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Learning good representations involves capturing the diverse ways in which data samples relate. Contrastive loss - an objective matching related samples - underlies methods from self-supervised to multimodal learning. Contrastive losses, however, can be viewed more broadly as modifying a similarity graph to indicate how samples should relate in the embedding space. This view reveals a shortcoming in contrastive learning: the similarity graph is binary, as only one sample is the related positive sample. Crucially, similarities \textit{across} samples are ignored. Based on this observation, we revise the standard contrastive loss to explicitly encode how a sample relates to others. We experiment with this new objective, called X -Sample Contrastive, to train vision models based on similarities in class or text caption descriptions. Our study spans three scales: ImageNet-1k with 1 million, CC3M with 3 million, and CC12M with 12 million samples. The representations learned via our objective outperform both contrastive self-supervised and vision-language models trained on the same data across a range of tasks. When training on CC12M, we outperform CLIP by on both ImageNet and ImageNet Real. Our objective appears to work particularly well in lower-data regimes, with gains over CLIP of on ImageNet and on ImageNet Real when training with CC3M. Finally, our objective seems to encourage the model to learn representations that separate objects from their attributes and backgrounds, with gains of - \% over CLIP on ImageNet9. We hope the proposed solution takes a small step towards developing richer learning objectives for understanding sample relations in foundation models. 

Supervised multi-modal learning involves mapping multiple modalities to a target label. Previous studies in this field have concentrated on capturing in isolation either the inter-modality dependencies (the relationships between different modalities and the label) or the intra-modality dependencies (the relationships within a single modality and the label). We argue that these conventional approaches that rely solely on either inter- or intra-modality dependencies may not be optimal in general. We view the multi-modal learning problem from the lens of generative models where we consider the target as a source of multiple modalities and the interaction between them. Towards that end, we propose inter- & intra-modality modeling (I2M2) framework, which captures and integrates both the inter- and intra-modality dependencies, leading to more accurate predictions. We evaluate our approach using real-world healthcare and vision-and-language datasets with state-of-the-art models, demonstrating superior performance over traditional methods focusing only on one type of modality dependency. 

Abstract Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorization for Gene Regulatory Network Inference (PMF-GRN). Using single-cell expression data, PMF-GRN infers latent factors capturing transcription factor activity and regulatory relationships. Using variational inference allows hyperparameter search for principled model selection and direct comparison to other generative models. We extensively test and benchmark our method using real single-cell datasets and synthetic data. We show that PMF-GRN infers GRNs more accurately than current state-of-the-art single-cell GRN inference methods, offering well-calibrated uncertainty estimates. 

Chest X-ray imaging is a widely accessible and non-invasive diagnostic tool for detecting thoracic abnormalities. While numerous AI models assist radiologists in interpreting these images, most overlook patients' historical data. To bridge this gap, we introduce Temporal MIMIC dataset, which integrates five years of patient history, including radiographic scans and reports from MIMIC-CXR and MIMIC-IV, encompassing 12,221 patients and thirteen pathologies. Building on this, we present HIST-AID, a framework that enhances automatic diagnostic accuracy using historical reports. HIST-AID emulates the radiologist's comprehensive approach, leveraging historical data to improve diagnostic accuracy. Our experiments demonstrate significant improvements, with AUROC increasing by 6.56% and AUPRC by 9.51% compared to models that rely solely on radiographic scans. These gains were consistently observed across diverse demographic groups, including variations in gender, age, and racial categories. We show that while recent data boost performance, older data may reduce accuracy due to changes in patient conditions. Our work paves the potential of incorporating historical data for more reliable automatic diagnosis, providing critical support for clinical decision-making. 

