Boulbaba Ben Amor

Jie Qin, Shuaihang Yuan, Jiaxin Chen et al.

Sketch-based 3D shape retrieval (SBSR) is an important yet challenging task, which has drawn more and more attention in recent years. Existing approaches address the problem in a restricted setting, without appropriately simulating real application scenarios. To mimic the realistic setting, in this track, we adopt large-scale sketches drawn by amateurs of different levels of drawing skills, as well as a variety of 3D shapes including not only CAD models but also models scanned from real objects. We define two SBSR tasks and construct two benchmarks consisting of more than 46,000 CAD models, 1,700 realistic models, and 145,000 sketches in total. Four teams participated in this track and submitted 15 runs for the two tasks, evaluated by 7 commonly-adopted metrics. We hope that, the benchmarks, the comparative results, and the open-sourced evaluation code will foster future research in this direction among the 3D object retrieval community.

Umaima Rahman, Raza Imam, Mohammad Yaqub et al.

In medical image classification, supervised learning is challenging due to the scarcity of labeled medical images. To address this, we leverage the visual-textual alignment within Vision-Language Models (VLMs) to enable unsupervised learning of a medical image classifier. In this work, we propose \underline{Med}ical \underline{Un}supervised \underline{A}daptation (\texttt{MedUnA}) of VLMs, where the LLM-generated descriptions for each class are encoded into text embeddings and matched with class labels via a cross-modal adapter. This adapter attaches to a visual encoder of \texttt{MedCLIP} and aligns the visual embeddings through unsupervised learning, driven by a contrastive entropy-based loss and prompt tuning. Thereby, improving performance in scenarios where textual information is more abundant than labeled images, particularly in the healthcare domain. Unlike traditional VLMs, \texttt{MedUnA} uses \textbf{unpaired images and text} for learning representations and enhances the potential of VLMs beyond traditional constraints. We evaluate the performance on three chest X-ray datasets and two multi-class datasets (diabetic retinopathy and skin lesions), showing significant accuracy gains over the zero-shot baseline. Our code is available at https://github.com/rumaima/meduna.

Syed Waqas Zamir, Wassim Hamidouche, Boulbaba Ben Amor et al.

Large Language Models (LLMs) exhibit strong multilingual capabilities, yet remain fundamentally constrained by the severe imbalance in global language resources. While over 7,000 languages are spoken worldwide, only a small subset (fewer than 100) has sufficient digital presence to meaningfully influence modern LLM training. This disparity leads to systematic underperformance, cultural misalignment, and limited accessibility for speakers of low-resource and extreme-low-resource languages. To address this gap, we introduce Bring Your Own Language (BYOL), a unified framework for scalable, language-aware LLM development tailored to each language's digital footprint. BYOL begins with a language resource classification that maps languages into four tiers (Extreme-Low, Low, Mid, High) using curated web-scale corpora, and uses this classification to select the appropriate integration pathway. For low-resource languages, we propose a full-stack data refinement and expansion pipeline that combines corpus cleaning, synthetic text generation, continual pretraining, and supervised finetuning. Applied to Chichewa and Maori, this pipeline yields language-specific LLMs that achieve approximately 12 percent average improvement over strong multilingual baselines across 12 benchmarks, while preserving English and multilingual capabilities via weight-space model merging. For extreme-low-resource languages, we introduce a translation-mediated inclusion pathway, and show on Inuktitut that a tailored machine translation system improves over a commercial baseline by 4 BLEU, enabling high-accuracy LLM access when direct language modeling is infeasible. Finally, we release human-translated versions of the Global MMLU-Lite benchmark in Chichewa, Maori, and Inuktitut, and make our codebase and models publicly available at https://github.com/microsoft/byol .

Aahan Singh, Engin Tekin, Maryam Nadeem et al.

