arXiv subjects

Kyunghyun Cho

Publications and source records attributed to Kyunghyun Cho.

At least 91 records · Page 5Linked to original sources

arXiv2024

Multiple Physics Pretraining for Physical Surrogate Models

We introduce multiple physics pretraining (MPP), an autoregressive task-agnostic pretraining approach for physical surrogate modeling of spatiotemporal systems with transformers. In MPP, rather than training one model on a specific physical system, we train a backbone model to predict the dynamics of multiple heterogeneous physical systems simultaneously in order to learn features that are broadly useful across systems and facilitate transfer. In order to learn effectively in this setting, we introduce a shared embedding and normalization strategy that projects the fields of multiple systems into a shared embedding space. We validate the efficacy of our approach on both pretraining and downstream tasks over a broad fluid mechanics-oriented benchmark. We show that a single MPP-pretrained transformer is able to match or outperform task-specific baselines on all pretraining sub-tasks without the need for finetuning. For downstream tasks, we demonstrate that finetuning MPP-trained models results in more accurate predictions across multiple time-steps on systems with previously unseen physical components or higher dimensional systems compared to training from scratch or finetuning pretrained video foundation models. We open-source our code and model weights trained at multiple scales for reproducibility.

cs.LG↗

arXiv2024

Jointly Modeling Inter- & Intra-Modality Dependencies for Multi-modal Learning

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.

cs.CV↗

arXiv2024

HIST-AID: Leveraging Historical Patient Reports for Enhanced Multi-Modal Automatic Diagnosis

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.

eess.IV↗

arXiv2024

Peer Reviews of Peer Reviews: A Randomized Controlled Trial and Other Experiments

Is it possible to reliably evaluate the quality of peer reviews? We study this question driven by two primary motivations -- incentivizing high-quality reviewing using assessed quality of reviews and measuring changes to review quality in experiments. We conduct a large scale study at the NeurIPS 2022 conference, a top-tier conference in machine learning, in which we invited (meta)-reviewers and authors to evaluate reviews given to submitted papers. First, we conduct a RCT to examine bias due to the length of reviews. We generate elongated versions of reviews by adding substantial amounts of non-informative content. Participants in the control group evaluate the original reviews, whereas participants in the experimental group evaluate the artificially lengthened versions. We find that lengthened reviews are scored (statistically significantly) higher quality than the original reviews. In analysis of observational data we find that authors are positively biased towards reviews recommending acceptance of their own papers, even after controlling for confounders of review length, quality, and different numbers of papers per author. We also measure disagreement rates between multiple evaluations of the same review of 28%-32%, which is comparable to that of paper reviewers at NeurIPS. Further, we assess the amount of miscalibration of evaluators of reviews using a linear model of quality scores and find that it is similar to estimates of miscalibration of paper reviewers at NeurIPS. Finally, we estimate the amount of variability in subjective opinions around how to map individual criteria to overall scores of review quality and find that it is roughly the same as that in the review of papers. Our results suggest that the various problems that exist in reviews of papers -- inconsistency, bias towards irrelevant factors, miscalibration, subjectivity -- also arise in reviewing of reviews.

cs.DL↗

arXiv2024

Preference Learning Algorithms Do Not Learn Preference Rankings

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.

cs.LG↗

arXiv2024

Generalizing to any diverse distribution: uniformity, gentle finetuning and rebalancing

As training datasets grow larger, we aspire to develop models that generalize well to any diverse test distribution, even if the latter deviates significantly from the training data. Various approaches like domain adaptation, domain generalization, and robust optimization attempt to address the out-of-distribution challenge by posing assumptions about the relation between training and test distribution. Differently, we adopt a more conservative perspective by accounting for the worst-case error across all sufficiently diverse test distributions within a known domain. Our first finding is that training on a uniform distribution over this domain is optimal. We also interrogate practical remedies when uniform samples are unavailable by considering methods for mitigating non-uniformity through finetuning and rebalancing. Our theory provides a mathematical grounding for previous observations on the role of entropy and rebalancing for o.o.d. generalization and foundation model training. We also provide new empirical evidence across tasks involving o.o.d. shifts which illustrate the broad applicability of our perspective.

cs.LG↗

arXiv2024

Non-convolutional Graph Neural Networks

Rethink convolution-based graph neural networks (GNN) -- they characteristically suffer from limited expressiveness, over-smoothing, and over-squashing, and require specialized sparse kernels for efficient computation. Here, we design a simple graph learning module entirely free of convolution operators, coined random walk with unifying memory (RUM) neural network, where an RNN merges the topological and semantic graph features along the random walks terminating at each node. Relating the rich literature on RNN behavior and graph topology, we theoretically show and experimentally verify that RUM attenuates the aforementioned symptoms and is more expressive than the Weisfeiler-Lehman (WL) isomorphism test. On a variety of node- and graph-level classification and regression tasks, RUM not only achieves competitive performance, but is also robust, memory-efficient, scalable, and faster than the simplest convolutional GNNs.

