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Eilif Muller

Publications and source records attributed to Eilif Muller.

12 recordsLinked to original sources

seq-JEPA: Autoregressive Predictive Learning of Invariant-Equivariant World Models

Joint-embedding self-supervised learning (SSL) commonly relies on transformations such as data augmentation and masking to learn visual representations, a task achieved by enforcing invariance or equivariance with respect to these transformations applied to two views of an image. This dominant two-view paradigm in SSL often limits the flexibility of learned representations for downstream adaptation by creating performance trade-offs between high-level invariance-demanding tasks such as image classification and more fine-grained equivariance-related tasks. In this work, we propose \emph{seq-JEPA}, a world modeling framework that introduces architectural inductive biases into joint-embedding predictive architectures to resolve this trade-off. Without relying on dual equivariance predictors or loss terms, seq-JEPA simultaneously learns two architecturally separate representations for equivariance- and invariance-demanding tasks. To do so, our model processes short sequences of different views (observations) of inputs. Each encoded view is concatenated with an embedding of the relative transformation (action) that produces the next observation in the sequence. These view-action pairs are passed through a transformer encoder that outputs an aggregate representation. A predictor head then conditions this aggregate representation on the upcoming action to predict the representation of the next observation. Empirically, seq-JEPA demonstrates strong performance on both equivariance- and invariance-demanding downstream tasks without sacrificing one for the other. Furthermore, it excels at tasks that inherently require aggregating a sequence of observations, such as path integration across actions and predictive learning across eye movements.

cs.CV

GitChameleon: Unmasking the Version-Switching Capabilities of Code Generation Models

The rapid evolution of software libraries presents a significant challenge for code generation models, which must adapt to frequent version updates while maintaining compatibility with previous versions. Existing code completion benchmarks often overlook this dynamic aspect, and the one that does consider it relies on static code prediction tasks without execution-based evaluation, offering a limited perspective on a model's practical usability. To address this gap, we introduce \textbf{\GitChameleon{}}, a novel, manually curated dataset comprising 116 Python code completion problems, each conditioned on specific library versions and accompanied by executable unit tests. \GitChameleon{} is designed to rigorously assess the ability of modern large language models (LLMs) to generate version-specific code that is not only syntactically correct but also functionally accurate upon execution. Our comprehensive evaluations reveal that state-of-the-art LLMs struggle with this task; for instance, \textbf{GPT-4o} achieves a pass@10 of only 39.9\% (43.7\% when provided with error feedback), highlighting the complexity of the problem and the limitations of current models. By providing an execution-based benchmark that emphasizes the dynamic nature of code libraries, \GitChameleon{} serves as a critical tool to advance the development of more adaptable and reliable code generation models. For facilitation for further exploration of version-conditioned code generation, we make our code repository publicly accessible at \url{https://github.com/NizarIslah/GitChameleon}.

cs.SE

Learning to combine top-down context and feed-forward representations under ambiguity with apical and basal dendrites

One of the hallmark features of neocortical anatomy is the presence of extensive top-down projections into primary sensory areas, with many impinging on the distal apical dendrites of pyramidal neurons. While it is known that they exert a modulatory effect, altering the gain of responses, their functional role remains an active area of research. It is hypothesized that these top-down projections carry contextual information that can help animals to resolve ambiguities in sensory data. One proposed mechanism of contextual integration is a non-linear integration of distinct input streams at apical and basal dendrites of pyramidal neurons. Computationally, however, it is yet to be demonstrated how such an architecture could leverage distinct compartments for flexible contextual integration and sensory processing when both sensory and context signals can be unreliable. Here, we implement an augmented deep neural network with distinct apical and basal compartments that integrates a) contextual information from top-down projections to apical compartments, and b) sensory representations driven by bottom-up projections to basal compartments, via a biophysically inspired rule. In addition, we develop a new multi-scenario contextual integration task using a generative image modeling approach. In addition to generalizing previous contextual integration tasks, it better captures the diversity of scenarios where neither contextual nor sensory information are fully reliable. To solve this task, this model successfully learns to select among integration strategies. We find that our model outperforms those without the "apical prior" when contextual information contradicts sensory input. Altogether, this suggests that the apical prior and biophysically inspired integration rule could be key components necessary for handling the ambiguities that animals encounter in the diverse contexts of the real world.

q-bio.NC

Generating Diverse Realistic Laughter for Interactive Art

We propose an interactive art project to make those rendered invisible by the COVID-19 crisis and its concomitant solitude reappear through the welcome melody of laughter, and connections created and explored through advanced laughter synthesis approaches. However, the unconditional generation of the diversity of human emotional responses in high-quality auditory synthesis remains an open problem, with important implications for the application of these approaches in artistic settings. We developed LaughGANter, an approach to reproduce the diversity of human laughter using generative adversarial networks (GANs). When trained on a dataset of diverse laughter samples, LaughGANter generates diverse, high quality laughter samples, and learns a latent space suitable for emotional analysis and novel artistic applications such as latent mixing/interpolation and emotional transfer.

