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Applications · Neuroscience, Cognitive Science

Berkay Döner, Thorir Mar Ingolfsson, Luca Benini, Yawei Li

Electroencephalography (EEG) offers a non-invasive lens into human brain activity, but building large‐scale models is hampered by $\textit{topological heterogeneity}$: each public corpus defines its own electrode layout, limiting generalization. We introduce $\textbf{LUNA}$ ($\textbf{L}$atent $\textbf{U}$nified $\textbf{N}$etwork $\textbf{A}$rchitecture), a self-supervised foundation model that reconciles disparate electrode geometries while scaling linearly---not quadratically---with channel count. LUNA compresses multi-channel EEG into a fixed-size, topology-agnostic latent space via learned queries and cross-attention. Downstream transformer blocks then operate exclusively on this latent representation using patch-wise temporal self-attention, decoupling computation from electrode count. Pre-trained on TUEG and Siena ($\>$21,000 h raw EEG across diverse montages) using a masked-patch reconstruction objective, LUNA transfers effectively to four downstream tasks: abnormality detection, artifact rejection, slowing classification, and emotion recognition. It demonstrates highly competitive performance across several benchmarks, achieving state-of-the-art results on TUAR and TUSL, e.g., $\textbf{0.921 AUROC}$ on TUAR, while reducing FLOPs by $\textbf{300}$$\times$ and trimming GPU memory use by up to $\textbf{10}$$\times$. Critically, these gains are consistent across all evaluated electrode configurations. Code is available at https://github.com/pulp-bio/biofoundation

Zhe Zhao, HaiBin Wen, Xianfu Liu, Rui Mao, Pengkun Wang, Liheng Yu, Linjiang Chen, Bo An, Qingfu Zhang, Yang Wang

Scientific discovery across diverse fields increasingly grapples with datasets exhibiting pathological long-tailed distributions: a few common phenomena overshadow a multitude of rare yet scientifically critical instances. Unlike standard benchmarks, these scientific datasets often feature extreme imbalance coupled with a modest number of classes and limited overall sample volume, rendering existing long-tailed recognition (LTR) techniques ineffective. Such methods, biased by majority classes or prone to overfitting on scarce tail data, frequently fail to identify the very instances—novel materials, rare disease biomarkers, faint astronomical signals—that drive scientific breakthroughs. This paper introduces a novel, end-to-end framework explicitly designed to address pathological long-tailed recognition in scientific contexts. Our approach synergizes a Balanced Supervised Contrastive Learning (B-SCL) mechanism, which enhances the representation of tail classes by dynamically re-weighting their contributions, with a Smooth Objective Regularization (SOR) strategy that manages the inherent tension between tail-class focus and overall classification performance. We introduce and analyze the real-world ZincFluor chemical dataset ($\mathcal{T}=137.54$) and synthetic benchmarks with controllable extreme imbalances (CIFAR-LT variants). Extensive evaluations demonstrate our method's superior ability to decipher these extremes. Notably, on ZincFluor, our approach achieves a Tail Top-2 accuracy of $66.84\%$, significantly outperforming existing techniques. On CIFAR-10-LT with an imbalance ratio of $1000$ ($\mathcal{T}=100$), our method achieves a tail-class accuracy of $38.99\%$, substantially leading the next best. These results underscore our framework's potential to unlock novel insights from complex, imbalanced scientific datasets, thereby accelerating discovery.

Applications · Genetics, Cell Biology, etc

Anna Foix-Romero, Craig Russell, Alexander Krull, Virginie Uhlmann

The shape of objects is an important source of visual information in a wide range of applications. One of the core challenges of shape quantification is to ensure that the extracted measurements remain invariant to transformations that preserve an object’s intrinsic geometry, such as changing its size, orientation, and position in the image. In this work, we introduce ShapeEmbed, a self-supervised representation learning framework designed to encode the contour of objects in 2D images, represented as a Euclidean distance matrix, into a shape descriptor that is invariant to translation, scaling, rotation, reflection, and point indexing. Our approach overcomes the limitations of traditional shape descriptors while improving upon existing state-of-the-art autoencoder-based approaches. We demonstrate that the descriptors learned by our framework outperform their competitors in shape classification tasks on natural and biological images. We envision our approach to be of particular relevance to biological imaging applications.

