arXiv subjects

Gabriel Bénédict

Publications and source records attributed to Gabriel Bénédict.

6 recordsLinked to original sources

arXiv2026

When Edit Flows are Edit Jumps: replicating Edit Flows and EvoFlows

Antibody lead optimization calls for a small, bounded set of edits to an existing candidate: substitutions, but also insertions and deletions. Edit-based generative models are the only ones that allocate such an edit budget without fixing the edit positions, the edit count, or the output length in advance. However, the existing approaches Edit Flows and EvoFlows did not release code or complete training specifications. Here, we show that both methods follow the same underlying process -- edits firing one at a time, at learned rates, in continuous time -- the pure-jump case of generator matching over finite sequences. With EditJumps we introduce the first open implementation of this framework, with a single generalist antibody editor trained on 1.66M Observed Antibody Space homolog pairs to propose homolog-like variants of a seed sequence, editing unseen leads zero-shot, without the per-family retraining original approaches require. Replicating this system from scratch exposes why open code is essential for generative biology: reconciling published edit distributions required reverse-engineering an undocumented rate-scaling hyperparameter that dictates realized mutation counts. Moreover, we show that published evaluation metrics are highly sensitive to reference sample size, frequently flipping method rankings. We release our full codebase, automated test suite, and configurations at: https://github.com/VisiumCH/editjumps

cs.LG↗

arXiv2025

SIM: Surface-based fMRI Analysis for Inter-Subject Multimodal Decoding from Movie-Watching Experiments

Current AI frameworks for brain decoding and encoding, typically train and test models within the same datasets. This limits their utility for brain computer interfaces (BCI) or neurofeedback, for which it would be useful to pool experiences across individuals to better simulate stimuli not sampled during training. A key obstacle to model generalisation is the degree of variability of inter-subject cortical organisation, which makes it difficult to align or compare cortical signals across participants. In this paper we address this through the use of surface vision transformers, which build a generalisable model of cortical functional dynamics, through encoding the topography of cortical networks and their interactions as a moving image across a surface. This is then combined with tri-modal self-supervised contrastive (CLIP) alignment of audio, video, and fMRI modalities to enable the retrieval of visual and auditory stimuli from patterns of cortical activity (and vice-versa). We validate our approach on 7T task-fMRI data from 174 healthy participants engaged in the movie-watching experiment from the Human Connectome Project (HCP). Results show that it is possible to detect which movie clips an individual is watching purely from their brain activity, even for individuals and movies not seen during training. Further analysis of attention maps reveals that our model captures individual patterns of brain activity that reflect semantic and visual systems. This opens the door to future personalised simulations of brain function. Code & pre-trained models will be made available at https://github.com/metrics-lab/sim, processed data for training will be available upon request at https://gin.g-node.org/Sdahan30/sim.

cs.LG↗

arXiv2023

RecFusion: A Binomial Diffusion Process for 1D Data for Recommendation

In this paper we propose RecFusion, which comprise a set of diffusion models for recommendation. Unlike image data which contain spatial correlations, a user-item interaction matrix, commonly utilized in recommendation, lacks spatial relationships between users and items. We formulate diffusion on a 1D vector and propose binomial diffusion, which explicitly models binary user-item interactions with a Bernoulli process. We show that RecFusion approaches the performance of complex VAE baselines on the core recommendation setting (top-n recommendation for binary non-sequential feedback) and the most common datasets (MovieLens and Netflix). Our proposed diffusion models that are specialized for 1D and/or binary setups have implications beyond recommendation systems, such as in the medical domain with MRI and CT scans.

cs.IR↗

arXiv2023

Gen-IR @ SIGIR 2023: The First Workshop on Generative Information Retrieval

Generative information retrieval (IR) has experienced substantial growth across multiple research communities (e.g., information retrieval, computer vision, natural language processing, and machine learning), and has been highly visible in the popular press. Theoretical, empirical, and actual user-facing products have been released that retrieve documents (via generation) or directly generate answers given an input request. We would like to investigate whether end-to-end generative models are just another trend or, as some claim, a paradigm change for IR. This necessitates new metrics, theoretical grounding, evaluation methods, task definitions, models, user interfaces, etc. The goal of this workshop (https://coda.io/@sigir/gen-ir) is to focus on previously explored Generative IR techniques like document retrieval and direct Grounded Answer Generation, while also offering a venue for the discussion and exploration of how Generative IR can be applied to new domains like recommendation systems, summarization, etc. The format of the workshop is interactive, including roundtable and keynote sessions and tends to avoid the one-sided dialogue of a mini-conference.

cs.IR↗

arXiv2022

sigmoidF1: A Smooth F1 Score Surrogate Loss for Multilabel Classification

Multiclass multilabel classification is the task of attributing multiple labels to examples via predictions. Current models formulate a reduction of the multilabel setting into either multiple binary classifications or multiclass classification, allowing for the use of existing loss functions (sigmoid, cross-entropy, logistic, etc.). Multilabel classification reductions do not accommodate for the prediction of varying numbers of labels per example and the underlying losses are distant estimates of the performance metrics. We propose a loss function, sigmoidF1, which is an approximation of the F1 score that (1) is smooth and tractable for stochastic gradient descent, (2) naturally approximates a multilabel metric, and (3) estimates label propensities and label counts. We show that any confusion matrix metric can be formulated with a smooth surrogate. We evaluate the proposed loss function on text and image datasets, and with a variety of metrics, to account for the complexity of multilabel classification evaluation. sigmoidF1 outperforms other loss functions on one text and two image datasets and several metrics. These results show the effectiveness of using inference-time metrics as loss functions for non-trivial classification problems like multilabel classification.

cs.LG↗

arXiv2022

RADio -- Rank-Aware Divergence Metrics to Measure Normative Diversity in News Recommendations

In traditional recommender system literature, diversity is often seen as the opposite of similarity, and typically defined as the distance between identified topics, categories or word models. However, this is not expressive of the social science's interpretation of diversity, which accounts for a news organization's norms and values and which we here refer to as normative diversity. We introduce RADio, a versatile metrics framework to evaluate recommendations according to these normative goals. RADio introduces a rank-aware Jensen Shannon (JS) divergence. This combination accounts for (i) a user's decreasing propensity to observe items further down a list and (ii) full distributional shifts as opposed to point estimates. We evaluate RADio's ability to reflect five normative concepts in news recommendations on the Microsoft News Dataset and six (neural) recommendation algorithms, with the help of our metadata enrichment pipeline. We find that RADio provides insightful estimates that can potentially be used to inform news recommender system design.

cs.IR↗