cs.LG

Predicting Infectiousness for Proactive Contact Tracing

The COVID-19 pandemic has spread rapidly worldwide, overwhelming manual contact tracing in many countries and resulting in widespread lockdowns for emergency containment. Large-scale digital contact tracing (DCT) has emerged as a potential solution to resume economic and social activity while minimizing spread of the virus. Various DCT methods have been proposed, each making trade-offs between privacy, mobility restrictions, and public health. The most common approach, binary contact tracing (BCT), models infection as a binary event, informed only by an individual's test results, with corresponding binary recommendations that either all or none of the individual's contacts quarantine. BCT ignores the inherent uncertainty in contacts and the infection process, which could be used to tailor messaging to high-risk individuals, and prompt proactive testing or earlier warnings. It also does not make use of observations such as symptoms or pre-existing medical conditions, which could be used to make more accurate infectiousness predictions. In this paper, we use a recently-proposed COVID-19 epidemiological simulator to develop and test methods that can be deployed to a smartphone to locally and proactively predict an individual's infectiousness (risk of infecting others) based on their contact history and other information, while respecting strong privacy constraints. Predictions are used to provide personalized recommendations to the individual via an app, as well as to send anonymized messages to the individual's contacts, who use this information to better predict their own infectiousness, an approach we call proactive contact tracing (PCT). We find a deep-learning based PCT method which improves over BCT for equivalent average mobility, suggesting PCT could help in safe re-opening and second-wave prevention.

cs.LG

Automated point-neuron simplification of data-driven microcircuit models

A method is presented for the reduction of morphologically detailed microcircuit models to a point-neuron representation without human intervention. The simplification occurs in a modular workflow, in the neighborhood of a user specified network activity state for the reference model, the "operating point". First, synapses are moved to the soma, correcting for dendritic filtering by low-pass filtering the delivered synaptic current. Filter parameters are computed numerically and independently for inhibitory and excitatory input using a Green's function approach. Next, point-neuron models for each neuron in the microcircuit are fit to their respective morphologically detailed counterparts. Here, generalized integrate-and-fire point neuron models are used, leveraging a recently published fitting toolbox. The fits are constrained by currents and voltages computed in the morphologically detailed partner neurons with soma corrected synapses at three depolarizations about the user specified operating point. The result is a simplified circuit which is well constrained by the reference circuit, and can be continuously updated as the latter iteratively integrates new data. The modularity of the approach makes it applicable also for other point-neuron and synapse models. The approach is demonstrated on a recently reported reconstruction of a neocortical microcircuit around an in vivo-like working point. The resulting simplified network model is benchmarked to the reference morphologically detailed microcircuit model for a range of simulated network protocols. The simplified network is found to be slightly more sub-critical than the reference, with otherwise good agreement for both quantitative and qualitative validations.

q-bio.NC

BluePyOpt: Leveraging open source software and cloud infrastructure to optimise model parameters in neuroscience

At many scales in neuroscience, appropriate mathematical models take the form of complex dynamical systems. Parametrising such models to conform to the multitude of available experimental constraints is a global nonlinear optimisation problem with a complex fitness landscape, requiring numerical techniques to find suitable approximate solutions. Stochastic optimisation approaches, such as evolutionary algorithms, have been shown to be effective, but often the setting up of such optimisations and the choice of a specific search algorithm and its parameters is non-trivial, requiring domain-specific expertise. Here we describe BluePyOpt, a Python package targeted at the broad neuroscience community to simplify this task. BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardises several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures. The versatility of the BluePyOpt framework is demonstrated by working through three representative neuroscience specific use cases.

q-bio.NC

Topological analysis of the connectome of digital reconstructions of neural microcircuits

A recent publication provides the network graph for a neocortical microcircuit comprising 8 million connections between 31,000 neurons (H. Markram, et al., Reconstruction and simulation of neocortical microcircuitry, Cell, 163 (2015) no. 2, 456-492). Since traditional graph-theoretical methods may not be sufficient to understand the immense complexity of such a biological network, we explored whether methods from algebraic topology could provide a new perspective on its structural and functional organization. Structural topological analysis revealed that directed graphs representing connectivity among neurons in the microcircuit deviated significantly from different varieties of randomized graph. In particular, the directed graphs contained in the order of $10^7$ simplices Ð groups of neurons with all-to-all directed connectivity. Some of these simplices contained up to 8 neurons, making them the most extreme neuronal clustering motif ever reported. Functional topological analysis of simulated neuronal activity in the microcircuit revealed novel spatio-temporal metrics that provide an effective classification of functional responses to qualitatively different stimuli. This study represents the first algebraic topological analysis of structural connectomics and connectomics-based spatio-temporal activity in a biologically realistic neural microcircuit. The methods used in the study show promise for more general applications in network science.

