arXiv subjects

Benjamin Wild

Publications and source records attributed to Benjamin Wild.

14 recordsLinked to original sources

arXiv2026

Beyond Objective Expressivity: Geometry Preservation in Multimodal Contrastive Learning

Contrastive learning is increasingly moving toward settings with three or more modalities instead of image-text pairs. Yet, extending models from pairwise to higher-order multimodal alignment can introduce optimization and representation challenges. We identify encoder Jacobian conditioning as a key factor in trimodal contrastive learning: poorly conditioned encoders exhibit collapsing or amplified singular-value spectra, leading to exploding Jacobian condition numbers and degraded multimodal alignment. We introduce geometry-preserving encoders (GPEs) by directly conditioning the Jacobian through regularization and demonstrating that simple modifications like LeakyReLU activations and residual paths recover these geometric benefits. Across a synthetic benchmark and four real-world datasets including missing modalities, improving Jacobian conditioning boosts retrieval and linear probe performance across multiple contrastive objectives, whereas expressive objectives yield little benefit in linear probes. More broadly, our results show that multimodal contrastive learning depends not only on objective expressivity, but also on the geometric and optimization properties of the underlying encoders.

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arXiv2026

Modeling Local, Global, and Cross-Modal Context in Multimodal 3D MRI

Brain MRI poses a fundamental challenge for machine learning: models must learn from high-dimensional 3D data spanning multiple co-registered modalities, despite the limited sample sizes typical of neuroimaging studies relative to the diversity in anatomy, pathology, and acquisition conditions. While multimodal imaging provides complementary information critical for clinical interpretation, effectively integrating these signals remains difficult. We propose Multimodal Intra- and Cross-Context Vision Transformer (MICViT), a 3D vision transformer that explicitly models both modality-specific representations and cross-modal interactions across local and global contexts. Concretely, MICViT combines four attention mechanisms: modality-specific local and global attention for intra-modal feature learning, and cross-modal local and global attention to capture interactions between modalities. We evaluate MICViT on brain age prediction across three heterogeneous datasets (UK Biobank, n=41,404; SOOP, n=1,062; Cam-CAN, n=613) using multiple MRI modalities (e.g. T1, FLAIR, DWI, SWI). MICViT consistently outperforms state-of-the-art CNN and transformer baselines in 3D settings. Notably, it benefits more strongly from multimodal inputs, yielding larger performance gains as additional modalities are incorporated. These results demonstrate that explicitly modeling intra- and cross-modal interactions is key to unlocking the full potential of multimodal brain MRI, highlighting a promising direction for representation learning in neuroimaging.

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arXiv2026

Hidden in the Multiplicative Interaction: Uncovering Fragility in Multimodal Contrastive Learning

Contrastive learning has become a standard approach for unsupervised learning from paired data, as demonstrated by CLIP for image-text matching. However, many domains involve more than two modalities and require objectives that capture higher-order dependencies beyond pairwise alignment. Symile extends CLIP to this setting by replacing the dot product with the multilinear inner product (MIP) over modality embeddings. In this work, we show that there is a fragility which ishidden in the multiplicative interaction: a single weakly informative, misaligned, or missing modality can propagate through the objective and distort cross-modal retrieval scores. We propose Gated Symile, a contrastive gating mechanism that adapts modality contributions on an attention-based, per-candidate basis. The gate suppresses unreliable inputs by interpolating embeddings toward learnable neutral directions with an explicit NULL option when reliable cross-modal alignment is unlikely. Across a controlled synthetic benchmark that uncovers this fragility and three real-world trimodal datasets, Gated Symile achieves higher top-1 retrieval accuracy than well-tuned state-of-the-art (sota) baselines. More broadly, our results highlight gating as a step toward robust multimodal contrastive learning beyond two modalities in the presence of noise, misalignment, or missing inputs.

