Kyunghyun Cho

Angelica Chen, Ravid Shwartz-Ziv, Kyunghyun Cho et al. · cmu, harvard

Most interpretability research in NLP focuses on understanding the behavior and features of a fully trained model. However, certain insights into model behavior may only be accessible by observing the trajectory of the training process. We present a case study of syntax acquisition in masked language models (MLMs) that demonstrates how analyzing the evolution of interpretable artifacts throughout training deepens our understanding of emergent behavior. In particular, we study Syntactic Attention Structure (SAS), a naturally emerging property of MLMs wherein specific Transformer heads tend to focus on specific syntactic relations. We identify a brief window in pretraining when models abruptly acquire SAS, concurrent with a steep drop in loss. This breakthrough precipitates the subsequent acquisition of linguistic capabilities. We then examine the causal role of SAS by manipulating SAS during training, and demonstrate that SAS is necessary for the development of grammatical capabilities. We further find that SAS competes with other beneficial traits during training, and that briefly suppressing SAS improves model quality. These findings offer an interpretation of a real-world example of both simplicity bias and breakthrough training dynamics.

Tianxing He, Jingyu Zhang, Tianle Wang et al.

In this work, we explore a useful but often neglected methodology for robustness analysis of text generation evaluation metrics: stress tests with synthetic data. Basically, we design and synthesize a wide range of potential errors and check whether they result in a commensurate drop in the metric scores. We examine a range of recently proposed evaluation metrics based on pretrained language models, for the tasks of open-ended generation, translation, and summarization. Our experiments reveal interesting insensitivities, biases, or even loopholes in existing metrics. For example, we find that BERTScore is confused by truncation errors in summarization, and MAUVE (built on top of GPT-2) is insensitive to errors at the beginning or middle of generations. Further, we investigate the reasons behind these blind spots and suggest practical workarounds for a more reliable evaluation of text generation. We have released our code and data at https://github.com/cloudygoose/blindspot_nlg.

Michael Y. Hu, Angelica Chen, Naomi Saphra et al. · cmu, harvard

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 $L_2$ 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.

Ningyuan Huang, Yash R. Deshpande, Yibo Liu et al. · amazon-science

We propose a method to make natural language understanding models more parameter efficient by storing knowledge in an external knowledge graph (KG) and retrieving from this KG using a dense index. Given (possibly multilingual) downstream task data, e.g., sentences in German, we retrieve entities from the KG and use their multimodal representations to improve downstream task performance. We use the recently released VisualSem KG as our external knowledge repository, which covers a subset of Wikipedia and WordNet entities, and compare a mix of tuple-based and graph-based algorithms to learn entity and relation representations that are grounded on the KG multimodal information. We demonstrate the usefulness of the learned entity representations on two downstream tasks, and show improved performance on the multilingual named entity recognition task by $0.3\%$--$0.7\%$ F1, while we achieve up to $2.5\%$ improvement in accuracy on the visual sense disambiguation task. All our code and data are available in: \url{https://github.com/iacercalixto/visualsem-kg}.

Weizhe Yuan, Kyunghyun Cho, Jason Weston

Natural language (NL) feedback offers rich insights into user experience. While existing studies focus on an instance-level approach, where feedback is used to refine specific examples, we introduce a framework for system-level use of NL feedback. We show how to use feedback to formalize system-level design decisions in a human-in-the-loop-process -- in order to produce better models. In particular this is done through: (i) metric design for tasks; and (ii) language model prompt design for refining model responses. We conduct two case studies of this approach for improving search query and dialog response generation, demonstrating the effectiveness of system-level feedback. We show the combination of system-level and instance-level feedback brings further gains, and that human written instance-level feedback results in more grounded refinements than GPT-3.5 written ones, underlying the importance of human feedback for building systems. We release our code and data at https://github.com/yyy-Apple/Sys-NL-Feedback.

Nathan C. Frey, Daniel Berenberg, Karina Zadorozhny et al. · berkeley

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our Discrete Walk-Jump Sampling formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the distributional conformity score to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100% of generated samples are successfully expressed and purified and 70% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

Nataša Tagasovska, Nathan C. Frey, Andreas Loukas et al. · berkeley

Deep generative models have emerged as a popular machine learning-based approach for inverse design problems in the life sciences. However, these problems often require sampling new designs that satisfy multiple properties of interest in addition to learning the data distribution. This multi-objective optimization becomes more challenging when properties are independent or orthogonal to each other. In this work, we propose a Pareto-compositional energy-based model (pcEBM), a framework that uses multiple gradient descent for sampling new designs that adhere to various constraints in optimizing distinct properties. We demonstrate its ability to learn non-convex Pareto fronts and generate sequences that simultaneously satisfy multiple desired properties across a series of real-world antibody design tasks.

Jeevesh Juneja, Rachit Bansal, Kyunghyun Cho et al. · cmu, harvard

It is widely accepted in the mode connectivity literature that when two neural networks are trained similarly on the same data, they are connected by a path through parameter space over which test set accuracy is maintained. Under some circumstances, including transfer learning from pretrained models, these paths are presumed to be linear. In contrast to existing results, we find that among text classifiers (trained on MNLI, QQP, and CoLA), some pairs of finetuned models have large barriers of increasing loss on the linear paths between them. On each task, we find distinct clusters of models which are linearly connected on the test loss surface, but are disconnected from models outside the cluster -- models that occupy separate basins on the surface. By measuring performance on specially-crafted diagnostic datasets, we find that these clusters correspond to different generalization strategies: one cluster behaves like a bag of words model under domain shift, while another cluster uses syntactic heuristics. Our work demonstrates how the geometry of the loss surface can guide models towards different heuristic functions.