Applications · Neuroscience, Cognitive Science

Antoine Collas, Ce Ju, Nicolas Salvy, Bertrand Thirion

Generating realistic brain connectivity matrices is key to analyzing population heterogeneity in brain organization, understanding disease, and augmenting data in challenging classification problems. Functional connectivity matrices lie in constrained spaces—such as the set of symmetric positive definite or correlation matrices—that can be modeled as Riemannian manifolds. However, using Riemannian tools typically requires redefining core operations (geodesics, norms, integration), making generative modeling computationally inefficient. In this work, we propose DiffeoCFM, an approach that enables conditional flow matching (CFM) on matrix manifolds by exploiting pullback metrics induced by global diffeomorphisms on Euclidean spaces. We show that Riemannian CFM with such metrics is equivalent to applying standard CFM after data transformation. This equivalence allows efficient vector field learning, and fast sampling with standard ODE solvers. We instantiate DiffeoCFM with two different settings: the matrix logarithm for covariance matrices and the normalized Cholesky decomposition for correlation matrices. We evaluate DiffeoCFM on three large-scale fMRI datasets with more than $4600$ scans from $2800$ subjects (ADNI, ABIDE, OASIS‑3) and two EEG motor imagery datasets with over $30000$ trials from $26$ subjects (BNCI2014‑002 and BNCI2015‑001). It enables fast training and achieves state-of-the-art performance, all while preserving manifold constraints. Code: https://github.com/antoinecollas/DiffeoCFM

Applications · Chemistry and Drug Discovery

Sebastian Ojeda, Rafael Velasquez, Nicolás Aparicio, Juanita Puentes, Paula Cárdenas, Nicolás Andrade, Gabriel González, Sergio Rincón, Carolina Muñoz-Camargo, Pablo Arbelaez

Antimicrobial peptides have emerged as promising molecules to combat antimicrobial resistance. However, fragmented datasets, inconsistent annotations, and the lack of standardized benchmarks hinder computational approaches and slow down the discovery of new candidates. To address these challenges, we present the Expanded Standardized Collection for Antimicrobial Peptide Evaluation (ESCAPE), an experimental framework integrating over 80.000 peptides from 27 validated repositories. Our dataset separates antimicrobial peptides from negative sequences and incorporates their functional annotations into a biologically coherent multilabel hierarchy, capturing activities across antibacterial, antifungal, antiviral, and antiparasitic classes. Building on ESCAPE, we propose a transformer-based model that leverages sequence and structural information to predict multiple functional activities of peptides. Our method achieves up to a 2.56% relative average improvement in mean Average Precision over the second-best method adapted for this task, establishing a new state-of-the-art multilabel peptide classification. ESCAPE provides a comprehensive and reproducible evaluation framework to advance AI-driven antimicrobial peptide research.

Computer Vision · Vision Models & Multimodal

Ziteng Wang, Siqi Yang, Limeng Qiao, Lin Ma

Despite the success of Vision-Language Models (VLMs) like CLIP in aligning vision and language, their proficiency in detailed, fine-grained visual comprehension remains a key challenge. We present CLIP-IN, a novel framework that bolsters CLIP's fine-grained perception through two core innovations. Firstly, we leverage instruction-editing datasets, originally designed for image manipulation, as a unique source of hard negative image-text pairs. Coupled with a symmetric hard negative contrastive loss, this enables the model to effectively distinguish subtle visual-semantic differences. Secondly, CLIP-IN incorporates long descriptive captions, utilizing rotary positional encodings to capture rich semantic context often missed by standard CLIP. Our experiments demonstrate that CLIP-IN achieves substantial gains on the MMVP benchmark and various fine-grained visual recognition tasks, without compromising robust zero-shot performance on broader classification and retrieval tasks. Critically, integrating CLIP-IN's visual representations into Multimodal Large Language Models significantly reduces visual hallucinations and enhances reasoning abilities. This work underscores the considerable potential of synergizing targeted, instruction-based contrastive learning with comprehensive descriptive information to elevate the fine-grained understanding of VLMs.

