MolMix: A Simple Yet Effective Baseline for Multimodal Molecular Representation Learning

In this work, we propose a simple transformer-based baseline for multimodal molecular representation learning, integrating three distinct modalities: SMILES strings, 2D graph representations, and 3D conformers of molecules. A key aspect of our approach is the aggregation of 3D conformers, allowing the model to account for the fact that molecules can adopt multiple conformations-an important factor for accurate molecular representation. The tokens for each modality are extracted using modality-specific encoders: a transformer for SMILES strings, a message-passing neural network for 2D graphs, and an equivariant neural network for 3D conformers. The flexibility and modularity of this framework enable easy adaptation and replacement of these encoders, making the model highly versatile for different molecular tasks. The extracted tokens are then combined into a unified multimodal sequence, which is processed by a downstream transformer for prediction tasks. To efficiently scale our model for large multimodal datasets, we utilize Flash Attention 2 and bfloat16 precision. Despite its simplicity, our approach achieves state-of-the-art results across multiple datasets, demonstrating its effectiveness as a strong baseline for multimodal molecular representation learning.

LoGra-Med: Long Context Multi-Graph Alignment for Medical Vision-Language Model

State-of-the-art medical multi-modal large language models (med-MLLM), like LLaVA-Med or BioMedGPT, leverage instruction-following data in pre-training. However, those models primarily focus on scaling the model size and data volume to boost performance while mainly relying on the autoregressive learning objectives. Surprisingly, we reveal that such learning schemes might result in a weak alignment between vision and language modalities, making these models highly reliant on extensive pre-training datasets - a significant challenge in medical domains due to the expensive and time-consuming nature of curating high-quality instruction-following instances. We address this with LoGra-Med, a new multi-graph alignment algorithm that enforces triplet correlations across image modalities, conversation-based descriptions, and extended captions. This helps the model capture contextual meaning, handle linguistic variability, and build cross-modal associations between visuals and text. To scale our approach, we designed an efficient end-to-end learning scheme using black-box gradient estimation, enabling faster LLaMa 7B training. Our results show LoGra-Med matches LLAVA-Med performance on 600K image-text pairs for Medical VQA and significantly outperforms it when trained on 10% of the data. For example, on VQA-RAD, we exceed LLAVA-Med by 20.13% and nearly match the 100% pre-training score (72.52% vs. 72.64%). We also surpass SOTA methods like BiomedGPT on visual chatbots and RadFM on zero-shot image classification with VQA, highlighting the effectiveness of multi-graph alignment.

Discrete Copula Diffusion

Discrete diffusion models have recently shown significant progress in modeling complex data, such as natural languages and DNA sequences. However, unlike diffusion models for continuous data, which can generate high-quality samples in just a few denoising steps, modern discrete diffusion models still require hundreds or even thousands of denoising steps to perform well. In this paper, we identify a fundamental limitation that prevents discrete diffusion models from achieving strong performance with fewer steps -- they fail to capture dependencies between output variables at each denoising step. To address this issue, we provide a formal explanation and introduce a general approach to supplement the missing dependency information by incorporating another deep generative model, termed the copula model. Our method does not require fine-tuning either the diffusion model or the copula model, yet it enables high-quality sample generation with significantly fewer denoising steps. When we apply this approach to autoregressive copula models, the combined model outperforms both models individually in unconditional and conditional text generation. Specifically, the hybrid model achieves better (un)conditional text generation using 8 to 32 times fewer denoising steps than the diffusion model alone. In addition to presenting an effective discrete diffusion generation algorithm, this paper emphasizes the importance of modeling inter-variable dependencies in discrete diffusion.