Grace Yang, Ming Cao, Lavender Y. Jiang et al.

Traditional evaluation metrics for classification in natural language processing such as accuracy and area under the curve fail to differentiate between models with different predictive behaviors despite their similar performance metrics. We introduce sensitivity score, a metric that scrutinizes models' behaviors at the vocabulary level to provide insights into disparities in their decision-making logic. We assess the sensitivity score on a set of representative words in the test set using two classifiers trained for hospital readmission classification with similar performance statistics. Our experiments compare the decision-making logic of clinicians and classifiers based on rank correlations of sensitivity scores. The results indicate that the language model's sensitivity score aligns better with the professionals than the xgboost classifier on tf-idf embeddings, which suggests that xgboost uses some spurious features. Overall, this metric offers a novel perspective on assessing models' robustness by quantifying their discrepancy with professional opinions. Our code is available on GitHub (https://github.com/nyuolab/Model_Sensitivity).

Richard Yuanzhe Pang, Stephen Roller, Kyunghyun Cho et al.

We study improving social conversational agents by learning from natural dialogue between users and a deployed model, without extra annotations. To implicitly measure the quality of a machine-generated utterance, we leverage signals like user response length, sentiment and reaction of the future human utterances in the collected dialogue episodes. Our experiments use the publicly released deployment data from BlenderBot (Xu et al., 2023). Human evaluation indicates improvements in our new models over baseline responses; however, we find that some proxy signals can lead to more generations with undesirable properties as well. For example, optimizing for conversation length can lead to more controversial or unfriendly generations compared to the baseline, whereas optimizing for positive sentiment or reaction can decrease these behaviors.

Yuanqing Wang, Kenichiro Takaba, Michael S. Chen et al.

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.

Naomi Saphra, Eve Fleisig, Kyunghyun Cho et al. · cmu, harvard

Many NLP researchers are experiencing an existential crisis triggered by the astonishing success of ChatGPT and other systems based on large language models (LLMs). After such a disruptive change to our understanding of the field, what is left to do? Taking a historical lens, we look for guidance from the first era of LLMs, which began in 2005 with large $n$-gram models for machine translation (MT). We identify durable lessons from the first era, and more importantly, we identify evergreen problems where NLP researchers can continue to make meaningful contributions in areas where LLMs are ascendant. We argue that disparities in scale are transient and researchers can work to reduce them; that data, rather than hardware, is still a bottleneck for many applications; that meaningful realistic evaluation is still an open problem; and that there is still room for speculative approaches.

Cal Peyser, Ronny Huang Andrew Rosenberg Tara N. Sainath, Michael Picheny et al.

The careful construction of audio representations has become a dominant feature in the design of approaches to many speech tasks. Increasingly, such approaches have emphasized "disentanglement", where a representation contains only parts of the speech signal relevant to transcription while discarding irrelevant information. In this paper, we construct a representation learning task based on joint modeling of ASR and TTS, and seek to learn a representation of audio that disentangles that part of the speech signal that is relevant to transcription from that part which is not. We present empirical evidence that successfully finding such a representation is tied to the randomness inherent in training. We then make the observation that these desired, disentangled solutions to the optimization problem possess unique statistical properties. Finally, we show that enforcing these properties during training improves WER by 24.5% relative on average for our joint modeling task. These observations motivate a novel approach to learning effective audio representations.

Nathan Ng, Neha Hulkund, Kyunghyun Cho et al.

Developing and deploying machine learning models safely depends on the ability to characterize and compare their abilities to generalize to new environments. Although recent work has proposed a variety of methods that can directly predict or theoretically bound the generalization capacity of a model, they rely on strong assumptions such as matching train/test distributions and access to model gradients. In order to characterize generalization when these assumptions are not satisfied, we propose neighborhood invariance, a measure of a classifier's output invariance in a local transformation neighborhood. Specifically, we sample a set of transformations and given an input test point, calculate the invariance as the largest fraction of transformed points classified into the same class. Crucially, our measure is simple to calculate, does not depend on the test point's true label, makes no assumptions about the data distribution or model, and can be applied even in out-of-domain (OOD) settings where existing methods cannot, requiring only selecting a set of appropriate data transformations. In experiments on robustness benchmarks in image classification, sentiment analysis, and natural language inference, we demonstrate a strong and robust correlation between our neighborhood invariance measure and actual OOD generalization on over 4,600 models evaluated on over 100 unique train/test domain pairs.

Karolis Martinkus, Jan Ludwiczak, Kyunghyun Cho et al.

We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new representation of protein structure, relies on a novel architecture for aligned proteins, and utilizes strong diffusion priors to improve the denoising process. Our approach improves protein diffusion by taking advantage of domain knowledge and physics-based constraints; handles sequence-length changes; and reduces memory complexity by an order of magnitude, enabling backbone and side chain generation. We validate AbDiffuser in silico and in vitro. Numerical experiments showcase the ability of AbDiffuser to generate antibodies that closely track the sequence and structural properties of a reference set. Laboratory experiments confirm that all 16 HER2 antibodies discovered were expressed at high levels and that 57.1% of the selected designs were tight binders.

Cal Peyser, Zhong Meng, Ke Hu et al.