cs.LG↗

arXiv2024

$\mathbb{X}$-Sample Contrastive Loss: Improving Contrastive Learning with Sample Similarity Graphs

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 $\mathbb{X}$-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 $0.6\%$ on both ImageNet and ImageNet Real. Our objective appears to work particularly well in lower-data regimes, with gains over CLIP of $16.8\%$ on ImageNet and $18.1\%$ 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 $3.3$-$5.6$\% 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.

cs.CV↗

arXiv2024

Generalization Measures for Zero-Shot Cross-Lingual Transfer

A model's capacity to generalize its knowledge to interpret unseen inputs with different characteristics is crucial to build robust and reliable machine learning systems. Language model evaluation tasks lack information metrics about model generalization and their applicability in a new setting is measured using task and language-specific downstream performance, which is often lacking in many languages and tasks. In this paper, we explore a set of efficient and reliable measures that could aid in computing more information related to the generalization capability of language models in cross-lingual zero-shot settings. In addition to traditional measures such as variance in parameters after training and distance from initialization, we also measure the effectiveness of sharpness in loss landscape in capturing the success in cross-lingual transfer and propose a novel and stable algorithm to reliably compute the sharpness of a model optimum that correlates to generalization.

cs.CL↗

arXiv2024

On the design space between molecular mechanics and machine learning force fields

A force field as accurate as quantum mechanics (QM) and as fast as molecular mechanics (MM), 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 towards this direction, where differentiable neural functions are parametrized to fit ab initio energies, and furthermore 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), as 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 explorations and designs of faster, albeit perhaps slightly less accurate MLFFs, in this review, we focus our attention on the design space (the speed-accuracy tradeoff) between MM and ML force fields. After a brief review of the building blocks 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, envision what the next generation of MLFF might look like.

physics.chem-ph↗

arXiv2024

Active and Passive Causal Inference Learning

This paper serves as a starting point for machine learning researchers, engineers and students who are interested in but not yet familiar with causal inference. We start by laying out an important set of assumptions that are collectively needed for causal identification, such as exchangeability, positivity, consistency and the absence of interference. From these assumptions, we build out a set of important causal inference techniques, which we do so by categorizing them into two buckets; active and passive approaches. We describe and discuss randomized controlled trials and bandit-based approaches from the active category. We then describe classical approaches, such as matching and inverse probability weighting, in the passive category, followed by more recent deep learning based algorithms. By finishing the paper with some of the missing aspects of causal inference from this paper, such as collider biases, we expect this paper to provide readers with a diverse set of starting points for further reading and research in causal inference and discovery.

cs.LG↗

arXiv2024

Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design

Machine learning (ML) has demonstrated significant promise in accelerating drug design. Active ML-guided optimization of therapeutic molecules typically relies on a surrogate model predicting the target property of interest. The model predictions are used to determine which designs to evaluate in the lab, and the model is updated on the new measurements to inform the next cycle of decisions. A key challenge is that the experimental feedback from each cycle inspires changes in the candidate proposal or experimental protocol for the next cycle, which lead to distribution shifts. To promote robustness to these shifts, we must account for them explicitly in the model training. We apply domain generalization (DG) methods to classify the stability of interactions between an antibody and antigen across five domains defined by design cycles. Our results suggest that foundational models and ensembling improve predictive performance on out-of-distribution domains. We publicly release our codebase extending the DG benchmark ``DomainBed,'' and the associated dataset of antibody sequences and structures emulating distribution shifts across design cycles.

q-bio.BM↗

arXiv2024

MentalAgora: A Gateway to Advanced Personalized Care in Mental Health through Multi-Agent Debating and Attribute Control

As mental health issues globally escalate, there is a tremendous need for advanced digital support systems. We introduce MentalAgora, a novel framework employing large language models enhanced by interaction between multiple agents for tailored mental health support. This framework operates through three stages: strategic debating, tailored counselor creation, and response generation, enabling the dynamic customization of responses based on individual user preferences and therapeutic needs. We conduct experiments utilizing a high-quality evaluation dataset TherapyTalk crafted with mental health professionals, shwoing that MentalAgora generates expert-aligned and user preference-enhanced responses. Our evaluations, including experiments and user studies, demonstrate that MentalAgora aligns with professional standards and effectively meets user preferences, setting a new benchmark for digital mental health interventions.