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arXiv2025

Fusion or Confusion? Multimodal Complexity Is Not All You Need

Multimodal learning has become a prominent research area, with the potential of substantial performance gains by combining information across modalities. At the same time, model development has trended toward increasingly complex deep learning architectures, motivated by the assumption that multimodal-specific methods improve performance. We challenge this assumption through a large-scale empirical study by reimplementing 19 high-impact multimodal methods across nine diverse datasets with up to 23 modalities. Under standardized experimental conditions, including hyperparameter tuning, weight initialization, cross-validation, and statistical testing, increased multimodal complexity often yields confusion rather than effective fusion of data modalities. Accordingly, complex multimodal architectures do not reliably outperform unimodal baselines and a Simple Baseline for Multimodal Learning (SimBaMM). Through a focused case study, we further demonstrate concrete methodological shortcomings even in top-tier multimodal learning publications, underscoring the need for standardized evaluation practices. In summary, we argue for a shift in focus for multimodal learning: away from the pursuit of architectural novelty and toward methodological rigor.

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arXiv2025

Cohort-Based Active Modality Acquisition

Real-world multimodal machine learning often faces missing, costly-to-acquire modalities, raising the problem of which samples to prioritize for additional acquisition under a budget. Prior work mainly studies per-sample or training-time acquisition while test-time, cohort-level acquisition is less explored. We propose Cohort-based Active Modality Acquisition (CAMA), a novel test-time cohort-level modality acquisition setting, and introduce imputation-based acquisition strategies that estimate the expected utility of acquiring a missing modality, along with upper-bound heuristics for benchmarking. Experiments on datasets with up to 15 modalities demonstrate that our proposed imputation-based strategies can more effectively guide the acquisition of an additional modality for selected samples compared with methods relying solely on pre-acquisition information, entropy-based guidance, or random selection. We showcase the real-world relevance and scalability of our method by demonstrating its ability to guide the acquisition of proteomics data for disease prediction in a large prospective cohort, the UK Biobank (UKB). Our work provides an effective approach for optimizing modality acquisition at the cohort level, enabling more effective use of resources in constrained settings.

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arXiv2025

JanusDNA: A Powerful Bi-directional Hybrid DNA Foundation Model

Large language models (LLMs) have revolutionized natural language processing and are increasingly applied to other sequential data types, including genetic sequences. However, adapting LLMs to genomics presents significant challenges. Capturing complex genomic interactions requires modeling long-range dependencies within DNA sequences, where interactions often span over 10,000 base pairs, even within a single gene, posing substantial computational burdens under conventional model architectures and training paradigms. Moreover, standard LLM training approaches are suboptimal for DNA: autoregressive training, while efficient, supports only unidirectional understanding. However, DNA is inherently bidirectional, e.g., bidirectional promoters regulate transcription in both directions and account for nearly 11% of human gene expression. Masked language models (MLMs) allow bidirectional understanding but are inefficient, as only masked tokens contribute to the loss per step. To address these limitations, we introduce JanusDNA, the first bidirectional DNA foundation model built upon a novel pretraining paradigm that combines the optimization efficiency of autoregressive modeling with the bidirectional comprehension of masked modeling. JanusDNA adopts a hybrid Mamba, Attention and Mixture of Experts (MoE) architecture, combining long-range modeling of Attention with efficient sequential learning of Mamba. MoE layers further scale model capacity via sparse activation while keeping computational cost low. Notably, JanusDNA processes up to 1 million base pairs at single nucleotide resolution on a single 80GB GPU. Extensive experiments and ablations show JanusDNA achieves new SOTA results on three genomic representation benchmarks, outperforming models with 250x more activated parameters. Code: https://github.com/Qihao-Duan/JanusDNA