The last year has seen astonishing progress in text-prompted image generation premised on the idea of a cross-modal representation space in which the text and image domains are represented jointly. In ASR, this idea has found application as joint speech-text encoders that can scale to the capacities of very large parameter models by being trained on both unpaired speech and text. While these methods show promise, they have required special treatment of the sequence-length mismatch inherent in speech and text, either by up-sampling heuristics or an explicit alignment model. In this work, we offer evidence that joint speech-text encoders naturally achieve consistent representations across modalities by disregarding sequence length, and argue that consistency losses could forgive length differences and simply assume the best alignment. We show that such a loss improves downstream WER in both a large-parameter monolingual and multilingual system.

Sang-Woo Lee, Sungdong Kim, Donghyeon Ko et al.

Task-oriented dialogue (TOD) systems are mainly based on the slot-filling-based TOD (SF-TOD) framework, in which dialogues are broken down into smaller, controllable units (i.e., slots) to fulfill a specific task. A series of approaches based on this framework achieved remarkable success on various TOD benchmarks. However, we argue that the current TOD benchmarks are limited to surrogate real-world scenarios and that the current TOD models are still a long way to cover the scenarios. In this position paper, we first identify current status and limitations of SF-TOD systems. After that, we explore the WebTOD framework, the alternative direction for building a scalable TOD system when a web/mobile interface is available. In WebTOD, the dialogue system learns how to understand the web/mobile interface that the human agent interacts with, powered by a large-scale language model.

Siavash Golkar, Jake Kovalic, Irina Espejo Morales et al.

Biological function emerges from coupled constraints across sequence, structure, regulation, evolution, and cellular context, yet most foundation models in biology are trained within one modality or for a fixed forward task. We present MIMIC, a generative multimodal foundation model trained on our newly curated and aligned dataset, LORE, linking nucleic acid, protein, evolutionary, structural, regulatory, and semantic/contextual modalities within partially observed biomolecular states. MIMIC uses a split-track encoder-decoder architecture to condition on arbitrary subsets of observed modalities and reconstruct or generate missing components of molecular state across the genome, transcriptome, and proteome. Multimodal conditioning consistently improves MIMIC's sequence reconstruction relative to sequence-only inputs, while its learned representations enable state-of-the-art performance on RNA and protein downstream tasks. MIMIC achieves state-of-the-art splicing prediction, and its joint generative formulation enables isoform-aware inference that further improves performance. Beyond prediction, the same generative framework supports constrained design. For RNA, MIMIC identifies corrective edits in a clinically relevant HBB splice-disrupting mutation without reverting it by using evolutionary and structural signals. For proteins, jointly conditioning on shape and surface chemistry of PD-L1 and hACE2 binding sites produces diverse, high-confidence sequences with strong in silico support for target binding. Finally, MIMIC uses experimental context as semantic conditioning to model assay-dependent RNA chemical probing, rather than treating context as a fixed output. Together, these results position MIMIC's aligned multimodal generative modeling as a strong foundation for unifying representation learning, conditional prediction, and constrained biomolecular design within a single model.

Nathan Ng, Ji Won Park, Jae Hyeon Lee et al.

Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate multiple subreads, or noisy observations of the same sequence. Denoising these subreads with alignment-based approaches often fails when too few subreads are available or error rates are too high. In this paper, we propose a novel method for blindly denoising sets of sequences without directly observing clean source sequence labels. Our method, Self-Supervised Set Learning (SSSL), gathers subreads together in an embedding space and estimates a single set embedding as the midpoint of the subreads in both the latent and sequence spaces. This set embedding represents the "average" of the subreads and can be decoded into a prediction of the clean sequence. In experiments on simulated long-read DNA data, SSSL methods denoise small reads of $\leq 6$ subreads with 17% fewer errors and large reads of $>6$ subreads with 8% fewer errors compared to the best baseline. On a real dataset of antibody sequences, SSSL improves over baselines on two self-supervised metrics, with a significant improvement on difficult small reads that comprise over 60% of the test set. By accurately denoising these reads, SSSL promises to better realize the potential of high-throughput DNA sequencing data for downstream scientific applications.

Cheolhyoung Lee, Kyunghyun Cho

Despite the recent success of stochastic gradient descent in deep learning, it is often difficult to train a deep neural network with an inappropriate choice of its initial parameters. Even if training is successful, it has been known that the initial parameter configuration may negatively impact generalization. In this paper, we propose an unsupervised algorithm to find good initialization for input data, given that a downstream task is d-way classification. We first notice that each parameter configuration in the parameter space corresponds to one particular downstream task of d-way classification. We then conjecture that the success of learning is directly related to how diverse downstream tasks are in the vicinity of the initial parameters. We thus design an algorithm that encourages small perturbation to the initial parameter configuration leads to a diverse set of d-way classification tasks. In other words, the proposed algorithm ensures a solution to any downstream task to be near the initial parameter configuration. We empirically evaluate the proposed algorithm on various tasks derived from MNIST with a fully connected network. In these experiments, we observe that our algorithm improves average test accuracy across most of these tasks, and that such improvement is greater when the number of labelled examples is small.