Preference learning algorithms (e.g., RLHF and DPO) are frequently used to steer LLMs to produce generations that are more preferred by humans, but our understanding of their inner workings is still limited. In this work, we study the conventional wisdom that preference learning trains models to assign higher likelihoods to more preferred outputs than less preferred outputs, measured via ranking accuracy. Surprisingly, we find that most state-of-the-art preference-tuned models achieve a ranking accuracy of less than 60% on common preference datasets. We furthermore derive the idealized ranking accuracy that a preference-tuned LLM would achieve if it optimized the DPO or RLHF objective perfectly. We demonstrate that existing models exhibit a significant alignment gap -- i.e., a gap between the observed and idealized ranking accuracies. We attribute this discrepancy to the DPO objective, which is empirically and theoretically ill-suited to fix even mild ranking errors in the reference model, and derive a simple and efficient formula for quantifying the difficulty of learning a given preference datapoint. Finally, we demonstrate that ranking accuracy strongly correlates with the empirically popular win rate metric when the model is close to the reference model used in the objective, shedding further light on the differences between on-policy (e.g., RLHF) and off-policy (e.g., DPO) preference learning algorithms. 

Language model performance depends on identifying the optimal mixture of data groups to train on (e.g., law, code, math). Prior work has proposed a diverse set of methods to efficiently learn mixture proportions, ranging from fitting regression models over training runs to dynamically updating proportions throughout training. Surprisingly, we find that no existing method consistently outperforms a simple stratified sampling baseline in terms of average test perplexity. To understand this inconsistency, we unify existing methods into a standard framework, showing they are equivalent to solving a common optimization problem: minimize average loss subject to a method-specific mixing law -- an implicit assumption on the relationship between loss and mixture proportions. This framework suggests that measuring the fidelity of a method's mixing law can offer insights into its performance. Empirically, we find that existing methods set their mixing law parameters inaccurately, resulting in the inconsistent mixing performance we observe. Using this insight, we derive a new online method named Aioli, which directly estimates the mixing law parameters throughout training and uses them to dynamically adjust proportions. Aioli outperforms stratified sampling on 6 out of 6 datasets by an average of 0.27 test perplexity points, whereas existing methods fail to consistently beat stratified sampling, doing up to 6.9 points worse. Moreover, in a practical setting where proportions are learned on shorter runs due to computational constraints, Aioli can dynamically adjust these proportions over the full training run, consistently improving performance over existing methods by up to 12.012 test perplexity points. 

The impact of randomness on model training is poorly understood. How do differences in data order and initialization actually manifest in the model, such that some training runs outperform others or converge faster? Furthermore, how can we interpret the resulting training dynamics and the phase transitions that characterize different trajectories? To understand the effect of randomness on the dynamics and outcomes of neural network training, we train models multiple times with different random seeds and compute a variety of metrics throughout training, such as the norm, mean, and variance of the neural network's weights. We then fit a hidden Markov model (HMM) over the resulting sequences of metrics. The HMM represents training as a stochastic process of transitions between latent states, providing an intuitive overview of significant changes during training. Using our method, we produce a low-dimensional, discrete representation of training dynamics on grokking tasks, image classification, and masked language modeling. We use the HMM representation to study phase transitions and identify latent "detour" states that slow down convergence. 

A force field as accurate as quantum mechanics (QMs) and as fast as molecular mechanics (MMs), with which one can simulate a biomolecular system efficiently enough and meaningfully enough to get quantitative insights, is among the most ardent dreams of biophysicists—a dream, nevertheless, not to be fulfilled any time soon. Machine learning force fields (MLFFs) represent a meaningful endeavor in this direction, where differentiable neural functions are parametrized to fit ab initio energies and forces through automatic differentiation. We argue that, as of now, the utility of the MLFF models is no longer bottlenecked by accuracy but primarily by their speed, as well as stability and generalizability—many recent variants, on limited chemical spaces, have long surpassed the chemical accuracy of 1 kcal/mol—the empirical threshold beyond which realistic chemical predictions are possible—though still magnitudes slower than MM. Hoping to kindle exploration and design of faster, albeit perhaps slightly less accurate MLFFs, in this review, we focus our attention on the technical design space (the speed-accuracy trade-off) between MM and ML force fields. After a brief review of the building blocks (from a machine learning-centric point of view) of force fields of either kind, we discuss the desired properties and challenges now faced by the force field development community, survey the efforts to make MM force fields more accurate and ML force fields faster, and envision what the next generation of MLFF might look like.