We use cookies to analyze the browsing and usage of our website and to personalize your experience. You can disable these technologies at any time, but this may limit certain functionalities of the site. Read our Privacy Policy for more information.
Setting cookies
You can enable and disable the types of cookies you wish to accept. However certain choices you make could affect the services offered on our sites (e.g. suggestions, personalised ads, etc.).
Essential cookies
These cookies are necessary for the operation of the site and cannot be deactivated. (Still active)
Analytics cookies
Do you accept the use of cookies to measure the audience of our sites?
Multimedia Player
Do you accept the use of cookies to display and allow you to watch the video content hosted by our partners (YouTube, etc.)?
Publications
Multi-Scale Representation Learning for Protein Fitness Prediction
Designing novel functional proteins crucially depends on accurately modeling their fitness landscape. Given the limited availability of func… (see more)tional annotations from wet-lab experiments, previous methods have primarily relied on self-supervised models trained on vast, unlabeled protein sequence or structure datasets. While initial protein representation learning studies solely focused on either sequence or structural features, recent hybrid architectures have sought to merge these modalities to harness their respective strengths. However, these sequence-structure models have so far achieved only incremental improvements when compared to the leading sequence-only approaches, highlighting unresolved challenges effectively leveraging these modalities together. Moreover, the function of certain proteins is highly dependent on the granular aspects of their surface topology, which have been overlooked by prior models.
To address these limitations, we introduce the Sequence-Structure-Surface Fitness (**S3F**) model — a novel multimodal representation learning framework that integrates protein features across several scales. Our approach combines sequence representations from a protein language model with Geometric Vector Perceptron networks encoding protein backbone and detailed surface topology. The proposed method achieves state-of-the-art fitness prediction on the ProteinGym benchmark encompassing 217 substitution deep mutational scanning assays, and provides insights into the determinants of protein function.
Our code is at https://github.com/DeepGraphLearning/S3F.
Generative Flow Networks (GFlowNets; GFNs) are a family of energy-based generative methods for combinatorial objects, capable of generating … (see more)diverse and high-utility samples. However, consistently biasing GFNs towards producing high-utility samples is non-trivial. In this work, we leverage connections between GFNs and reinforcement learning (RL) and propose to combine the GFN policy with an action-value estimate,
The rapid progress in generative models has resulted in impressive leaps in generation quality, blurring the lines between synthetic and rea… (see more)l data. Web-scale datasets are now prone to the inevitable contamination by synthetic data, directly impacting the training of future generated models. Already, some theoretical results on self-consuming generative models (a.k.a., iterative retraining) have emerged in the literature, showcasing that either model collapse or stability could be possible depending on the fraction of generated data used at each retraining step. However, in practice, synthetic data is often subject to human feedback and curated by users before being used and uploaded online. For instance, many interfaces of popular text-to-image generative models, such as Stable Diffusion or Midjourney, produce several variations of an image for a given query which can eventually be curated by the users. In this paper, we theoretically study the impact of data curation on iterated retraining of generative models and show that it can be seen as an \emph{implicit preference optimization mechanism}. However, unlike standard preference optimization, the generative model does not have access to the reward function or negative samples needed for pairwise comparisons. Moreover, our study doesn't require access to the density function, only to samples. We prove that, if the data is curated according to a reward model, then the expected reward of the iterative retraining procedure is maximized. We further provide theoretical results on the stability of the retraining loop when using a positive fraction of real data at each step. Finally, we conduct illustrative experiments on both synthetic datasets and on CIFAR10 showing that such a procedure amplifies biases of the reward model.
Current research in adversarial robustness of LLMs focuses on discrete input manipulations in the natural language space, which can be direc… (see more)tly transferred to closed-source models. However, this approach neglects the steady progression of open-source models. As open-source models advance in capability, ensuring their safety also becomes increasingly imperative. Yet, attacks tailored to open-source LLMs that exploit full model access remain largely unexplored. We address this research gap and propose the embedding space attack, which directly attacks the continuous embedding representation of input tokens. We find that embedding space attacks circumvent model alignments and trigger harmful behaviors more efficiently than discrete attacks or model fine-tuning. Furthermore, we present a novel threat model in the context of unlearning and show that embedding space attacks can extract supposedly deleted information from unlearned LLMs across multiple datasets and models. Our findings highlight embedding space attacks as an important threat model in open-source LLMs. Trigger Warning: the appendix contains LLM-generated text with violence and harassment.
Source-free domain adaptation (SFDA) is a challenging problem in object detection, where a pre-trained source model is adapted to a new targ… (see more)et domain without using any source domain data for privacy and efficiency reasons. Most state-of-the-art SFDA methods for object detection have been proposed for Faster-RCNN, a detector that is known to have high computational complexity. This paper focuses on domain adaptation techniques for real-world vision systems, particularly for the YOLO family of single-shot detectors known for their fast baselines and practical applications. Our proposed SFDA method - Source-Free YOLO (SF-YOLO) - relies on a teacher-student framework in which the student receives images with a learned, target domain-specific augmentation, allowing the model to be trained with only unlabeled target data and without requiring feature alignment. A challenge with self-training using a mean-teacher architecture in the absence of labels is the rapid decline of accuracy due to noisy or drifting pseudo-labels. To address this issue, a teacher-to-student communication mechanism is introduced to help stabilize the training and reduce the reliance on annotated target data for model selection. Despite its simplicity, our approach is competitive with state-of-the-art detectors on several challenging benchmark datasets, even sometimes outperforming methods that use source data for adaptation.