Eugene Choi, Kyunghyun Cho, Cheolhyoung Lee

Recent large-scale neural autoregressive sequence models have shown impressive performances on a variety of natural language generation tasks. However, their generated sequences often exhibit degenerate properties such as non-termination, undesirable repetition, and premature termination, when generated with decoding algorithms such as greedy search, beam search, top-$k$ sampling, and nucleus sampling. In this paper, we focus on the problem of non-terminating sequences resulting from an incomplete decoding algorithm. We first define an incomplete probable decoding algorithm which includes greedy search, top-$k$ sampling, and nucleus sampling, beyond the incomplete decoding algorithm originally put forward by Welleck et al. (2020). We then propose a non-monotonic self-terminating language model, which significantly relaxes the constraint of monotonically increasing termination probability in the originally proposed self-terminating language model by Welleck et al. (2020), to address the issue of non-terminating sequences when using incomplete probable decoding algorithms. We prove that our proposed model prevents non-terminating sequences when using not only incomplete probable decoding algorithms but also beam search. We empirically validate our model on sequence completion tasks with various architectures.

Divyam Madaan, Daniel Sodickson, Kyunghyun Cho et al.

Magnetic Resonance Imaging (MRI) is considered the gold standard of medical imaging because of the excellent soft-tissue contrast exhibited in the images reconstructed by the MRI pipeline, which in-turn enables the human radiologist to discern many pathologies easily. More recently, Deep Learning (DL) models have also achieved state-of-the-art performance in diagnosing multiple diseases using these reconstructed images as input. However, the image reconstruction process within the MRI pipeline, which requires the use of complex hardware and adjustment of a large number of scanner parameters, is highly susceptible to noise of various forms, resulting in arbitrary artifacts within the images. Furthermore, the noise distribution is not stationary and varies within a machine, across machines, and patients, leading to varying artifacts within the images. Unfortunately, DL models are quite sensitive to these varying artifacts as it leads to changes in the input data distribution between the training and testing phases. The lack of robustness of these models against varying artifacts impedes their use in medical applications where safety is critical. In this work, we focus on improving the generalization performance of these models in the presence of multiple varying artifacts that manifest due to the complexity of the MR data acquisition. In our experiments, we observe that Batch Normalization, a widely used technique during the training of DL models for medical image analysis, is a significant cause of performance degradation in these changing environments. As a solution, we propose to use other normalization techniques, such as Group Normalization and Layer Normalization (LN), to inject robustness into model performance against varying image artifacts. Through a systematic set of experiments, we show that GN and LN provide better accuracy for various MR artifacts and distribution shifts.

Buxin Su, Jiayao Zhang, Natalie Collina et al. · princeton

We conducted an experiment during the review process of the 2023 International Conference on Machine Learning (ICML), asking authors with multiple submissions to rank their papers based on perceived quality. In total, we received 1,342 rankings, each from a different author, covering 2,592 submissions. In this paper, we present an empirical analysis of how author-provided rankings could be leveraged to improve peer review processes at machine learning conferences. We focus on the Isotonic Mechanism, which calibrates raw review scores using the author-provided rankings. Our analysis shows that these ranking-calibrated scores outperform the raw review scores in estimating the ground truth ``expected review scores'' in terms of both squared and absolute error metrics. Furthermore, we propose several cautious, low-risk applications of the Isotonic Mechanism and author-provided rankings in peer review, including supporting senior area chairs in overseeing area chairs' recommendations, assisting in the selection of paper awards, and guiding the recruitment of emergency reviewers.

Ji Won Park, Samuel Stanton, Saeed Saremi et al.

Bayesian optimization offers a sample-efficient framework for navigating the exploration-exploitation trade-off in the vast design space of biological sequences. Whereas it is possible to optimize the various properties of interest jointly using a multi-objective acquisition function, such as the expected hypervolume improvement (EHVI), this approach does not account for objectives with a hierarchical dependency structure. We consider a common use case where some regions of the Pareto frontier are prioritized over others according to a specified $\textit{partial ordering}$ in the objectives. For instance, when designing antibodies, we would like to maximize the binding affinity to a target antigen only if it can be expressed in live cell culture -- modeling the experimental dependency in which affinity can only be measured for antibodies that can be expressed and thus produced in viable quantities. In general, we may want to confer a partial ordering to the properties such that each property is optimized conditioned on its parent properties satisfying some feasibility condition. To this end, we present PropertyDAG, a framework that operates on top of the traditional multi-objective BO to impose this desired ordering on the objectives, e.g. expression $\rightarrow$ affinity. We demonstrate its performance over multiple simulated active learning iterations on a penicillin production task, toy numerical problem, and a real-world antibody design task.

Jang-Hyun Kim, Claudia Skok Gibbs, Sangdoo Yun et al.

We propose a novel machine learning approach for inferring causal variables of a target variable from observations. Our focus is on directly inferring a set of causal factors without requiring full causal graph reconstruction, which is computationally challenging in large-scale systems. The identified causal set consists of all potential regulators of the target variable under experimental settings, enabling efficient regulation through intervention. To achieve this, we train a neural network using supervised learning on simulated data to infer causality. By employing a subsampled-ensemble inference strategy, our approach scales with linear complexity in the number of variables, efficiently scaling up to thousands of variables. Empirical results demonstrate superior performance in identifying causal relationships within large-scale gene regulatory networks, outperforming existing methods that emphasize full-graph discovery. We validate our model's generalization capability across out-of-distribution graph structures and generating mechanisms, including gene regulatory networks of E. coli and the human K562 cell line. Implementation codes are available at https://github.com/snu-mllab/Targeted-Cause-Discovery.

Daniel Berenberg, Jae Hyeon Lee, Simon Kelow et al.