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arXiv2025

Large Language Models are Powerful Electronic Health Record Encoders

Electronic Health Records (EHRs) offer considerable potential for clinical prediction, but their complexity and heterogeneity challenge traditional machine learning. Domain-specific EHR foundation models trained on unlabeled EHR data have shown improved predictive accuracy and generalization. However, their development is constrained by limited data access and site-specific vocabularies. We convert EHR data into plain text by replacing medical codes with natural-language descriptions, enabling general-purpose Large Language Models (LLMs) to produce high-dimensional embeddings for downstream prediction tasks without access to private medical training data. LLM-based embeddings perform on par with a specialized EHR foundation model, CLMBR-T-Base, across 15 clinical tasks from the EHRSHOT benchmark. In an external validation using the UK Biobank, an LLM-based model shows statistically significant improvements for some tasks, which we attribute to higher vocabulary coverage and slightly better generalization. Overall, we reveal a trade-off between the computational efficiency of specialized EHR models and the portability and data independence of LLM-based embeddings.

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arXiv2023

Diffsurv: Differentiable sorting for censored time-to-event data

Survival analysis is a crucial semi-supervised task in machine learning with numerous real-world applications, particularly in healthcare. Currently, the most common approach to survival analysis is based on Cox's partial likelihood, which can be interpreted as a ranking model optimized on a lower bound of the concordance index. This relation between ranking models and Cox's partial likelihood considers only pairwise comparisons. Recent work has developed differentiable sorting methods which relax this pairwise independence assumption, enabling the ranking of sets of samples. However, current differentiable sorting methods cannot account for censoring, a key factor in many real-world datasets. To address this limitation, we propose a novel method called Diffsurv. We extend differentiable sorting methods to handle censored tasks by predicting matrices of possible permutations that take into account the label uncertainty introduced by censored samples. We contrast this approach with methods derived from partial likelihood and ranking losses. Our experiments show that Diffsurv outperforms established baselines in various simulated and real-world risk prediction scenarios. Additionally, we demonstrate the benefits of the algorithmic supervision enabled by Diffsurv by presenting a novel method for top-k risk prediction that outperforms current methods.

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arXiv2021

The Multi-Agent Behavior Dataset: Mouse Dyadic Social Interactions

Multi-agent behavior modeling aims to understand the interactions that occur between agents. We present a multi-agent dataset from behavioral neuroscience, the Caltech Mouse Social Interactions (CalMS21) Dataset. Our dataset consists of trajectory data of social interactions, recorded from videos of freely behaving mice in a standard resident-intruder assay. To help accelerate behavioral studies, the CalMS21 dataset provides benchmarks to evaluate the performance of automated behavior classification methods in three settings: (1) for training on large behavioral datasets all annotated by a single annotator, (2) for style transfer to learn inter-annotator differences in behavior definitions, and (3) for learning of new behaviors of interest given limited training data. The dataset consists of 6 million frames of unlabeled tracked poses of interacting mice, as well as over 1 million frames with tracked poses and corresponding frame-level behavior annotations. The challenge of our dataset is to be able to classify behaviors accurately using both labeled and unlabeled tracking data, as well as being able to generalize to new settings.

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arXiv2018

BioTracker: An Open-Source Computer Vision Framework for Visual Animal Tracking

The study of animal behavior increasingly relies on (semi-) automatic methods for the extraction of relevant behavioral features from video or picture data. To date, several specialized software products exist to detect and track animals' positions in simple (laboratory) environments. Tracking animals in their natural environments, however, often requires substantial customization of the image processing algorithms to the problem-specific image characteristics. Here we introduce BioTracker, an open-source computer vision framework, that provides programmers with core functionalities that are essential parts of a tracking software, such as video I/O, graphics overlays and mouse and keyboard interfaces. BioTracker additionally provides a number of different tracking algorithms suitable for a variety of image recording conditions. The main feature of BioTracker is however the straightforward implementation of new problem-specific tracking modules and vision algorithms that can build upon BioTracker's core functionalities. With this open-source framework the scientific community can accelerate their research and focus on the development of new vision algorithms.