cs.CL↗

arXiv2024

Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms

There is a growing body of work seeking to replicate the success of machine learning (ML) on domains like computer vision (CV) and natural language processing (NLP) to applications involving biophysical data. One of the key ingredients of prior successes in CV and NLP was the broad acceptance of difficult benchmarks that distilled key subproblems into approachable tasks that any junior researcher could investigate, but good benchmarks for biophysical domains are rare. This scarcity is partially due to a narrow focus on benchmarks which simulate biophysical data; we propose instead to carefully abstract biophysical problems into simpler ones with key geometric similarities. In particular we propose a new class of closed-form test functions for biophysical sequence optimization, which we call Ehrlich functions. We provide empirical results demonstrating these functions are interesting objects of study and can be non-trivial to solve with a standard genetic optimization baseline.

cs.LG↗

arXiv2024

Iterative Reasoning Preference Optimization

Iterative preference optimization methods have recently been shown to perform well for general instruction tuning tasks, but typically make little improvement on reasoning tasks (Yuan et al., 2024, Chen et al., 2024). In this work we develop an iterative approach that optimizes the preference between competing generated Chain-of-Thought (CoT) candidates by optimizing for winning vs. losing reasoning steps that lead to the correct answer. We train using a modified DPO loss (Rafailov et al., 2023) with an additional negative log-likelihood term, which we find to be crucial. We show reasoning improves across repeated iterations of this scheme. While only relying on examples in the training set, our approach results in increasing accuracy on GSM8K, MATH, and ARC-Challenge for Llama-2-70B-Chat, outperforming other Llama-2-based models not relying on additionally sourced datasets. For example, we see a large improvement from 55.6% to 81.6% on GSM8K and an accuracy of 88.7% with majority voting out of 32 samples.

cs.CL↗

arXiv2024

Following Length Constraints in Instructions

Aligned instruction following models can better fulfill user requests than their unaligned counterparts. However, it has been shown that there is a length bias in evaluation of such models, and that training algorithms tend to exploit this bias by learning longer responses. In this work we show how to train models that can be controlled at inference time with instructions containing desired length constraints. Such models are superior in length instructed evaluations, outperforming standard instruction following models such as GPT4, Llama 3 and Mixtral.

cs.CL↗

arXiv2024

Training Greedy Policy for Proposal Batch Selection in Expensive Multi-Objective Combinatorial Optimization

Active learning is increasingly adopted for expensive multi-objective combinatorial optimization problems, but it involves a challenging subset selection problem, optimizing the batch acquisition score that quantifies the goodness of a batch for evaluation. Due to the excessively large search space of the subset selection problem, prior methods optimize the batch acquisition on the latent space, which has discrepancies with the actual space, or optimize individual acquisition scores without considering the dependencies among candidates in a batch instead of directly optimizing the batch acquisition. To manage the vast search space, a simple and effective approach is the greedy method, which decomposes the problem into smaller subproblems, yet it has difficulty in parallelization since each subproblem depends on the outcome from the previous ones. To this end, we introduce a novel greedy-style subset selection algorithm that optimizes batch acquisition directly on the combinatorial space by sequential greedy sampling from the greedy policy, specifically trained to address all greedy subproblems concurrently. Notably, our experiments on the red fluorescent proteins design task show that our proposed method achieves the baseline performance in 1.69x fewer queries, demonstrating its efficiency.

cs.LG↗

arXiv2024

AstroCLIP: A Cross-Modal Foundation Model for Galaxies

We present AstroCLIP, a single, versatile model that can embed both galaxy images and spectra into a shared, physically meaningful latent space. These embeddings can then be used - without any model fine-tuning - for a variety of downstream tasks including (1) accurate in-modality and cross-modality semantic similarity search, (2) photometric redshift estimation, (3) galaxy property estimation from both images and spectra, and (4) morphology classification. Our approach to implementing AstroCLIP consists of two parts. First, we embed galaxy images and spectra separately by pretraining separate transformer-based image and spectrum encoders in self-supervised settings. We then align the encoders using a contrastive loss. We apply our method to spectra from the Dark Energy Spectroscopic Instrument and images from its corresponding Legacy Imaging Survey. Overall, we find remarkable performance on all downstream tasks, even relative to supervised baselines. For example, for a task like photometric redshift prediction, we find similar performance to a specifically-trained ResNet18, and for additional tasks like physical property estimation (stellar mass, age, metallicity, and sSFR), we beat this supervised baseline by 19\% in terms of $R^2$. We also compare our results to a state-of-the-art self-supervised single-modal model for galaxy images, and find that our approach outperforms this benchmark by roughly a factor of two on photometric redshift estimation and physical property prediction in terms of $R^2$, while remaining roughly in-line in terms of morphology classification. Ultimately, our approach represents the first cross-modal self-supervised model for galaxies, and the first self-supervised transformer-based architectures for galaxy images and spectra.

astro-ph.IM↗