Revolutionizing drug discovery demands more than just understanding molecular interactions - it requires generative models that can design novel ligands tailored to specific biological targets. While chemical Language Models (cLMs) have made strides in learning molecular properties, most fail to incorporate target-specific insights, restricting their ability to drive de-novo ligand generation. Chem42, a cutting-edge family of generative chemical Language Models, is designed to bridge this gap. By integrating atomic-level interactions with multimodal inputs from Prot42, a complementary protein Language Model, Chem42 achieves a sophisticated cross-modal representation of molecular structures, interactions, and binding patterns. This innovative framework enables the creation of structurally valid, synthetically accessible ligands with enhanced target specificity. Evaluations across diverse protein targets confirm that Chem42 surpasses existing approaches in chemical validity, target-aware design, and predicted binding affinity. By reducing the search space of viable drug candidates, Chem42 could accelerate the drug discovery pipeline, offering a powerful generative AI tool for precision medicine. Our Chem42 models set a new benchmark in molecule property prediction, conditional molecule generation, and target-aware ligand design. The models are publicly available at huggingface.co/inceptionai.

Kirill Vishniakov, Boulbaba Ben Amor, Engin Tekin et al.

We introduce Gene42, a novel family of Genomic Foundation Models (GFMs) designed to manage context lengths of up to 192,000 base pairs (bp) at a single-nucleotide resolution. Gene42 models utilize a decoder-only (LLaMA-style) architecture with a dense self-attention mechanism. Initially trained on fixed-length sequences of 4,096 bp, our models underwent continuous pretraining to extend the context length to 192,000 bp. This iterative extension allowed for the comprehensive processing of large-scale genomic data and the capture of intricate patterns and dependencies within the human genome. Gene42 is the first dense attention model capable of handling such extensive long context lengths in genomics, challenging state-space models that often rely on convolutional operators among other mechanisms. Our pretrained models exhibit notably low perplexity values and high reconstruction accuracy, highlighting their strong ability to model genomic data. Extensive experiments on various genomic benchmarks have demonstrated state-of-the-art performance across multiple tasks, including biotype classification, regulatory region identification, chromatin profiling prediction, variant pathogenicity prediction, and species classification. The models are publicly available at huggingface.co/inceptionai.

Clément Christophe, Praveen K Kanithi, Prateek Munjal et al.

This study presents a comprehensive analysis and comparison of two predominant fine-tuning methodologies - full-parameter fine-tuning and parameter-efficient tuning - within the context of medical Large Language Models (LLMs). We developed and refined a series of LLMs, based on the Llama-2 architecture, specifically designed to enhance medical knowledge retrieval, reasoning, and question-answering capabilities. Our experiments systematically evaluate the effectiveness of these tuning strategies across various well-known medical benchmarks. Notably, our medical LLM Med42 showed an accuracy level of 72% on the US Medical Licensing Examination (USMLE) datasets, setting a new standard in performance for openly available medical LLMs. Through this comparative analysis, we aim to identify the most effective and efficient method for fine-tuning LLMs in the medical domain, thereby contributing significantly to the advancement of AI-driven healthcare applications.

Mohammad Amaan Sayeed, Engin Tekin, Maryam Nadeem et al.

Unlocking the next generation of biotechnology and therapeutic innovation demands overcoming the inherent complexity and resource-intensity of conventional protein engineering methods. Recent GenAI-powered computational techniques often rely on the availability of the target protein's 3D structures and specific binding sites to generate high-affinity binders, constraints exhibited by models such as AlphaProteo and RFdiffusion. In this work, we explore the use of Protein Language Models (pLMs) for high-affinity binder generation. We introduce Prot42, a novel family of Protein Language Models (pLMs) pretrained on vast amounts of unlabeled protein sequences. By capturing deep evolutionary, structural, and functional insights through an advanced auto-regressive, decoder-only architecture inspired by breakthroughs in natural language processing, Prot42 dramatically expands the capabilities of computational protein design based on language only. Remarkably, our models handle sequences up to 8,192 amino acids, significantly surpassing standard limitations and enabling precise modeling of large proteins and complex multi-domain sequences. Demonstrating powerful practical applications, Prot42 excels in generating high-affinity protein binders and sequence-specific DNA-binding proteins. Our innovative models are publicly available, offering the scientific community an efficient and precise computational toolkit for rapid protein engineering.

Hao Huang, Boulbaba Ben Amor, Xichan Lin et al.

