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Mar 11

CortexCompile: Harnessing Cortical-Inspired Architectures for Enhanced Multi-Agent NLP Code Synthesis

Current approaches to automated code generation often rely on monolithic models that lack real-time adaptability and scalability. This limitation is particularly evident in complex programming tasks that require dynamic adjustment and efficiency. The integration of neuroscience principles into Natural Language Processing (NLP) has the potential to revolutionize automated code generation. This paper presents CortexCompile, a novel modular system inspired by the specialized functions of the human brain's cortical regions. By emulating the distinct roles of the Prefrontal Cortex, Parietal Cortex, Temporal Lobe, and Motor Cortex, CortexCompile achieves significant advancements in scalability, efficiency, and adaptability compared to traditional monolithic models like GPT-4o. The system's architecture features a Task Orchestration Agent that manages dynamic task delegation and parallel processing, facilitating the generation of highly accurate and optimized code across increasingly complex programming tasks. Experimental evaluations demonstrate that CortexCompile consistently outperforms GPT-4o in development time, accuracy, and user satisfaction, particularly in tasks involving real-time strategy games and first-person shooters. These findings underscore the viability of neuroscience-inspired architectures in addressing the limitations of current NLP models, paving the way for more efficient and human-like AI systems.

LaVCa: LLM-assisted Visual Cortex Captioning

Understanding the property of neural populations (or voxels) in the human brain can advance our comprehension of human perceptual and cognitive processing capabilities and contribute to developing brain-inspired computer models. Recent encoding models using deep neural networks (DNNs) have successfully predicted voxel-wise activity. However, interpreting the properties that explain voxel responses remains challenging because of the black-box nature of DNNs. As a solution, we propose LLM-assisted Visual Cortex Captioning (LaVCa), a data-driven approach that uses large language models (LLMs) to generate natural-language captions for images to which voxels are selective. By applying LaVCa for image-evoked brain activity, we demonstrate that LaVCa generates captions that describe voxel selectivity more accurately than the previously proposed method. Furthermore, the captions generated by LaVCa quantitatively capture more detailed properties than the existing method at both the inter-voxel and intra-voxel levels. Furthermore, a more detailed analysis of the voxel-specific properties generated by LaVCa reveals fine-grained functional differentiation within regions of interest (ROIs) in the visual cortex and voxels that simultaneously represent multiple distinct concepts. These findings offer profound insights into human visual representations by assigning detailed captions throughout the visual cortex while highlighting the potential of LLM-based methods in understanding brain representations. Please check out our webpage at https://sites.google.com/view/lavca-llm/

Brain Diffusion for Visual Exploration: Cortical Discovery using Large Scale Generative Models

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach -- Brain Diffusion for Visual Exploration ("BrainDiVE") -- builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.

Diffeomorphic Mesh Deformation via Efficient Optimal Transport for Cortical Surface Reconstruction

Mesh deformation plays a pivotal role in many 3D vision tasks including dynamic simulations, rendering, and reconstruction. However, defining an efficient discrepancy between predicted and target meshes remains an open problem. A prevalent approach in current deep learning is the set-based approach which measures the discrepancy between two surfaces by comparing two randomly sampled point-clouds from the two meshes with Chamfer pseudo-distance. Nevertheless, the set-based approach still has limitations such as lacking a theoretical guarantee for choosing the number of points in sampled point-clouds, and the pseudo-metricity and the quadratic complexity of the Chamfer divergence. To address these issues, we propose a novel metric for learning mesh deformation. The metric is defined by sliced Wasserstein distance on meshes represented as probability measures that generalize the set-based approach. By leveraging probability measure space, we gain flexibility in encoding meshes using diverse forms of probability measures, such as continuous, empirical, and discrete measures via varifold representation. After having encoded probability measures, we can compare meshes by using the sliced Wasserstein distance which is an effective optimal transport distance with linear computational complexity and can provide a fast statistical rate for approximating the surface of meshes. To the end, we employ a neural ordinary differential equation (ODE) to deform the input surface into the target shape by modeling the trajectories of the points on the surface. Our experiments on cortical surface reconstruction demonstrate that our approach surpasses other competing methods in multiple datasets and metrics.

