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Publications
Data harmonization for Advancing research on Personalized Rehabilitation Interventions for Patients with Traumatic Brain Injury and Stroke: A proof of concept
Stroke and traumatic brain injury (TBI) are leading causes of morbidity and mortality, affecting survivors’ mobility and social participat… (voir plus)ion. Although personalized interventions could positively impact survivors' recovery, the effectiveness of such interventions remains unclear. Open-access data repositories can provide access to multiple shared data which could help uncover new evidence of effective interventions; however, harmonizing data between different studies requires many steps to make it possible given the various methods of data collection, intervention characteristics and population sociodemographic profile. This proof-of-concept study aimed to describe the steps and anchors that contributed to the development of guiding frameworks to harmonize data across different studies. Data were extracted from the Federal Interagency Traumatic Brain Injury Research (FITBIR) repository and stored on an online cloud platform. The outcome measures were mapped to mobility determinants using the International Classification of Functioning, Disability, and Health (ICF) and Webber framework. The intervention's effect was categorized according to the Minimal Clinically Important Difference (MCID)s of the measures administered. The study proposed a novel framework for intervention features, which aims to enhance our understanding of the mechanisms of action and potential impact of rehabilitation interventions. The framework classified interventions based on their nature, context, specific body systems, dosage, caregiver assistance, and behaviour change strategies. In conclusion, this study demonstrated the feasibility of harmonizing data extracted from different sources in the FITBIR repository. Leveraging existing open databases offers tremendous opportunities to advance research on personalized interventions for patients with TBI and stroke and inform decision-making during transitions.
Despite extensive research on adversarial training strategies to improve robustness, the decisions of even the most robust deep learning mod… (voir plus)els can still be quite sensitive to imperceptible perturbations, creating serious risks when deploying them for high-stakes real-world applications. While detecting such cases may be critical, evaluating a model's vulnerability at a per-instance level using adversarial attacks is computationally too intensive and unsuitable for real-time deployment scenarios. The input space margin is the exact score to detect non-robust samples and is intractable for deep neural networks. This paper introduces the concept of margin consistency -- a property that links the input space margins and the logit margins in robust models -- for efficient detection of vulnerable samples. First, we establish that margin consistency is a necessary and sufficient condition to use a model's logit margin as a score for identifying non-robust samples. Next, through comprehensive empirical analysis of various robustly trained models on CIFAR10 and CIFAR100 datasets, we show that they indicate strong margin consistency with a strong correlation between their input space margins and the logit margins. Then, we show that we can effectively use the logit margin to confidently detect brittle decisions with such models and accurately estimate robust accuracy on an arbitrarily large test set by estimating the input margins only on a small subset. Finally, we address cases where the model is not sufficiently margin-consistent by learning a pseudo-margin from the feature representation. Our findings highlight the potential of leveraging deep representations to efficiently assess adversarial vulnerability in deployment scenarios.
We propose a general framework for automating data-structure design and apply it to the problem of nearest neighbor search. Our model adapts… (voir plus) to the underlying data distribution and provides fine-grained control over query and space complexity, enabling the discovery of solutions tailored to problem-specific constraints. We are able to reverse-engineer learned algorithms in several settings. In 1D, the model discovers optimal distribution (in)dependent algorithms such as binary search and variants of interpolation search. In higher dimensions, the model learns solutions that resemble K-d trees in some regimes, while in others, have elements of locality-sensitive hashing.
Mixtures of Experts (MoEs) have gained prominence in (self-)supervised learning due to their enhanced inference efficiency, adaptability to … (voir plus)distributed training, and modularity. Previous research has illustrated that MoEs can significantly boost Deep Reinforcement Learning (DRL) performance by expanding the network's parameter count while reducing dormant neurons, thereby enhancing the model's learning capacity and ability to deal with non-stationarity. In this work, we shed more light on MoEs' ability to deal with non-stationarity and investigate MoEs in DRL settings with"amplified"non-stationarity via multi-task training, providing further evidence that MoEs improve learning capacity. In contrast to previous work, our multi-task results allow us to better understand the underlying causes for the beneficial effect of MoE in DRL training, the impact of the various MoE components, and insights into how best to incorporate them in actor-critic-based DRL networks. Finally, we also confirm results from previous work.
Test-time augmentation (TTA) is a well-known technique employed during the testing phase of computer vision tasks. It involves aggregating m… (voir plus)ultiple augmented versions of input data. Combining predictions using a simple average formulation is a common and straightforward approach after performing TTA. This paper introduces a novel framework for optimizing TTA, called BayTTA (Bayesian-based TTA), which is based on Bayesian Model Averaging (BMA). First, we generate a model list associated with different variations of the input data created through TTA. Then, we use BMA to combine model predictions weighted by their respective posterior probabilities. Such an approach allows one to take into account model uncertainty, and thus to enhance the predictive performance of the related machine learning or deep learning model. We evaluate the performance of BayTTA on various public data, including three medical image datasets comprising skin cancer, breast cancer, and chest X-ray images and two well-known gene editing datasets, CRISPOR and GUIDE-seq. Our experimental results indicate that BayTTA can be effectively integrated into state-of-the-art deep learning models used in medical image analysis as well as into some popular pre-trained CNN models such as VGG-16, MobileNetV2, DenseNet201, ResNet152V2, and InceptionRes-NetV2, leading to the enhancement in their accuracy and robustness performance.