Deep generative modeling for biological sequences presents a unique challenge in reconciling the bias-variance trade-off between explicit biological insight and model flexibility. The deep manifold sampler was recently proposed as a means to iteratively sample variable-length protein sequences by exploiting the gradients from a function predictor. We introduce an alternative approach to this guided sampling procedure, multi-segment preserving sampling, that enables the direct inclusion of domain-specific knowledge by designating preserved and non-preserved segments along the input sequence, thereby restricting variation to only select regions. We present its effectiveness in the context of antibody design by training two models: a deep manifold sampler and a GPT-2 language model on nearly six million heavy chain sequences annotated with the IGHV1-18 gene. During sampling, we restrict variation to only the complementarity-determining region 3 (CDR3) of the input. We obtain log probability scores from a GPT-2 model for each sampled CDR3 and demonstrate that multi-segment preserving sampling generates reasonable designs while maintaining the desired, preserved regions.

Ji Won Park, Nataša Tagasovska, Michael Maser et al.

Many scientific and industrial applications require the joint optimization of multiple, potentially competing objectives. Multi-objective Bayesian optimization (MOBO) is a sample-efficient framework for identifying Pareto-optimal solutions. At the heart of MOBO is the acquisition function, which determines the next candidate to evaluate by navigating the best compromises among the objectives. In this paper, we show a natural connection between non-dominated solutions and the extreme quantile of the joint cumulative distribution function (CDF). Motivated by this link, we propose the Pareto-compliant CDF indicator and the associated acquisition function, BOtied. BOtied inherits desirable invariance properties of the CDF, and an efficient implementation with copulas allows it to scale to many objectives. Our experiments on a variety of synthetic and real-world problems demonstrate that BOtied outperforms state-of-the-art MOBO acquisition functions while being computationally efficient for many objectives.

Zihan Wang, Kangrui Wang, Qineng Wang et al.

Training large language models (LLMs) as interactive agents presents unique challenges including long-horizon decision making and interacting with stochastic environment feedback. While reinforcement learning (RL) has enabled progress in static tasks, multi-turn agent RL training remains underexplored. We propose StarPO (State-Thinking-Actions-Reward Policy Optimization), a general framework for trajectory-level agent RL, and introduce RAGEN, a modular system for training and evaluating LLM agents. Our study on four stylized environments reveals three core findings. First, our agent RL training shows a recurring mode of Echo Trap where reward variance cliffs and gradient spikes; we address this with StarPO-S, a stabilized variant with trajectory filtering, critic incorporation, and gradient stabilization. Second, we find the shaping of RL rollouts would benefit from diverse initial states, medium interaction granularity and more frequent sampling. Third, we show that without fine-grained, reasoning-aware reward signals, agent reasoning hardly emerge through multi-turn RL and they may show shallow strategies or hallucinated thoughts. Code and environments are available at https://github.com/RAGEN-AI/RAGEN.

Yuanqing Wang, Kyunghyun Cho

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.

Nataša Tagasovska, Ji Won Park, Matthieu Kirchmeyer et al.

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.

Weizhe Yuan, Jane Yu, Song Jiang et al.

Scaling reasoning capabilities beyond traditional domains such as math and coding is hindered by the lack of diverse and high-quality questions. To overcome this limitation, we introduce a scalable approach for generating diverse and challenging reasoning questions, accompanied by reference answers. We present NaturalReasoning, a comprehensive dataset comprising 2.8 million questions that span multiple domains, including STEM fields (e.g., Physics, Computer Science), Economics, Social Sciences, and more. We demonstrate the utility of the questions in NaturalReasoning through knowledge distillation experiments which show that NaturalReasoning can effectively elicit and transfer reasoning capabilities from a strong teacher model. Furthermore, we demonstrate that NaturalReasoning is also effective for unsupervised self-training using external reward models or self-rewarding. To foster future work, we publicly release NaturalReasoning at https://huggingface.co/datasets/facebook/natural_reasoning.

Hongyi Zheng, Yixin Zhu, Lavender Yao Jiang et al.

Recent advances in large language models have led to renewed interest in natural language processing in healthcare using the free text of clinical notes. One distinguishing characteristic of clinical notes is their long time span over multiple long documents. The unique structure of clinical notes creates a new design choice: when the context length for a language model predictor is limited, which part of clinical notes should we choose as the input? Existing studies either choose the inputs with domain knowledge or simply truncate them. We propose a framework to analyze the sections with high predictive power. Using MIMIC-III, we show that: 1) predictive power distribution is different between nursing notes and discharge notes and 2) combining different types of notes could improve performance when the context length is large. Our findings suggest that a carefully selected sampling function could enable more efficient information extraction from clinical notes.

Richard Yuanzhe Pang, Weizhe Yuan, Kyunghyun Cho et al. · meta-ai

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.

Seyoung Song, Haneul Yoo, Jiho Jin et al.