BrainSCUBA: Fine-Grained Natural Language Captions of Visual Cortex Selectivity

Understanding the functional organization of higher visual cortex is a central focus in neuroscience. Past studies have primarily mapped the visual and semantic selectivity of neural populations using hand-selected stimuli, which may potentially bias results towards pre-existing hypotheses of visual cortex functionality. Moving beyond conventional approaches, we introduce a data-driven method that generates natural language descriptions for images predicted to maximally activate individual voxels of interest. Our method -- Semantic Captioning Using Brain Alignments ("BrainSCUBA") -- builds upon the rich embedding space learned by a contrastive vision-language model and utilizes a pre-trained large language model to generate interpretable captions. We validate our method through fine-grained voxel-level captioning across higher-order visual regions. We further perform text-conditioned image synthesis with the captions, and show that our images are semantically coherent and yield high predicted activations. Finally, to demonstrate how our method enables scientific discovery, we perform exploratory investigations on the distribution of "person" representations in the brain, and discover fine-grained semantic selectivity in body-selective areas. Unlike earlier studies that decode text, our method derives voxel-wise captions of semantic selectivity. Our results show that BrainSCUBA is a promising means for understanding functional preferences in the brain, and provides motivation for further hypothesis-driven investigation of visual cortex.

Adaptive coding efficiency in recurrent cortical circuits via gain control

Sensory systems across all modalities and species exhibit adaptation to continuously changing input statistics. Individual neurons have been shown to modulate their response gains so as to maximize information transmission in different stimulus contexts. Experimental measurements have revealed additional, nuanced sensory adaptation effects including changes in response maxima and minima, tuning curve repulsion from the adapter stimulus, and stimulus-driven response decorrelation. Existing explanations of these phenomena rely on changes in inter-neuronal synaptic efficacy, which, while more flexible, are unlikely to operate as rapidly or reversibly as single neuron gain modulations. Using published V1 population adaptation data, we show that propagation of single neuron gain changes in a recurrent network is sufficient to capture the entire set of observed adaptation effects. We propose a novel adaptive efficient coding objective with which single neuron gains are modulated, maximizing the fidelity of the stimulus representation while minimizing overall activity in the network. From this objective, we analytically derive a set of gains that optimize the trade-off between preserving information about the stimulus and conserving metabolic resources. Our model generalizes well-established concepts of single neuron adaptive gain control to recurrent populations, and parsimoniously explains experimental adaptation data.

Aligned with LLM: a new multi-modal training paradigm for encoding fMRI activity in visual cortex

Recently, there has been a surge in the popularity of pre trained large language models (LLMs) (such as GPT-4), sweeping across the entire Natural Language Processing (NLP) and Computer Vision (CV) communities. These LLMs have demonstrated advanced multi-modal understanding capabilities and showcased strong performance across various benchmarks. The LLM has started to embody traits of artificial general intelligence, which holds vital guidance for enhancing brain-like characteristics within visual encoding models. Hence, This paper proposes a new multi-modal training paradigm, aligning with LLM, for encoding fMRI activity in visual cortex. Based on this paradigm, we trained an encoding model in fMRI data named the LLM-Visual Encoding Model (LLM-VEM). Specifically, we utilize LLM (miniGPT4) to generate descriptive text for all stimulus images, forming a high-quality textual description set. Moreover, we use the pre-trained text encoder (CLIP) to process these detailed descriptions, obtaining the text embedding features. Next, we use the contrast loss function to minimize the distance between the image embedding features and the text embedding features to complete the alignment operation of the stimulus image and text information. With the assistance of the pre-trained LLM, this alignment process facilitates better learning of the visual encoding model, resulting in higher precision. The final experimental results indicate that our training paradigm has significantly aided in enhancing the performance of the visual encoding model.