State-of-the-art results in large language models (LLMs) often rely on scale, which becomes computationally expensive. This has sparked a re… (voir plus)search agenda to reduce these models' parameter counts and computational costs without significantly impacting their performance. Our study focuses on transformer-based LLMs, specifically targeting the computationally intensive feedforward networks (FFNs), which are less studied than attention blocks. We consider three structured linear parameterizations of the FFN using efficient low-rank and block-diagonal matrices. In contrast to many previous works that examined these approximations, our study i) explores these structures from a training-from-scratch perspective, ii) scales up to 1.3B parameters, and iii) is conducted within recent Transformer-based LLMs rather than convolutional architectures. We demonstrate that these structures can lead to actual computational gains in various scenarios, including online decoding when using a pre-merge technique. Additionally, we propose a novel training regime, called \textit{self-guided training}, aimed at improving the poor training dynamics that these approximations exhibit when used from initialization. Interestingly, the scaling performance of structured matrices is explored, revealing steeper curves in scaling training FLOPs, along with a favorable scaling trend in the overtraining regime. Specifically, we show that wide and structured networks can utilize training FLOPs more efficiently, with fewer parameters and lower loss than dense models at their optimal trade-off. Our code is available at https://github.com/CLAIRE-Labo/StructuredFFN/tree/main.
Understanding the mechanisms behind decisions taken by large foundation models in sequential tasks is critical to ensuring that such systems… (voir plus) operate transparently and safely. However, interpretability methods have not yet been applied extensively to large-scale agents based on reinforcement learning. In this work, we perform exploratory analysis on the Video PreTraining (VPT) Minecraft playing agent, one of the largest open-source vision-based agents. We try to illuminate its reasoning mechanisms by applying various interpretability techniques. First, we analyze the attention mechanism while the agent solves its training task --- crafting a diamond pickaxe. The agent seems to pay attention to the 4 last frames and several key-frames further back. This provides clues as to how it maintains coherence in the task that takes 3-10 minutes, despite the agent's short memory span of only six seconds. Second, we perform various interventions, which help us uncover a worrying case of goal misgeneralization: VPT mistakenly identifies a villager wearing brown clothes as a tree trunk and punches it to death, when positioned stationary under green tree leaves. We demonstrate similar misbehavior in a related agent (STEVE-1), which motivates the use of VPT as a model organism for large-scale vision-based agent interpretability.
Methods for machine unlearning in large language models seek to remove undesirable knowledge or capabilities without compromising general la… (voir plus)nguage modeling performance.
This work investigates the use of mechanistic interpretability to improve the precision and effectiveness of unlearning.
We demonstrate that localizing unlearning to components with particular mechanisms in factual recall leads to more robust unlearning across different input/output formats, relearning, and latent knowledge, and reduces unintended side effects compared to nonlocalized unlearning.
Additionally, we analyze the strengths and weaknesses of different automated (rather than manual) interpretability methods for guiding unlearning, finding that their corresponding unlearned models require smaller edit sizes to achieve unlearning but are much less robust.
Methods for machine unlearning in large language models seek to remove undesirable knowledge or capabilities without compromising general la… (voir plus)nguage modeling performance.
This work investigates the use of mechanistic interpretability to improve the precision and effectiveness of unlearning.
We demonstrate that localizing unlearning to components with particular mechanisms in factual recall leads to more robust unlearning across different input/output formats, relearning, and latent knowledge, and reduces unintended side effects compared to nonlocalized unlearning.
Additionally, we analyze the strengths and weaknesses of different automated (rather than manual) interpretability methods for guiding unlearning, finding that their corresponding unlearned models require smaller edit sizes to achieve unlearning but are much less robust.
Automated sensors have potential to standardize and expand the monitoring of insects across the globe. As one of the most scalable and faste… (voir plus)st developing sensor technologies, we describe a framework for automated, image-based monitoring of nocturnal insects—from sensor development and field deployment to workflows for data processing and publishing. Sensors comprise a light to attract insects, a camera for collecting images and a computer for scheduling, data storage and processing. Metadata is important to describe sampling schedules that balance the capture of relevant ecological information against power and data storage limitations. Large data volumes of images from automated systems necessitate scalable and effective data processing. We describe computer vision approaches for the detection, tracking and classification of insects, including models built from existing aggregations of labelled insect images. Data from automated camera systems necessitate approaches that account for inherent biases. We advocate models that explicitly correct for bias in species occurrence or abundance estimates resulting from the imperfect detection of species or individuals present during sampling occasions. We propose ten priorities towards a step-change in automated monitoring of nocturnal insects, a vital task in the face of rapid biodiversity loss from global threats. This article is part of the theme issue ‘Towards a toolkit for global insect biodiversity monitoring’.
2024-06-24
Philosophical Transactions of the Royal Society B: Biological Sciences (publié)
Molecular discovery, when formulated as an optimization problem, presents significant computational challenges because optimization objectiv… (voir plus)es can be non-differentiable. Evolutionary Algorithms (EAs), often used to optimize black-box objectives in molecular discovery, traverse chemical space by performing random mutations and crossovers, leading to a large number of expensive objective evaluations. In this work, we ameliorate this shortcoming by incorporating chemistry-aware Large Language Models (LLMs) into EAs. Namely, we redesign crossover and mutation operations in EAs using LLMs trained on large corpora of chemical information. We perform extensive empirical studies on both commercial and open-source models on multiple tasks involving property optimization, molecular rediscovery, and structure-based drug design, demonstrating that the joint usage of LLMs with EAs yields superior performance over all baseline models across single- and multi-objective settings. We demonstrate that our algorithm improves both the quality of the final solution and convergence speed, thereby reducing the number of required objective evaluations. Our code is available at http://github.com/zoom-wang112358/MOLLEO