A Looming Replication Crisis in Evaluating Behavior in Language Models? Evidence and Solutions

In an era where large language models (LLMs) are increasingly integrated into a wide range of everyday applications, research into these models' behavior has surged. However, due to the novelty of the field, clear methodological guidelines are lacking. This raises concerns about the replicability and generalizability of insights gained from research on LLM behavior. In this study, we discuss the potential risk of a replication crisis and support our concerns with a series of replication experiments focused on prompt engineering techniques purported to influence reasoning abilities in LLMs. We tested GPT-3.5, GPT-4o, Gemini 1.5 Pro, Claude 3 Opus, Llama 3-8B, and Llama 3-70B, on the chain-of-thought, EmotionPrompting, ExpertPrompting, Sandbagging, as well as Re-Reading prompt engineering techniques, using manually double-checked subsets of reasoning benchmarks including CommonsenseQA, CRT, NumGLUE, ScienceQA, and StrategyQA. Our findings reveal a general lack of statistically significant differences across nearly all techniques tested, highlighting, among others, several methodological weaknesses in previous research. We propose a forward-looking approach that includes developing robust methodologies for evaluating LLMs, establishing sound benchmarks, and designing rigorous experimental frameworks to ensure accurate and reliable assessments of model outputs.

Active Learning for Neural PDE Solvers

Solving partial differential equations (PDEs) is a fundamental problem in engineering and science. While neural PDE solvers can be more efficient than established numerical solvers, they often require large amounts of training data that is costly to obtain. Active Learning (AL) could help surrogate models reach the same accuracy with smaller training sets by querying classical solvers with more informative initial conditions and PDE parameters. While AL is more common in other domains, it has yet to be studied extensively for neural PDE solvers. To bridge this gap, we introduce AL4PDE, a modular and extensible active learning benchmark. It provides multiple parametric PDEs and state-of-the-art surrogate models for the solver-in-the-loop setting, enabling the evaluation of existing and the development of new AL methods for PDE solving. We use the benchmark to evaluate batch active learning algorithms such as uncertainty- and feature-based methods. We show that AL reduces the average error by up to 71% compared to random sampling and significantly reduces worst-case errors. Moreover, AL generates similar datasets across repeated runs, with consistent distributions over the PDE parameters and initial conditions. The acquired datasets are reusable, providing benefits for surrogate models not involved in the data generation.

Dude: Dual Distribution-Aware Context Prompt Learning For Large Vision-Language Model

Prompt learning methods are gaining increasing attention due to their ability to customize large vision-language models to new domains using pre-trained contextual knowledge and minimal training data. However, existing works typically rely on optimizing unified prompt inputs, often struggling with fine-grained classification tasks due to insufficient discriminative attributes. To tackle this, we consider a new framework based on a dual context of both domain-shared and class-specific contexts, where the latter is generated by Large Language Models (LLMs) such as GPTs. Such dual prompt methods enhance the model's feature representation by joining implicit and explicit factors encoded in LLM knowledge. Moreover, we formulate the Unbalanced Optimal Transport (UOT) theory to quantify the relationships between constructed prompts and visual tokens. Through partial matching, UOT can properly align discrete sets of visual tokens and prompt embeddings under different mass distributions, which is particularly valuable for handling irrelevant or noisy elements, ensuring that the preservation of mass does not restrict transport solutions. Furthermore, UOT's characteristics integrate seamlessly with image augmentation, expanding the training sample pool while maintaining a reasonable distance between perturbed images and prompt inputs. Extensive experiments across few-shot classification and adapter settings substantiate the superiority of our model over current state-of-the-art baselines.

Vectorized Conditional Neural Fields: A Framework for Solving Time-dependent Parametric Partial Differential Equations

Transformer models are increasingly used for solving Partial Differential Equations (PDEs). Several adaptations have been proposed, all of which suffer from the typical problems of Transformers, such as quadratic memory and time complexity. Furthermore, all prevalent architectures for PDE solving lack at least one of several desirable properties of an ideal surrogate model, such as (i) generalization to PDE parameters not seen during training, (ii) spatial and temporal zero-shot super-resolution, (iii) continuous temporal extrapolation, (iv) support for 1D, 2D, and 3D PDEs, and (v) efficient inference for longer temporal rollouts. To address these limitations, we propose Vectorized Conditional Neural Fields (VCNeFs), which represent the solution of time-dependent PDEs as neural fields. Contrary to prior methods, however, VCNeFs compute, for a set of multiple spatio-temporal query points, their solutions in parallel and model their dependencies through attention mechanisms. Moreover, VCNeF can condition the neural field on both the initial conditions and the parameters of the PDEs. An extensive set of experiments demonstrates that VCNeFs are competitive with and often outperform existing ML-based surrogate models.

