properties of human causal cognition and, crucially, how those properties are adaptive in the niche in which humans live, we hope that future work at the intersection of machine learning and causality will leverage more human-like inductive biases to create more capable, controllable, and interpretable systems.

cs.AI↗

arXiv2024

Neural decoding from stereotactic EEG: accounting for electrode variability across subjects

Deep learning based neural decoding from stereotactic electroencephalography (sEEG) would likely benefit from scaling up both dataset and model size. To achieve this, combining data across multiple subjects is crucial. However, in sEEG cohorts, each subject has a variable number of electrodes placed at distinct locations in their brain, solely based on clinical needs. Such heterogeneity in electrode number/placement poses a significant challenge for data integration, since there is no clear correspondence of the neural activity recorded at distinct sites between individuals. Here we introduce seegnificant: a training framework and architecture that can be used to decode behavior across subjects using sEEG data. We tokenize the neural activity within electrodes using convolutions and extract long-term temporal dependencies between tokens using self-attention in the time dimension. The 3D location of each electrode is then mixed with the tokens, followed by another self-attention in the electrode dimension to extract effective spatiotemporal neural representations. Subject-specific heads are then used for downstream decoding tasks. Using this approach, we construct a multi-subject model trained on the combined data from 21 subjects performing a behavioral task. We demonstrate that our model is able to decode the trial-wise response time of the subjects during the behavioral task solely from neural data. We also show that the neural representations learned by pretraining our model across individuals can be transferred in a few-shot manner to new subjects. This work introduces a scalable approach towards sEEG data integration for multi-subject model training, paving the way for cross-subject generalization for sEEG decoding.

eess.SP↗

arXiv2024

Empirical influence functions to understand the logic of fine-tuning

Understanding the process of learning in neural networks is crucial for improving their performance and interpreting their behavior. This can be approximately understood by asking how a model's output is influenced when we fine-tune on a new training sample. There are desiderata for such influences, such as decreasing influence with semantic distance, sparseness, noise invariance, transitive causality, and logical consistency. Here we use the empirical influence measured using fine-tuning to demonstrate how individual training samples affect outputs. We show that these desiderata are violated for both for simple convolutional networks and for a modern LLM. We also illustrate how prompting can partially rescue this failure. Our paper presents an efficient and practical way of quantifying how well neural networks learn from fine-tuning stimuli. Our results suggest that popular models cannot generalize or perform logic in the way they appear to.

cs.LG↗

arXiv2023

A large language model-assisted education tool to provide feedback on open-ended responses

Open-ended questions are a favored tool among instructors for assessing student understanding and encouraging critical exploration of course material. Providing feedback for such responses is a time-consuming task that can lead to overwhelmed instructors and decreased feedback quality. Many instructors resort to simpler question formats, like multiple-choice questions, which provide immediate feedback but at the expense of personalized and insightful comments. Here, we present a tool that uses large language models (LLMs), guided by instructor-defined criteria, to automate responses to open-ended questions. Our tool delivers rapid personalized feedback, enabling students to quickly test their knowledge and identify areas for improvement. We provide open-source reference implementations both as a web application and as a Jupyter Notebook widget that can be used with instructional coding or math notebooks. With instructor guidance, LLMs hold promise to enhance student learning outcomes and elevate instructional methodologies.

cs.CY↗

arXiv2023

Prospective Learning: Principled Extrapolation to the Future

Learning is a process which can update decision rules, based on past experience, such that future performance improves. Traditionally, machine learning is often evaluated under the assumption that the future will be identical to the past in distribution or change adversarially. But these assumptions can be either too optimistic or pessimistic for many problems in the real world. Real world scenarios evolve over multiple spatiotemporal scales with partially predictable dynamics. Here we reformulate the learning problem to one that centers around this idea of dynamic futures that are partially learnable. We conjecture that certain sequences of tasks are not retrospectively learnable (in which the data distribution is fixed), but are prospectively learnable (in which distributions may be dynamic), suggesting that prospective learning is more difficult in kind than retrospective learning. We argue that prospective learning more accurately characterizes many real world problems that (1) currently stymie existing artificial intelligence solutions and/or (2) lack adequate explanations for how natural intelligences solve them. Thus, studying prospective learning will lead to deeper insights and solutions to currently vexing challenges in both natural and artificial intelligences.