While Korean historical documents are invaluable cultural heritage, understanding those documents requires in-depth Hanja expertise. Hanja is an ancient language used in Korea before the 20th century, whose characters were borrowed from old Chinese but had evolved in Korea for centuries. Modern Koreans and Chinese cannot understand Korean historical documents without substantial additional help, and while previous efforts have produced some Korean and English translations, this requires in-depth expertise, and so most of the documents are not translated into any modern language. To address this gap, we present HERITAGE, the first open-source Hanja NLP toolkit to assist in understanding and translating the unexplored Korean historical documents written in Hanja. HERITAGE is a web-based platform providing model predictions of three critical tasks in historical document understanding via Hanja language models: punctuation restoration, named entity recognition, and machine translation (MT). HERITAGE also provides an interactive glossary, which provides the character-level reading of the Hanja characters in modern Korean, as well as character-level English definition. HERITAGE serves two purposes. First, anyone interested in these documents can get a general understanding from the model predictions and the interactive glossary, especially MT outputs in Korean and English. Second, since the model outputs are not perfect, Hanja experts can revise them to produce better annotations and translations. This would boost the translation efficiency and potentially lead to most of the historical documents being translated into modern languages, lowering the barrier on unexplored Korean historical documents.

Sungmin Cha, Kyunghyun Cho

Continual learning (CL) aims to train a model on a sequence of tasks (i.e., a CL scenario) while balancing the trade-off between plasticity (learning new tasks) and stability (retaining prior knowledge). The dominantly adopted conventional evaluation protocol for CL algorithms selects the best hyperparameters (e.g., learning rate, mini-batch size, regularization strengths, etc.) within a given scenario and then evaluates the algorithms using these hyperparameters in the same scenario. However, this protocol has significant shortcomings: it overestimates the CL capacity of algorithms and relies on unrealistic hyperparameter tuning, which is not feasible for real-world applications. From the fundamental principles of evaluation in machine learning, we argue that the evaluation of CL algorithms should focus on assessing the generalizability of their CL capacity to unseen scenarios. Based on this, we propose the Generalizable Two-phase Evaluation Protocol (GTEP) consisting of hyperparameter tuning and evaluation phases. Both phases share the same scenario configuration (e.g., number of tasks) but are generated from different datasets. Hyperparameters of CL algorithms are tuned in the first phase and applied in the second phase to evaluate the algorithms. We apply this protocol to class-incremental learning, both with and without pretrained models. Across more than 8,000 experiments, our results show that most state-of-the-art algorithms fail to replicate their reported performance, highlighting that their CL capacity has been significantly overestimated in the conventional evaluation protocol. Our implementation can be found in https://github.com/csm9493/GTEP.

Benjamin Stadnick, Jan Witowski, Vishwaesh Rajiv et al.

Artificial intelligence (AI) is showing promise in improving clinical diagnosis. In breast cancer screening, recent studies show that AI has the potential to improve early cancer diagnosis and reduce unnecessary workup. As the number of proposed models and their complexity grows, it is becoming increasingly difficult to re-implement them. To enable reproducibility of research and to enable comparison between different methods, we release a meta-repository containing models for classification of screening mammograms. This meta-repository creates a framework that enables the evaluation of AI models on any screening mammography data set. At its inception, our meta-repository contains five state-of-the-art models with open-source implementations and cross-platform compatibility. We compare their performance on seven international data sets. Our framework has a flexible design that can be generalized to other medical image analysis tasks. The meta-repository is available at https://www.github.com/nyukat/mammography_metarepository.

William F. Whitney, Min Jae Song, David Brandfonbrener et al.

We consider the problem of evaluating representations of data for use in solving a downstream task. We propose to measure the quality of a representation by the complexity of learning a predictor on top of the representation that achieves low loss on a task of interest, and introduce two methods, surplus description length (SDL) and $\varepsilon$ sample complexity ($\varepsilon$SC). In contrast to prior methods, which measure the amount of information about the optimal predictor that is present in a specific amount of data, our methods measure the amount of information needed from the data to recover an approximation of the optimal predictor up to a specified tolerance. We present a framework to compare these methods based on plotting the validation loss versus evaluation dataset size (the "loss-data" curve). Existing measures, such as mutual information and minimum description length probes, correspond to slices and integrals along the data axis of the loss-data curve, while ours correspond to slices and integrals along the loss axis. We provide experiments on real data to compare the behavior of each of these methods over datasets of varying size along with a high performance open source library for representation evaluation at https://github.com/willwhitney/reprieve.

Moin Nadeem, Tianxing He, Kyunghyun Cho et al.

This work studies the widely adopted ancestral sampling algorithms for auto-regressive language models, which is not widely studied in the literature. We use the quality-diversity (Q-D) trade-off to investigate three popular sampling algorithms (top-k, nucleus and tempered sampling). We focus on the task of open-ended language generation. We first show that the existing sampling algorithms have similar performance. After carefully inspecting the transformations defined by different sampling algorithms, we identify three key properties that are shared among them: entropy reduction, order preservation, and slope preservation. To validate the importance of the identified properties, we design two sets of new sampling algorithms: one set in which each algorithm satisfies all three properties, and one set in which each algorithm violates at least one of the properties. We compare their performance with existing sampling algorithms, and find that violating the identified properties could lead to drastic performance degradation, as measured by the Q-D trade-off. On the other hand, we find that the set of sampling algorithms that satisfies these properties performs on par with the existing sampling algorithms. Our data and code are available at https://github.com/moinnadeem/characterizing-sampling-algorithms

Houda Alberts, Teresa Huang, Yash Deshpande et al.