The KiTS21 Challenge: Automatic segmentation of kidneys, renal tumors, and renal cysts in corticomedullary-phase CT

This paper presents the challenge report for the 2021 Kidney and Kidney Tumor Segmentation Challenge (KiTS21) held in conjunction with the 2021 international conference on Medical Image Computing and Computer Assisted Interventions (MICCAI). KiTS21 is a sequel to its first edition in 2019, and it features a variety of innovations in how the challenge was designed, in addition to a larger dataset. A novel annotation method was used to collect three separate annotations for each region of interest, and these annotations were performed in a fully transparent setting using a web-based annotation tool. Further, the KiTS21 test set was collected from an outside institution, challenging participants to develop methods that generalize well to new populations. Nonetheless, the top-performing teams achieved a significant improvement over the state of the art set in 2019, and this performance is shown to inch ever closer to human-level performance. An in-depth meta-analysis is presented describing which methods were used and how they faired on the leaderboard, as well as the characteristics of which cases generally saw good performance, and which did not. Overall KiTS21 facilitated a significant advancement in the state of the art in kidney tumor segmentation, and provides useful insights that are applicable to the field of semantic segmentation as a whole.

Enhancing the Stability of LLM-based Speech Generation Systems through Self-Supervised Representations

Large Language Models (LLMs) are one of the most promising technologies for the next era of speech generation systems, due to their scalability and in-context learning capabilities. Nevertheless, they suffer from multiple stability issues at inference time, such as hallucinations, content skipping or speech repetitions. In this work, we introduce a new self-supervised Voice Conversion (VC) architecture which can be used to learn to encode transitory features, such as content, separately from stationary ones, such as speaker ID or recording conditions, creating speaker-disentangled representations. Using speaker-disentangled codes to train LLMs for text-to-speech (TTS) allows the LLM to generate the content and the style of the speech only from the text, similarly to humans, while the speaker identity is provided by the decoder of the VC model. Results show that LLMs trained over speaker-disentangled self-supervised representations provide an improvement of 4.7pp in speaker similarity over SOTA entangled representations, and a word error rate (WER) 5.4pp lower. Furthermore, they achieve higher naturalness than human recordings of the LibriTTS test-other dataset. Finally, we show that using explicit reference embedding negatively impacts intelligibility (stability), with WER increasing by 14pp compared to the model that only uses text to infer the style.

Textualized and Feature-based Models for Compound Multimodal Emotion Recognition in the Wild

Systems for multimodal emotion recognition (ER) are commonly trained to extract features from different modalities (e.g., visual, audio, and textual) that are combined to predict individual basic emotions. However, compound emotions often occur in real-world scenarios, and the uncertainty of recognizing such complex emotions over diverse modalities is challenging for feature-based models As an alternative, emerging multimodal large language models (LLMs) like BERT and LLaMA rely on explicit non-verbal cues that may be translated from different non-textual modalities (e.g., audio and visual) into text. Textualization of modalities augments data with emotional cues to help the LLM encode the interconnections between all modalities in a shared text space. In such text-based models, prior knowledge of ER tasks is leveraged to textualize relevant nonverbal cues such as audio tone from vocal expressions, and action unit intensity from facial expressions. Since the pre-trained weights are publicly available for many LLMs, training on large-scale datasets is unnecessary, allowing fine-tuning for downstream tasks such as compound ER (CER). This paper compares the potential of text- and feature-based approaches for compound multimodal ER in videos. Experiments were conducted on the challenging C-EXPR-DB dataset in the wild for CER, and contrasted with results on the MELD dataset for basic ER. Our results indicate that multimodal textualization provides lower accuracy than feature-based models on C-EXPR-DB, where text transcripts are captured in the wild. However, higher accuracy can be achieved when the video data has rich transcripts. Our code is available.

Do As I Can, Not As I Say: Grounding Language in Robotic Affordances

Large language models can encode a wealth of semantic knowledge about the world. Such knowledge could be extremely useful to robots aiming to act upon high-level, temporally extended instructions expressed in natural language. However, a significant weakness of language models is that they lack real-world experience, which makes it difficult to leverage them for decision making within a given embodiment. For example, asking a language model to describe how to clean a spill might result in a reasonable narrative, but it may not be applicable to a particular agent, such as a robot, that needs to perform this task in a particular environment. We propose to provide real-world grounding by means of pretrained skills, which are used to constrain the model to propose natural language actions that are both feasible and contextually appropriate. The robot can act as the language model's "hands and eyes," while the language model supplies high-level semantic knowledge about the task. We show how low-level skills can be combined with large language models so that the language model provides high-level knowledge about the procedures for performing complex and temporally-extended instructions, while value functions associated with these skills provide the grounding necessary to connect this knowledge to a particular physical environment. We evaluate our method on a number of real-world robotic tasks, where we show the need for real-world grounding and that this approach is capable of completing long-horizon, abstract, natural language instructions on a mobile manipulator. The project's website and the video can be found at https://say-can.github.io/.