Analyzing the structure of proteins is a key part of understanding their functions and thus their role in biology at the molecular level. In addition, design new proteins in a methodical way is a major engineering challenge. In this work, we introduce a joint geometric-neural networks approach for comparing, deforming and generating 3D protein structures. Viewing protein structures as 3D open curves, we adopt the Square Root Velocity Function (SRVF) representation and leverage its suitable geometric properties along with Deep Residual Networks (ResNets) for a joint registration and comparison. Our ResNets handle better large protein deformations while being more computationally efficient. On top of the mathematical framework, we further design a Geometric Variational Auto-Encoder (G-VAE), that once trained, maps original, previously unseen structures, into a low-dimensional (latent) hyper-sphere. Motivated by the spherical structure of the pre-shape space, we naturally adopt the von Mises-Fisher (vMF) distribution to model our hidden variables. We test the effectiveness of our models by generating novel protein structures and predicting completions of corrupted protein structures. Experimental results show that our method is able to generate plausible structures, different from the structures in the training data.

Hao Huang, Boulbaba Ben Amor, Xichan Lin et al.

Non-linear (large) time warping is a challenging source of nuisance in time-series analysis. In this paper, we propose a novel diffeomorphic temporal transformer network for both pairwise and joint time-series alignment. Our ResNet-TW (Deep Residual Network for Time Warping) tackles the alignment problem by compositing a flow of incremental diffeomorphic mappings. Governed by the flow equation, our Residual Network (ResNet) builds smooth, fluid and regular flows of velocity fields and consequently generates smooth and invertible transformations (i.e. diffeomorphic warping functions). Inspired by the elegant Large Deformation Diffeomorphic Metric Mapping (LDDMM) framework, the final transformation is built by the flow of time-dependent vector fields which are none other than the building blocks of our Residual Network. The latter is naturally viewed as an Eulerian discretization schema of the flow equation (an ODE). Once trained, our ResNet-TW aligns unseen data by a single inexpensive forward pass. As we show in experiments on both univariate (84 datasets from UCR archive) and multivariate time-series (MSR Action-3D, Florence-3D and MSR Daily Activity), ResNet-TW achieves competitive performance in joint alignment and classification.

Qingkai Zhen, Di Huang, Yunhong Wang et al.

In this paper, an effective pipeline to automatic 4D Facial Expression Recognition (4D FER) is proposed. It combines two growing but disparate ideas in Computer Vision -- computing the spatial facial deformations using tools from Riemannian geometry and magnifying them using temporal filtering. The flow of 3D faces is first analyzed to capture the spatial deformations based on the recently-developed Riemannian approach, where registration and comparison of neighboring 3D faces are led jointly. Then, the obtained temporal evolution of these deformations are fed into a magnification method in order to amplify the facial activities over the time. The latter, main contribution of this paper, allows revealing subtle (hidden) deformations which enhance the emotion classification performance. We evaluated our approach on BU-4DFE dataset, the state-of-art 94.18% average performance and an improvement that exceeds 10% in classification accuracy, after magnifying extracted geometric features (deformations), are achieved.

Boulbaba Ben Amor, Sylvain Arguillère, Ling Shao

In deformable registration, the geometric framework - large deformation diffeomorphic metric mapping or LDDMM, in short - has inspired numerous techniques for comparing, deforming, averaging and analyzing shapes or images. Grounded in flows, which are akin to the equations of motion used in fluid dynamics, LDDMM algorithms solve the flow equation in the space of plausible deformations, i.e. diffeomorphisms. In this work, we make use of deep residual neural networks to solve the non-stationary ODE (flow equation) based on a Euler's discretization scheme. The central idea is to represent time-dependent velocity fields as fully connected ReLU neural networks (building blocks) and derive optimal weights by minimizing a regularized loss function. Computing minimizing paths between deformations, thus between shapes, turns to find optimal network parameters by back-propagating over the intermediate building blocks. Geometrically, at each time step, ResNet-LDDMM searches for an optimal partition of the space into multiple polytopes, and then computes optimal velocity vectors as affine transformations on each of these polytopes. As a result, different parts of the shape, even if they are close (such as two fingers of a hand), can be made to belong to different polytopes, and therefore be moved in different directions without costing too much energy. Importantly, we show how diffeomorphic transformations, or more precisely bilipshitz transformations, are predicted by our algorithm. We illustrate these ideas on diverse registration problems of 3D shapes under complex topology-preserving transformations. We thus provide essential foundations for more advanced shape variability analysis under a novel joint geometric-neural networks Riemannian-like framework, i.e. ResNet-LDDMM.