An exciting frontier in natural language understanding (NLU) and generation (NLG) calls for (vision-and-) language models that can efficiently access external structured knowledge repositories. However, many existing knowledge bases only cover limited domains, or suffer from noisy data, and most of all are typically hard to integrate into neural language pipelines. To fill this gap, we release VisualSem: a high-quality knowledge graph (KG) which includes nodes with multilingual glosses, multiple illustrative images, and visually relevant relations. We also release a neural multi-modal retrieval model that can use images or sentences as inputs and retrieves entities in the KG. This multi-modal retrieval model can be integrated into any (neural network) model pipeline. We encourage the research community to use VisualSem for data augmentation and/or as a source of grounding, among other possible uses. VisualSem as well as the multi-modal retrieval models are publicly available and can be downloaded in this URL: https://github.com/iacercalixto/visualsem

Yiqiu Shen, Nan Wu, Jason Phang et al.

Medical images differ from natural images in significantly higher resolutions and smaller regions of interest. Because of these differences, neural network architectures that work well for natural images might not be applicable to medical image analysis. In this work, we extend the globally-aware multiple instance classifier, a framework we proposed to address these unique properties of medical images. This model first uses a low-capacity, yet memory-efficient, network on the whole image to identify the most informative regions. It then applies another higher-capacity network to collect details from chosen regions. Finally, it employs a fusion module that aggregates global and local information to make a final prediction. While existing methods often require lesion segmentation during training, our model is trained with only image-level labels and can generate pixel-level saliency maps indicating possible malignant findings. We apply the model to screening mammography interpretation: predicting the presence or absence of benign and malignant lesions. On the NYU Breast Cancer Screening Dataset, consisting of more than one million images, our model achieves an AUC of 0.93 in classifying breasts with malignant findings, outperforming ResNet-34 and Faster R-CNN. Compared to ResNet-34, our model is 4.1x faster for inference while using 78.4% less GPU memory. Furthermore, we demonstrate, in a reader study, that our model surpasses radiologist-level AUC by a margin of 0.11. The proposed model is available online: https://github.com/nyukat/GMIC.

Rodrigo Nogueira, Kyunghyun Cho

Recently, neural models pretrained on a language modeling task, such as ELMo (Peters et al., 2017), OpenAI GPT (Radford et al., 2018), and BERT (Devlin et al., 2018), have achieved impressive results on various natural language processing tasks such as question-answering and natural language inference. In this paper, we describe a simple re-implementation of BERT for query-based passage re-ranking. Our system is the state of the art on the TREC-CAR dataset and the top entry in the leaderboard of the MS MARCO passage retrieval task, outperforming the previous state of the art by 27% (relative) in MRR@10. The code to reproduce our results is available at https://github.com/nyu-dl/dl4marco-bert

Konrad Zolna, Krzysztof J. Geras, Kyunghyun Cho

Currently available methods for extracting saliency maps identify parts of the input which are the most important to a specific fixed classifier. We show that this strong dependence on a given classifier hinders their performance. To address this problem, we propose classifier-agnostic saliency map extraction, which finds all parts of the image that any classifier could use, not just one given in advance. We observe that the proposed approach extracts higher quality saliency maps than prior work while being conceptually simple and easy to implement. The method sets the new state of the art result for localization task on the ImageNet data, outperforming all existing weakly-supervised localization techniques, despite not using the ground truth labels at the inference time. The code reproducing the results is available at https://github.com/kondiz/casme . The final version of this manuscript is published in Computer Vision and Image Understanding and is available online at https://doi.org/10.1016/j.cviu.2020.102969 .

Francesco Visin, Marco Ciccone, Adriana Romero et al.

We propose a structured prediction architecture, which exploits the local generic features extracted by Convolutional Neural Networks and the capacity of Recurrent Neural Networks (RNN) to retrieve distant dependencies. The proposed architecture, called ReSeg, is based on the recently introduced ReNet model for image classification. We modify and extend it to perform the more challenging task of semantic segmentation. Each ReNet layer is composed of four RNN that sweep the image horizontally and vertically in both directions, encoding patches or activations, and providing relevant global information. Moreover, ReNet layers are stacked on top of pre-trained convolutional layers, benefiting from generic local features. Upsampling layers follow ReNet layers to recover the original image resolution in the final predictions. The proposed ReSeg architecture is efficient, flexible and suitable for a variety of semantic segmentation tasks. We evaluate ReSeg on several widely-used semantic segmentation datasets: Weizmann Horse, Oxford Flower, and CamVid; achieving state-of-the-art performance. Results show that ReSeg can act as a suitable architecture for semantic segmentation tasks, and may have further applications in other structured prediction problems. The source code and model hyperparameters are available on https://github.com/fvisin/reseg.

Max W. Shen, Ewa Nowara, Michael Maser et al.

While data augmentation is widely used to train symmetry-agnostic models, it remains unclear how quickly and effectively they learn to respect symmetries. We investigate this by deriving a principled measure of equivariance error that, for convex losses, calculates the percent of total loss attributable to imperfections in learned symmetry. We focus our empirical investigation to 3D-rotation equivariance on high-dimensional molecular tasks (flow matching, force field prediction, denoising voxels) and find that models reduce equivariance error quickly to $\leq$2\% held-out loss within 1k-10k training steps, a result robust to model and dataset size. This happens because learning 3D-rotational equivariance is an easier learning task, with a smoother and better-conditioned loss landscape, than the main prediction task. For 3D rotations, the loss penalty for non-equivariant models is small throughout training, so they may achieve lower test loss than equivariant models per GPU-hour unless the equivariant ``efficiency gap'' is narrowed. We also experimentally and theoretically investigate the relationships between relative equivariance error, learning gradients, and model parameters.