Computer Vision · Classification and Understanding

Thomas Eiter, Katsumi Inoue, Nelson Higuera, Sota Moriyama

Integrating logical constraints into object detection models for autonomous driving (AD) is a promising way to enhance their compliance with rules and thereby increase the safety of the system. T-norms have been utilized to calculate the constrained loss, i.e., the violations of logical constraints as losses. While prior works have statically selected a few t-norms, we conduct an extensive experimental study to identify the most effective choices, as suboptimal t-norms can lead to undesired model behavior. To this end, we present MOD-ECL, a neurosymbolic framework that implements a wide range of t-norms and applies them in an adaptive manner. It includes an algorithm that selects well-performing t-norms during training and a scheduler that regulates the impact of the constrained loss. We evaluate its effectiveness on the ROAD-R and ROAD-Waymo-R datasets for object detection in AD, using attached common-sense constraints. Our results show that careful selection of parameters is crucial for effective constrained loss behavior. Moreover, our framework not only reduces constraint violations but also, in some cases, improves detection performance. Additionally, our methods offer fine-grained control over the trade-off between accuracy and constraint violation.

Computer Vision · Classification and Understanding

Yujin Jeong, Arnas Uselis, Seong Joon Oh, Anna Rohrbach

Understanding visual scenes is fundamental to human intelligence. While discriminative models have significantly advanced computer vision, they often struggle with compositional understanding. In contrast, recent generative text-to-image diffusion models excel at synthesizing complex scenes, suggesting inherent compositional capabilities.Building on this, zero-shot diffusion classifiers have been proposed to repurpose diffusion models for discriminative tasks. While prior work offered promising results in discriminative compositional scenarios, these results remain preliminary due to a small number of benchmarks and a relatively shallow analysis of conditions under which the models succeed. To address this, we present a comprehensive study of the discriminative capabilities of diffusion classifiers on a wide range of compositional tasks. Specifically, our study covers three diffusion models (SD 1.5, 2.0, and, for the first time, 3-m) spanning 10 datasets and over 30 tasks. Further, we shed light on the role that target dataset domains play in respective performance; to isolate the domain effects, we introduce a new diagnostic benchmark \textsc{Self-Bench} comprised of images created by diffusion models themselves. Finally, we explore the importance of timestep weighting and uncover a relationship between domain gap and timestep sensitivity, particularly for SD3-m.To sum up, diffusion classifiers understand compositionality, but conditions apply! Code and dataset are available at https://github.com/eugene6923/Diffusion-Classifiers-Compositionality

Applications · Physics

Jinlin Xiang, Minho Choi, Yubo Zhang, Zhihao Zhou, Arka Majumdar, Eli Shlizerman

Hybrid Optical Neural Networks (ONNs, typically consisting of an optical frontend and a digital backend) offer an energy-efficient alternative to fully digital deep networks for real-time, power-constrained systems. However, their adoption is limited by two main challenges: the accuracy gap compared to large-scale networks during training, and discrepancies between simulated and fabricated systems that further degrade accuracy. While previous work has proposed end-to-end optimizations for specific datasets (e.g., MNIST) and optical systems, these approaches typically lack generalization across tasks and hardware designs. To address these limitations, we propose a task-agnostic and hardware-agnostic pipeline that supports image classification and segmentation across diverse optical systems. To assist optical system design before training, we design the metasurface layout based on fabrication constraints. For training, we introduce Neural Tangent Knowledge Distillation (NTKD), which aligns optical models with electronic teacher networks, thereby narrowing the accuracy gap. After fabrication, NTKD also guides fine-tuning of the digital backend to compensate for implementation errors. Experiments on multiple datasets (e.g., MNIST, CIFAR, Carvana Masking) and hardware configurations show that our pipeline consistently improves ONN performance and enables practical deployment in both pre-fabrication simulations and physical implementations.