Probabilistic Graph Rewiring via Virtual Nodes

Message-passing graph neural networks (MPNNs) have emerged as a powerful paradigm for graph-based machine learning. Despite their effectiveness, MPNNs face challenges such as under-reaching and over-squashing, where limited receptive fields and structural bottlenecks hinder information flow in the graph. While graph transformers hold promise in addressing these issues, their scalability is limited due to quadratic complexity regarding the number of nodes, rendering them impractical for larger graphs. Here, we propose \emph{implicitly rewired message-passing neural networks} (IPR-MPNNs), a novel approach that integrates \emph{implicit} probabilistic graph rewiring into MPNNs. By introducing a small number of virtual nodes, i.e., adding additional nodes to a given graph and connecting them to existing nodes, in a differentiable, end-to-end manner, IPR-MPNNs enable long-distance message propagation, circumventing quadratic complexity. Theoretically, we demonstrate that IPR-MPNNs surpass the expressiveness of traditional MPNNs. Empirically, we validate our approach by showcasing its ability to mitigate under-reaching and over-squashing effects, achieving state-of-the-art performance across multiple graph datasets. Notably, IPR-MPNNs outperform graph transformers while maintaining significantly faster computational efficiency.

Accelerating Transformers with Spectrum-Preserving Token Merging

Increasing the throughput of the Transformer architecture, a foundational component used in numerous state-of-the-art models for vision and language tasks (e.g., GPT, LLaVa), is an important problem in machine learning. One recent and effective strategy is to merge token representations within Transformer models, aiming to reduce computational and memory requirements while maintaining accuracy. Prior works have proposed algorithms based on Bipartite Soft Matching (BSM), which divides tokens into distinct sets and merges the top k similar tokens. However, these methods have significant drawbacks, such as sensitivity to token-splitting strategies and damage to informative tokens in later layers. This paper presents a novel paradigm called PiToMe, which prioritizes the preservation of informative tokens using an additional metric termed the energy score. This score identifies large clusters of similar tokens as high-energy, indicating potential candidates for merging, while smaller (unique and isolated) clusters are considered as low-energy and preserved. Experimental findings demonstrate that PiToMe saved from 40-60\% FLOPs of the base models while exhibiting superior off-the-shelf performance on image classification (0.5\% average performance drop of ViT-MAE-H compared to 2.6\% as baselines), image-text retrieval (0.3\% average performance drop of CLIP on Flickr30k compared to 4.5\% as others), and analogously in visual questions answering with LLaVa-7B. Furthermore, PiToMe is theoretically shown to preserve intrinsic spectral properties of the original token space under mild conditions

Learning to Discretize Denoising Diffusion ODEs

Diffusion Probabilistic Models (DPMs) are powerful generative models showing competitive performance in various domains, including image synthesis and 3D point cloud generation. However, sampling from pre-trained DPMs involves multiple neural function evaluations (NFE) to transform Gaussian noise samples into images, resulting in higher computational costs compared to single-step generative models such as GANs or VAEs. Therefore, a crucial problem is to reduce NFE while preserving generation quality. To this end, we propose LD3, a lightweight framework for learning time discretization while sampling from the diffusion ODE encapsulated by DPMs. LD3 can be combined with various diffusion ODE solvers and consistently improves performance without retraining resource-intensive neural networks. We demonstrate analytically and empirically that LD3 enhances sampling efficiency compared to distillation-based methods, without the extensive computational overhead. We evaluate our method with extensive experiments on 5 datasets, covering unconditional and conditional sampling in both pixel-space and latent-space DPMs. For example, in about 5 minutes of training on a single GPU, our method reduces the FID score from 6.63 to 2.68 on CIFAR10 (7 NFE), and in around 20 minutes, decreases the FID from 8.51 to 5.03 on class-conditional ImageNet-256 (5 NFE). LD3 complements distillation methods, offering a more efficient approach to sampling from pre-trained diffusion models.