Diantong Li, Kyunghyun Cho, Chong Liu

Bayesian Optimization (BO) is an efficient tool for optimizing black-box functions, but its theoretical guarantees typically hold in the asymptotic regime. In many critical real-world applications such as drug discovery or materials design, where each evaluation can be very costly and time-consuming, BO becomes impractical for many evaluations. In this paper, we introduce the Procedure-inFormed BO (ProfBO) algorithm, which solves black-box optimization with remarkably few function evaluations. At the heart of our algorithmic design are Markov Decision Process (MDP) priors that model optimization trajectories from related source tasks, thereby capturing procedural knowledge on efficient optimization. We embed these MDP priors into a prior-fitted neural network and employ model-agnostic meta-learning for fast adaptation to new target tasks. Experiments on real-world Covid and Cancer benchmarks and hyperparameter tuning tasks demonstrate that ProfBO consistently outperforms state-of-the-art methods by achieving high-quality solutions with significantly fewer evaluations, making it ready for practical deployment.

Aya Abdelsalam Ismail, Tuomas Oikarinen, Amy Wang et al.

We introduce Concept Bottleneck Protein Language Models (CB-pLM), a generative masked language model with a layer where each neuron corresponds to an interpretable concept. Our architecture offers three key benefits: i) Control: We can intervene on concept values to precisely control the properties of generated proteins, achieving a 3 times larger change in desired concept values compared to baselines. ii) Interpretability: A linear mapping between concept values and predicted tokens allows transparent analysis of the model's decision-making process. iii) Debugging: This transparency facilitates easy debugging of trained models. Our models achieve pre-training perplexity and downstream task performance comparable to traditional masked protein language models, demonstrating that interpretability does not compromise performance. While adaptable to any language model, we focus on masked protein language models due to their importance in drug discovery and the ability to validate our model's capabilities through real-world experiments and expert knowledge. We scale our CB-pLM from 24 million to 3 billion parameters, making them the largest Concept Bottleneck Models trained and the first capable of generative language modeling.

Ji Won Park, Robert Tibshirani, Kyunghyun Cho

Many risk-sensitive applications require well-calibrated prediction sets over multiple, potentially correlated target variables, for which the prediction algorithm may report correlated errors. In this work, we aim to construct the conformal prediction set accounting for the joint correlation structure of the vector-valued non-conformity scores. Drawing from the rich literature on multivariate quantiles and semiparametric statistics, we propose an algorithm to estimate the $1-α$ quantile of the scores, where $α$ is the user-specified miscoverage rate. In particular, we flexibly estimate the joint cumulative distribution function (CDF) of the scores using nonparametric vine copulas and improve the asymptotic efficiency of the quantile estimate using its influence function. The vine decomposition allows our method to scale well to a large number of targets. As well as guaranteeing asymptotically exact coverage, our method yields desired coverage and competitive efficiency on a range of real-world regression problems, including those with missing-at-random labels in the calibration set.

Micah Goldblum, Anima Anandkumar, Richard Baraniuk et al.

The goal of this series is to chronicle opinions and issues in the field of machine learning as they stand today and as they change over time. The plan is to host this survey periodically until the AI singularity paperclip-frenzy-driven doomsday, keeping an updated list of topical questions and interviewing new community members for each edition. In this issue, we probed people's opinions on interpretable AI, the value of benchmarking in modern NLP, the state of progress towards understanding deep learning, and the future of academia.

Lucius E. J. Bynum, Kyunghyun Cho

In this work, we present sequence-driven structural causal models (SD-SCMs), a framework for specifying causal models with user-defined structure and language-model-defined mechanisms. We characterize how an SD-SCM enables sampling from observational, interventional, and counterfactual distributions according to the desired causal structure. We then leverage this procedure to propose a new type of benchmark for causal inference methods, generating individual-level counterfactual data to test treatment effect estimation. We create an example benchmark consisting of thousands of datasets, and test a suite of popular estimation methods for average, conditional average, and individual treatment effect estimation. We find under this benchmark that (1) causal methods outperform non-causal methods and that (2) even state-of-the-art methods struggle with individualized effect estimation, suggesting this benchmark captures some inherent difficulties in causal estimation. Apart from generating data, this same technique can underpin the auditing of language models for (un)desirable causal effects, such as misinformation or discrimination. We believe SD-SCMs can serve as a useful tool in any application that would benefit from sequential data with controllable causal structure.

Mallory Knodel, Andrés Fábrega, Daniella Ferrari et al.

End-to-end encryption (E2EE) has become the gold standard for securing communications, bringing strong confidentiality and privacy guarantees to billions of users worldwide. However, the current push towards widespread integration of artificial intelligence (AI) models, including in E2EE systems, raises some serious security concerns. This work performs a critical examination of the (in)compatibility of AI models and E2EE applications. We explore this on two fronts: (1) the integration of AI "assistants" within E2EE applications, and (2) the use of E2EE data for training AI models. We analyze the potential security implications of each, and identify conflicts with the security guarantees of E2EE. Then, we analyze legal implications of integrating AI models in E2EE applications, given how AI integration can undermine the confidentiality that E2EE promises. Finally, we offer a list of detailed recommendations based on our technical and legal analyses, including: technical design choices that must be prioritized to uphold E2EE security; how service providers must accurately represent E2EE security; and best practices for the default behavior of AI features and for requesting user consent. We hope this paper catalyzes an informed conversation on the tensions that arise between the brisk deployment of AI and the security offered by E2EE, and guides the responsible development of new AI features.