Amor Ben Tanfous, Hassen Drira, Boulbaba Ben Amor

The detection and tracking of human landmarks in video streams has gained in reliability partly due to the availability of affordable RGB-D sensors. The analysis of such time-varying geometric data is playing an important role in the automatic human behavior understanding. However, suitable shape representations as well as their temporal evolution, termed trajectories, often lie to nonlinear manifolds. This puts an additional constraint (i.e., nonlinearity) in using conventional Machine Learning techniques. As a solution, this paper accommodates the well-known Sparse Coding and Dictionary Learning approach to study time-varying shapes on the Kendall shape spaces of 2D and 3D landmarks. We illustrate effective coding of 3D skeletal sequences for action recognition and 2D facial landmark sequences for macro- and micro-expression recognition. To overcome the inherent nonlinearity of the shape spaces, intrinsic and extrinsic solutions were explored. As main results, shape trajectories give rise to more discriminative time-series with suitable computational properties, including sparsity and vector space structure. Extensive experiments conducted on commonly-used datasets demonstrate the competitiveness of the proposed approaches with respect to state-of-the-art.

Anis Kacem, Mohamed Daoudi, Boulbaba Ben Amor et al.

In this paper, we propose a novel space-time geometric representation of human landmark configurations and derive tools for comparison and classification. We model the temporal evolution of landmarks as parametrized trajectories on the Riemannian manifold of positive semidefinite matrices of fixed-rank. Our representation has the benefit to bring naturally a second desirable quantity when comparing shapes, the spatial covariance, in addition to the conventional affine-shape representation. We derived then geometric and computational tools for rate-invariant analysis and adaptive re-sampling of trajectories, grounding on the Riemannian geometry of the underlying manifold. Specifically, our approach involves three steps: (1) landmarks are first mapped into the Riemannian manifold of positive semidefinite matrices of fixed-rank to build time-parameterized trajectories; (2) a temporal warping is performed on the trajectories, providing a geometry-aware (dis-)similarity measure between them; (3) finally, a pairwise proximity function SVM is used to classify them, incorporating the (dis-)similarity measure into the kernel function. We show that such representation and metric achieve competitive results in applications as action recognition and emotion recognition from 3D skeletal data, and facial expression recognition from videos. Experiments have been conducted on several publicly available up-to-date benchmarks.

Anis Kacem, Mohamed Daoudi, Boulbaba Ben Amor et al.

In this paper, we study the problem of facial expression recognition using a novel space-time geometric representation. We describe the temporal evolution of facial landmarks as parametrized trajectories on the Riemannian manifold of positive semidefinite matrices of fixed-rank. Our representation has the advantage to bring naturally a second desirable quantity when comparing shapes -- the spatial covariance -- in addition to the conventional affine-shape representation. We derive then geometric and computational tools for rate-invariant analysis and adaptive re-sampling of trajectories, grounding on the Riemannian geometry of the manifold. Specifically, our approach involves three steps: 1) facial landmarks are first mapped into the Riemannian manifold of positive semidefinite matrices of rank 2, to build time-parameterized trajectories; 2) a temporal alignment is performed on the trajectories, providing a geometry-aware (dis-)similarity measure between them; 3) finally, pairwise proximity function SVM (ppfSVM) is used to classify them, incorporating the latter (dis-)similarity measure into the kernel function. We show the effectiveness of the proposed approach on four publicly available benchmarks (CK+, MMI, Oulu-CASIA, and AFEW). The results of the proposed approach are comparable to or better than the state-of-the-art methods when involving only facial landmarks.