cs.LG↗

arXiv2023

Comparing dendritic trees with actual trees

Since they became observable, neuron morphologies have been informally compared with biological trees but they are studied by distinct communities, neuroscientists, and ecologists. The apparent structural similarity suggests there may be common quantitative rules and constraints. However, there are also reasons to believe they should be different. For example, while the environments of trees may be relatively simple, neurons are constructed by a complex iterative program where synapses are made and pruned. This complexity may make neurons less self-similar than trees. Here we test this hypothesis by comparing the features of segmented sub-trees with those of the whole tree. We indeed find more self-similarity within actual trees than neurons. At the same time, we find that many other features are somewhat comparable across the two. Investigation of shapes and behaviors promises new ways of conceptualizing the form-function link.

q-bio.NC↗

arXiv2022

Neural Networks as Paths through the Space of Representations

Deep neural networks implement a sequence of layer-by-layer operations that are each relatively easy to understand, but the resulting overall computation is generally difficult to understand. We consider a simple hypothesis for interpreting the layer-by-layer construction of useful representations: perhaps the role of each layer is to reformat information to reduce the "distance" to the desired outputs. With this framework, the layer-wise computation implemented by a deep neural network can be viewed as a path through a high-dimensional representation space. We formalize this intuitive idea of a "path" by leveraging recent advances in *metric* representational similarity. We extend existing representational distance methods by computing geodesics, angles, and projections of representations, going beyond mere layer distances. We then demonstrate these tools by visualizing and comparing the paths taken by ResNet and VGG architectures on CIFAR-10. We conclude by sketching additional ways that this kind of representational geometry can be used to understand and interpret network training, and to describe novel kinds of similarities between different models.

cs.LG↗

arXiv2022

Clustering units in neural networks: upstream vs downstream information

It has been hypothesized that some form of "modular" structure in artificial neural networks should be useful for learning, compositionality, and generalization. However, defining and quantifying modularity remains an open problem. We cast the problem of detecting functional modules into the problem of detecting clusters of similar-functioning units. This begs the question of what makes two units functionally similar. For this, we consider two broad families of methods: those that define similarity based on how units respond to structured variations in inputs ("upstream"), and those based on how variations in hidden unit activations affect outputs ("downstream"). We conduct an empirical study quantifying modularity of hidden layer representations of simple feedforward, fully connected networks, across a range of hyperparameters. For each model, we quantify pairwise associations between hidden units in each layer using a variety of both upstream and downstream measures, then cluster them by maximizing their "modularity score" using established tools from network science. We find two surprising results: first, dropout dramatically increased modularity, while other forms of weight regularization had more modest effects. Second, although we observe that there is usually good agreement about clusters within both upstream methods and downstream methods, there is little agreement about the cluster assignments across these two families of methods. This has important implications for representation-learning, as it suggests that finding modular representations that reflect structure in inputs (e.g. disentanglement) may be a distinct goal from learning modular representations that reflect structure in outputs (e.g. compositionality).

cs.LG↗

arXiv2021

Object Based Attention Through Internal Gating

Object-based attention is a key component of the visual system, relevant for perception, learning, and memory. Neurons tuned to features of attended objects tend to be more active than those associated with non-attended objects. There is a rich set of models of this phenomenon in computational neuroscience. However, there is currently a divide between models that successfully match physiological data but can only deal with extremely simple problems and models of attention used in computer vision. For example, attention in the brain is known to depend on top-down processing, whereas self-attention in deep learning does not. Here, we propose an artificial neural network model of object-based attention that captures the way in which attention is both top-down and recurrent. Our attention model works well both on simple test stimuli, such as those using images of handwritten digits, and on more complex stimuli, such as natural images drawn from the COCO dataset. We find that our model replicates a range of findings from neuroscience, including attention-invariant tuning, inhibition of return, and attention-mediated scaling of activity. Understanding object based attention is both computationally interesting and a key problem for computational neuroscience.

q-bio.NC↗