q-bio.NC

Cellular Adaptation Accounts for the Sparse and Reliable Sensory Stimulus Representation

Most neurons in peripheral sensory pathways initially respond vigorously when a preferred stimulus is presented, but adapt as stimulation continues. It is unclear how this phenomenon affects stimulus representation in the later stages of cortical sensory processing. Here, we show that a temporally sparse and reliable stimulus representation develops naturally in a network with adapting neurons. We find that cellular adaptation plays a critical role in the transient reduction of the trial-by-trial variability of cortical spiking, providing an explanation for a wide-spread and hitherto unexplained phenomenon by a simple mechanism. In insect olfaction, cellular adaptation is sufficient to explain the emergence of the temporally sparse and reliable stimulus representation in the mushroom body, independent of inhibitory mechanisms. Our results reveal a computational principle that relates neuronal firing rate adaptation to temporal sparse coding and variability suppression in nervous systems with a sequential processing architecture.

q-bio.NC

A Comprehensive Workflow for General-Purpose Neural Modeling with Highly Configurable Neuromorphic Hardware Systems

In this paper we present a methodological framework that meets novel requirements emerging from upcoming types of accelerated and highly configurable neuromorphic hardware systems. We describe in detail a device with 45 million programmable and dynamic synapses that is currently under development, and we sketch the conceptual challenges that arise from taking this platform into operation. More specifically, we aim at the establishment of this neuromorphic system as a flexible and neuroscientifically valuable modeling tool that can be used by non-hardware-experts. We consider various functional aspects to be crucial for this purpose, and we introduce a consistent workflow with detailed descriptions of all involved modules that implement the suggested steps: The integration of the hardware interface into the simulator-independent model description language PyNN; a fully automated translation between the PyNN domain and appropriate hardware configurations; an executable specification of the future neuromorphic system that can be seamlessly integrated into this biology-to-hardware mapping process as a test bench for all software layers and possible hardware design modifications; an evaluation scheme that deploys models from a dedicated benchmark library, compares the results generated by virtual or prototype hardware devices with reference software simulations and analyzes the differences. The integration of these components into one hardware-software workflow provides an ecosystem for ongoing preparative studies that support the hardware design process and represents the basis for the maturity of the model-to-hardware mapping software. The functionality and flexibility of the latter is proven with a variety of experimental results.

q-bio.NC

Adaptation Reduces Variability of the Neuronal Population Code

Sequences of events in noise-driven excitable systems with slow variables often show serial correlations among their intervals of events. Here, we employ a master equation for general non-renewal processes to calculate the interval and count statistics of superimposed processes governed by a slow adaptation variable. For an ensemble of spike-frequency adapting neurons this results in the regularization of the population activity and an enhanced post-synaptic signal decoding. We confirm our theoretical results in a population of cortical neurons.

physics.bio-ph

Sequential Sparsening by Successive Adaptation in Neural Populations

In the principal cells of the insect mushroom body, the Kenyon cells (KC), olfactory information is represented by a spatially and temporally sparse code. Each odor stimulus will activate only a small portion of neurons and each stimulus leads to only a short phasic response following stimulus onset irrespective of the actual duration of a constant stimulus. The mechanisms responsible for the sparse code in the KCs are yet unresolved. Here, we explore the role of the neuron-intrinsic mechanism of spike-frequency adaptation (SFA) in producing temporally sparse responses to sensory stimulation in higher processing stages. Our single neuron model is defined through a conductance-based integrate-and-fire neuron with spike-frequency adaptation [1]. We study a fully connected feed-forward network architecture in coarse analogy to the insect olfactory pathway. A first layer of ten neurons represents the projection neurons (PNs) of the antenna lobe. All PNs receive a step-like input from the olfactory receptor neurons, which was realized by independent Poisson processes. The second layer represents 100 KCs which converge onto ten neurons in the output layer which represents the population of mushroom body extrinsic neurons (ENs). Our simulation result matches with the experimental observations. In particular, intracellular recordings of PNs show a clear phasic-tonic response that outlasts the stimulus [2] while extracellular recordings from KCs in the locust express sharp transient responses [3]. We conclude that the neuron-intrinsic mechanism is can explain a progressive temporal response sparsening in the insect olfactory system. Further experimental work is needed to test this hypothesis empirically. [1] Muller et. al., Neural Comput, 19(11):2958-3010, 2007. [2] Assisi et. al., Nat Neurosci, 10(9):1176-1184, 2007. [3] Krofczik et. al. Front. Comput. Neurosci., 2(9), 2009.

physics.bio-ph