Applications · Neuroscience, Cognitive Science

Leonie Bossemeyer, Samuel Heinrich, Grant Van Horn, Oisin Mac Aodha

Mastering fine-grained visual recognition, essential in many expert domains, can require that specialists undergo years of dedicated training. Modeling the progression of such expertize in humans remains challenging, and accurately inferring a human learner’s knowledge state is a key step toward understanding visual learning. We introduce CleverBirds, a large-scale knowledge tracing benchmark for fine-grained bird species recognition. Collected by the citizen-science platform eBird, it offers insight into how individuals acquire expertize in complex fine-grained classification. More than 40,000 participants have engaged in the quiz, answering over 17 million multiple-choice questions spanning over 10,000 bird species, with long-range learning patterns across an average of 400 questions per participant. We release this dataset to support the development and evaluation of new methods for visual knowledge tracing. We show that tracking learners' knowledge is challenging, especially across participant subgroups and question types, with different forms of contextual information offering varying degrees of predictive benefit. CleverBirds is among the largest benchmark of its kind, offering a substantially higher number of learnable concepts. With it, we hope to enable new avenues for studying the development of visual expertize over time and across individuals.

Applications · Time Series

Bosong Huang, Ming Jin, Yuxuan Liang, Johan Barthelemy, Debo Cheng, Qingsong Wen, Chenghao Liu, Shirui Pan

Explaining time series classification models is crucial, particularly in high-stakes applications such as healthcare and finance, where transparency and trust play a critical role. Although numerous time series classification methods have identified key subsequences, known as shapelets, as core features for achieving state-of-the-art performance and validating their pivotal role in classification outcomes, existing post-hoc time series explanation (PHTSE) methods primarily focus on timestep-level feature attribution. These explanation methods overlook the fundamental prior that classification outcomes are predominantly driven by key shapelets. To bridge this gap, we present ShapeX, an innovative framework that segments time series into meaningful shapelet-driven segments and employs Shapley values to assess their saliency. At the core of ShapeX lies the Shapelet Describe-and-Detect (SDD) framework, which effectively learns a diverse set of shapelets essential for classification. We further demonstrate that ShapeX produces explanations which reveal causal relationships instead of just correlations, owing to the atomicity properties of shapelets. Experimental results on both synthetic and real-world datasets demonstrate that ShapeX outperforms existing methods in identifying the most relevant subsequences, enhancing both the precision and causal fidelity of time series explanations.

Computer Vision · Segmentation

Naga Venkata Sai Jitin Jami, Thomas Altstidl, Jonas Mueller, Jindong Li, Dario Zanca, Bjoern Eskofier, Heike Leutheuser

Random splitting of datasets in image segmentation often leads to unrepresentative test sets, resulting in biased evaluations and poor model generalization. While stratified sampling has proven effective for addressing label distribution imbalance in classification tasks, extending these ideas to segmentation remains challenging due to the multi-label structure and class imbalance typically present in such data. Building on existing stratification concepts, we introduce Iterative Pixel Stratification (IPS), a straightforward, label-aware sampling method tailored for segmentation tasks. Additionally, we present Wasserstein-Driven Evolutionary Stratification (WDES), a novel genetic algorithm designed to minimize the Wasserstein distance, thereby optimizing the similarity of label distributions across dataset splits. We prove that WDES is globally optimal given enough generations. Using newly proposed statistical heterogeneity metrics, we evaluate both methods against random sampling and find that WDES consistently produces more representative splits. Applying WDES across diverse segmentation tasks, including street scenes, medical imaging, and satellite imagery, leads to lower performance variance and improved model evaluation. Our results also highlight the particular value of WDES in handling small, imbalanced, and low-diversity datasets, where conventional splitting strategies are most prone to bias.

Applications · Neuroscience, Cognitive Science

Yassine El Ouahidi, Jonathan Lys, Philipp Thölke, Nicolas Farrugia, Bastien Pasdeloup, Vincent Gripon, Karim Jerbi, Giulia Lioi

Foundation models have transformed AI by reducing reliance on task-specific data through large-scale pretraining. While successful in language and vision, their adoption in EEG has lagged due to the heterogeneity of public datasets, which are collected under varying protocols, devices, and electrode configurations. Existing EEG foundation models struggle to generalize across these variations, often restricting pretraining to a single setup, resulting in suboptimal performance, in particular under linear probing. We present REVE (Representation for EEG with Versatile Embeddings), a pretrained model explicitly designed to generalize across diverse EEG signals. REVE introduces a novel 4D positional encoding scheme that enables it to process signals of arbitrary length and electrode arrangement. Using a masked autoencoding objective, we pretrain REVE on over 60,000 hours of EEG data from 92 datasets spanning 25,000 subjects, representing the largest EEG pretraining effort to date. REVE achieves state-of-the-art results on 10 downstream EEG tasks, including motor imagery classification, seizure detection, sleep staging, cognitive load estimation, and emotion recognition. With little to no fine-tuning, it demonstrates strong generalization, and nuanced spatio-temporal modeling. We release code, pretrained weights, and tutorials to support standardized EEG research and accelerate progress in clinical neuroscience.