Helping LLMs Improve Code Generation Using Feedback from Testing and Static Analysis

Large Language Models (LLMs) are one of the most promising developments in the field of artificial intelligence, and the software engineering community has readily noticed their potential role in the software development life-cycle. Developers routinely ask LLMs to generate code snippets, increasing productivity but also potentially introducing ownership, privacy, correctness, and security issues. Previous work highlighted how code generated by mainstream commercial LLMs is often not safe, containing vulnerabilities, bugs, and code smells. In this paper, we present a framework that leverages testing and static analysis to assess the quality, and guide the self-improvement, of code generated by general-purpose, open-source LLMs. First, we ask LLMs to generate C code to solve a number of programming tasks. Then we employ ground-truth tests to assess the (in)correctness of the generated code, and a static analysis tool to detect potential safety vulnerabilities. Next, we assess the models ability to evaluate the generated code, by asking them to detect errors and vulnerabilities. Finally, we test the models ability to fix the generated code, providing the reports produced during the static analysis and incorrectness evaluation phases as feedback. Our results show that models often produce incorrect code, and that the generated code can include safety issues. Moreover, they perform very poorly at detecting either issue. On the positive side, we observe a substantial ability to fix flawed code when provided with information about failed tests or potential vulnerabilities, indicating a promising avenue for improving the safety of LLM-based code generation tools.

The LHCb ultra-fast simulation option, Lamarr: design and validation

Detailed detector simulation is the major consumer of CPU resources at LHCb, having used more than 90% of the total computing budget during Run 2 of the Large Hadron Collider at CERN. As data is collected by the upgraded LHCb detector during Run 3 of the LHC, larger requests for simulated data samples are necessary, and will far exceed the pledged resources of the experiment, even with existing fast simulation options. An evolution of technologies and techniques to produce simulated samples is mandatory to meet the upcoming needs of analysis to interpret signal versus background and measure efficiencies. In this context, we propose Lamarr, a Gaudi-based framework designed to offer the fastest solution for the simulation of the LHCb detector. Lamarr consists of a pipeline of modules parameterizing both the detector response and the reconstruction algorithms of the LHCb experiment. Most of the parameterizations are made of Deep Generative Models and Gradient Boosted Decision Trees trained on simulated samples or alternatively, where possible, on real data. Embedding Lamarr in the general LHCb Gauss Simulation framework allows combining its execution with any of the available generators in a seamless way. Lamarr has been validated by comparing key reconstructed quantities with Detailed Simulation. Good agreement of the simulated distributions is obtained with two-order-of-magnitude speed-up of the simulation phase.

The WMDP Benchmark: Measuring and Reducing Malicious Use With Unlearning

The White House Executive Order on Artificial Intelligence highlights the risks of large language models (LLMs) empowering malicious actors in developing biological, cyber, and chemical weapons. To measure these risks of malicious use, government institutions and major AI labs are developing evaluations for hazardous capabilities in LLMs. However, current evaluations are private, preventing further research into mitigating risk. Furthermore, they focus on only a few, highly specific pathways for malicious use. To fill these gaps, we publicly release the Weapons of Mass Destruction Proxy (WMDP) benchmark, a dataset of 4,157 multiple-choice questions that serve as a proxy measurement of hazardous knowledge in biosecurity, cybersecurity, and chemical security. WMDP was developed by a consortium of academics and technical consultants, and was stringently filtered to eliminate sensitive information prior to public release. WMDP serves two roles: first, as an evaluation for hazardous knowledge in LLMs, and second, as a benchmark for unlearning methods to remove such hazardous knowledge. To guide progress on unlearning, we develop CUT, a state-of-the-art unlearning method based on controlling model representations. CUT reduces model performance on WMDP while maintaining general capabilities in areas such as biology and computer science, suggesting that unlearning may be a concrete path towards reducing malicious use from LLMs. We release our benchmark and code publicly at https://wmdp.ai