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arXiv2018

Automatic localization and decoding of honeybee markers using deep convolutional neural networks

The honeybee is a fascinating model animal to investigate how collective behavior emerges from (inter-)actions of thousands of individuals. Bees may acquire unique memories throughout their lives. These experiences affect social interactions even over large time frames. Tracking and identifying all bees in the colony over their lifetimes therefore may likely shed light on the interplay of individual differences and colony behavior. This paper proposes a software pipeline based on two deep convolutional neural networks for the localization and decoding of custom binary markers that honeybees carry from their first to the last day in their life. We show that this approach outperforms similar systems proposed in recent literature. By opening this software for the public, we hope that the resulting datasets will help advancing the understanding of honeybee collective intelligence.

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arXiv2018

Tracking all members of a honey bee colony over their lifetime

Computational approaches to the analysis of collective behavior in social insects increasingly rely on motion paths as an intermediate data layer from which one can infer individual behaviors or social interactions. Honey bees are a popular model for learning and memory. Previous experience has been shown to affect and modulate future social interactions. So far, no lifetime history observations have been reported for all bees of a colony. In a previous work we introduced a tracking system customized to track up to $4000$ bees over several weeks. In this contribution we present an in-depth description of the underlying multi-step algorithm which both produces the motion paths, and also improves the marker decoding accuracy significantly. We automatically tracked ${\sim}2000$ marked honey bees over 10 weeks with inexpensive recording hardware using markers without any error correction bits. We found that the proposed two-step tracking reduced incorrect ID decodings from initially ${\sim}13\%$ to around $2\%$ post-tracking. Alongside this paper, we publish the first trajectory dataset for all bees in a colony, extracted from ${\sim} 4$ million images. We invite researchers to join the collective scientific effort to investigate this intriguing animal system. All components of our system are open-source.

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arXiv2017

Automatic detection and decoding of honey bee waggle dances

The waggle dance is one of the most popular examples of animal communication. Forager bees direct their nestmates to profitable resources via a complex motor display. Essentially, the dance encodes the polar coordinates to the resource in the field. Unemployed foragers follow the dancer's movements and then search for the advertised spots in the field. Throughout the last decades, biologists have employed different techniques to measure key characteristics of the waggle dance and decode the information it conveys. Early techniques involved the use of protractors and stopwatches to measure the dance orientation and duration directly from the observation hive. Recent approaches employ digital video recordings and manual measurements on screen. However, manual approaches are very time-consuming. Most studies, therefore, regard only small numbers of animals in short periods of time. We have developed a system capable of automatically detecting, decoding and mapping communication dances in real-time. In this paper, we describe our recording setup, the image processing steps performed for dance detection and decoding and an algorithm to map dances to the field. The proposed system performs with a detection accuracy of 90.07\%. The decoded waggle orientation has an average error of -2.92{\deg} ($\pm$ 7.37{\deg} ), well within the range of human error. To evaluate and exemplify the system's performance, a group of bees was trained to an artificial feeder, and all dances in the colony were automatically detected, decoded and mapped. The system presented here is the first of this kind made publicly available, including source code and hardware specifications. We hope this will foster quantitative analyses of the honey bee waggle dance.

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arXiv2016

RenderGAN: Generating Realistic Labeled Data

Deep Convolutional Neuronal Networks (DCNNs) are showing remarkable performance on many computer vision tasks. Due to their large parameter space, they require many labeled samples when trained in a supervised setting. The costs of annotating data manually can render the use of DCNNs infeasible. We present a novel framework called RenderGAN that can generate large amounts of realistic, labeled images by combining a 3D model and the Generative Adversarial Network framework. In our approach, image augmentations (e.g. lighting, background, and detail) are learned from unlabeled data such that the generated images are strikingly realistic while preserving the labels known from the 3D model. We apply the RenderGAN framework to generate images of barcode-like markers that are attached to honeybees. Training a DCNN on data generated by the RenderGAN yields considerably better performance than training it on various baselines.

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