Optimization · Optimization and Learning under Uncertainty

Daniel Ovalle, Lorenz Biegler, Ignacio Grossmann, Carl Laird, Mateo Dulce Rubio

We propose Conformal Mixed-Integer Constraint Learning (C-MICL), a novel framework that provides probabilistic feasibility guarantees for data-driven constraints in optimization problems. While standard Mixed-Integer Constraint Learning methods often violate the true constraints due to model error or data limitations, our C-MICL approach leverages conformal prediction to ensure feasible solutions are ground-truth feasible with probability at least $1{-}\alpha$, under a conditional independence assumption. The proposed framework supports both regression and classification tasks without requiring access to the true constraint function, while avoiding the scalability issues associated with ensemble-based heuristics. Experiments on real-world applications demonstrate that C-MICL consistently achieves target feasibility rates, maintains competitive objective performance, and significantly reduces computational cost compared to existing methods. Our work bridges mathematical optimization and machine learning, offering a principled approach to incorporate uncertainty-aware constraints into decision-making with rigorous statistical guarantees.

Deep Learning · Graph Neural Networks

Ben Finkelshtein, Ismail Ilkan Ceylan, Michael Bronstein, Ron Levie

Graph machine learning architectures are typically tailored to specific tasks on specific datasets, which hinders their broader applicability. This has led to a new quest in graph machine learning: \emph{how to build graph foundation models (GFMs)} capable of generalizing across arbitrary graphs and features? In this work, we present a recipe for designing GFMs for node-level tasks from first principles. The key ingredient underpinning our study is a systematic investigation of the symmetries that a graph foundation model must respect. In a nutshell, we argue that label permutation-equivariance alongside feature permutation-invariance are necessary in addition to the common node permutation-equivariance on each local neighborhood of the graph. To this end, we first characterize the space of linear transformations that are equivariant to permutations of nodes and labels, and invariant to permutations of features. We then prove that the resulting network is a universal approximator on multisets that respect the aforementioned symmetries. Our recipe uses such layers on the multiset of features induced by the local neighborhood of the graph to obtain a class of graph foundation models for node property prediction. We validate our approach through extensive experiments on 29 real-world node classification datasets, demonstrating both strong zero-shot empirical performance and consistent improvement as the number of training graphs increases.

General Machine Learning · Representation Learning

Yuxuan Zhou, Heng Li, Zhi-Qi Cheng, Xudong Yan, Yifei Dong, Mario Fritz, Margret Keuper

Label Smoothing (LS) is widely adopted to reduce overconfidence in neural network predictions and improve generalization. Despite these benefits, recent studies reveal two critical issues with LS. First, LS induces overconfidence in misclassified samples. Second, it compacts feature representations into overly tight clusters, diluting intra-class diversity, although the precise cause of this phenomenon remained elusive. In this paper, we analytically decompose the LS-induced loss, exposing two key terms: (i) a regularization term that dampens overconfidence only when the prediction is correct, and (ii) an error-amplification term that arises under misclassifications. This latter term compels the network to reinforce incorrect predictions with undue certainty, exacerbating representation collapse. To address these shortcomings, we propose Max Suppression (MaxSup), which applies uniform regularization to both correct and incorrect predictions by penalizing the top-1 logit rather than the ground-truth logit. Through extensive feature-space analyses, we show that MaxSup restores intra-class variation and sharpens inter-class boundaries. Experiments on large-scale image classification and multiple downstream tasks confirm that MaxSup is a more robust alternative to LS.Code and reproducibility scripts are available at https://github.com/ZhouYuxuanYX/Maximum-Suppression-Regularization.