Barkour: Benchmarking Animal-level Agility with Quadruped Robots

Animals have evolved various agile locomotion strategies, such as sprinting, leaping, and jumping. There is a growing interest in developing legged robots that move like their biological counterparts and show various agile skills to navigate complex environments quickly. Despite the interest, the field lacks systematic benchmarks to measure the performance of control policies and hardware in agility. We introduce the Barkour benchmark, an obstacle course to quantify agility for legged robots. Inspired by dog agility competitions, it consists of diverse obstacles and a time based scoring mechanism. This encourages researchers to develop controllers that not only move fast, but do so in a controllable and versatile way. To set strong baselines, we present two methods for tackling the benchmark. In the first approach, we train specialist locomotion skills using on-policy reinforcement learning methods and combine them with a high-level navigation controller. In the second approach, we distill the specialist skills into a Transformer-based generalist locomotion policy, named Locomotion-Transformer, that can handle various terrains and adjust the robot's gait based on the perceived environment and robot states. Using a custom-built quadruped robot, we demonstrate that our method can complete the course at half the speed of a dog. We hope that our work represents a step towards creating controllers that enable robots to reach animal-level agility.

Anatomical Foundation Models for Brain MRIs

Deep Learning (DL) in neuroimaging has become increasingly relevant for detecting neurological conditions and neurodegenerative disorders. One of the most predominant biomarkers in neuroimaging is represented by brain age, which has been shown to be a good indicator for different conditions, such as Alzheimer's Disease. Using brain age for weakly supervised pre-training of DL models in transfer learning settings has also recently shown promising results, especially when dealing with data scarcity of different conditions. On the other hand, anatomical information of brain MRIs (e.g. cortical thickness) can provide important information for learning good representations that can be transferred to many downstream tasks. In this work, we propose AnatCL, an anatomical foundation model for brain MRIs that i.) leverages anatomical information in a weakly contrastive learning approach, and ii.) achieves state-of-the-art performances across many different downstream tasks. To validate our approach we consider 12 different downstream tasks for the diagnosis of different conditions such as Alzheimer's Disease, autism spectrum disorder, and schizophrenia. Furthermore, we also target the prediction of 10 different clinical assessment scores using structural MRI data. Our findings show that incorporating anatomical information during pre-training leads to more robust and generalizable representations. Pre-trained models can be found at: https://github.com/EIDOSLAB/AnatCL.

The Expressive Leaky Memory Neuron: an Efficient and Expressive Phenomenological Neuron Model Can Solve Long-Horizon Tasks

Biological cortical neurons are remarkably sophisticated computational devices, temporally integrating their vast synaptic input over an intricate dendritic tree, subject to complex, nonlinearly interacting internal biological processes. A recent study proposed to characterize this complexity by fitting accurate surrogate models to replicate the input-output relationship of a detailed biophysical cortical pyramidal neuron model and discovered it needed temporal convolutional networks (TCN) with millions of parameters. Requiring these many parameters, however, could stem from a misalignment between the inductive biases of the TCN and cortical neuron's computations. In light of this, and to explore the computational implications of leaky memory units and nonlinear dendritic processing, we introduce the Expressive Leaky Memory (ELM) neuron model, a biologically inspired phenomenological model of a cortical neuron. Remarkably, by exploiting such slowly decaying memory-like hidden states and two-layered nonlinear integration of synaptic input, our ELM neuron can accurately match the aforementioned input-output relationship with under ten thousand trainable parameters. To further assess the computational ramifications of our neuron design, we evaluate it on various tasks with demanding temporal structures, including the Long Range Arena (LRA) datasets, as well as a novel neuromorphic dataset based on the Spiking Heidelberg Digits dataset (SHD-Adding). Leveraging a larger number of memory units with sufficiently long timescales, and correspondingly sophisticated synaptic integration, the ELM neuron displays substantial long-range processing capabilities, reliably outperforming the classic Transformer or Chrono-LSTM architectures on LRA, and even solving the Pathfinder-X task with over 70% accuracy (16k context length).