Applications · Everything Else

Changlun Li, Yao SHI, Chen Wang, Qiqi Duan, Runke RUAN, Weijie Huang, Haonan Long, Lijun Huang, Nan Tang, Yuyu Luo

Large Language Models (LLMs) have demonstrated notable capabilities across financial tasks, including financial report summarization, earnings call transcript analysis, and asset classification. However, their real-world effectiveness in managing complex fund investment remains inadequately assessed. A fundamental limitation of existing benchmarks for evaluating LLM-driven trading strategies is their reliance on historical back-testing, inadvertently enabling LLMs to "time travel"—leveraging future information embedded in their training corpora, thus resulting in possible information leakage and overly optimistic performance estimates. To address this issue, we introduce DeepFund, a live fund benchmark tool designed to rigorously evaluate LLM in real-time market conditions. Utilizing a multi-agent architecture, DeepFund connects directly with real-time stock market data—specifically data published after each model’s pretraining cutoff—to ensure fair and leakage-free evaluations. Empirical tests on nine flagship LLMs from leading global institutions across multiple investment dimensions—including ticker-level analysis, investment decision-making, portfolio management, and risk control—reveal significant practical challenges. Notably, even cutting-edge models such as DeepSeek-V3 and Claude-3.7-Sonnet incur net trading losses within DeepFund real-time evaluation environment, underscoring the present limitations of LLMs for active fund management. Our code is available at https://github.com/HKUSTDial/DeepFund.

Theory · Learning Theory

Zihao Tang, Boyuan Wang, Chuan Wen, Jiaye Teng

Conformal prediction is widely adopted in uncertainty quantification, due to its post-hoc, distribution-free, and model-agnostic properties. In the realm of modern deep learning, researchers have proposed Feature Conformal Prediction (FCP), which deploys conformal prediction in a feature space, yielding reduced band lengths. However, the practical utility of FCP is limited due to the time-consuming non-linear operations required to transform confidence bands from feature space to output space. In this paper, we present Fast Feature Conformal Prediction (FFCP), a method that accelerates FCP by leveraging a first-order Taylor expansion to approximate these non-linear operations. The proposed FFCP introduces a novel non-conformity score that is both effective and efficient for real-world applications. Empirical validations showcase that FFCP performs comparably with FCP (both outperforming the vanilla version) while achieving a significant reduction in computational time by approximately 50x in both regression and classification tasks.

Computer Vision · Classification and Understanding

Xinyi Huang, Kangfei Zhao, Long-Kai Huang

Model editing offers a promising paradigm for efficiently and precisely updating knowledge in pre-trained transformers without costly retraining. While extensively studied in language models (LMs), model editing for vision transformers (ViTs) remains underexplored. Existing methods typically adapt LM-based techniques by modifying the multi-layer perceptron (MLP) modules, overlooking the unique characteristics of ViTs. In this work, we show that ViT predictions are more strongly influenced by the multi-head self-attention (MSA) modules than by the MLPs. Building on this observation, we propose a two-stage framework for editing ViTs. First, we identify which attention heads are most responsible for incorrect predictions. Next, we selectively remove the corresponding features to correct the model’s prediction. To further balance error correction with predictive stability on unrelated data, we learn a projection matrix that refines the image representations. Extensive experiments across multiple real-world datasets and model editing benchmarks demonstrate that our method consistently outperforms existing model editing methods for ViTs, achieving superior generalization and locality. Our code is available at https://github.com/shanghxy/Model-editing-for-vision-transformers.

Applications · Chemistry and Drug Discovery

Haydn Jones, Natalie Maus, Josh magnus Ludan, Maggie Huan, Jiaming Liang, Marcelo Der Torossian Torres, Jiatao Liang, Zachary Ives, Yoseph Barash, Cesar de la Fuente-Nunez 等

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis across diverse models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had a high probability of being mutagenic. In this work, we introduce Medex, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. Medex consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or RefSeq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLaVA architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). Medex is highly effective for creating models with strong priors: in supervised prediction problems that use our data for pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with Medex can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset on HuggingFace at https://huggingface.co/datasets/DocAndDesign/Medex, and will provide expanded versions as the available literature grows.