Yair Schiff

Brian Belgodere, Vijil Chenthamarakshan, Payel Das et al. · ibm-research

With the prospect of automating a number of chemical tasks with high fidelity, chemical language processing models are emerging at a rapid speed. Here, we present a cloud-based real-time platform that allows users to virtually screen molecules of interest. For this purpose, molecular embeddings inferred from a recently proposed large chemical language model, named MolFormer, are leveraged. The platform currently supports three tasks: nearest neighbor retrieval, chemical space visualization, and property prediction. Based on the functionalities of this platform and results obtained, we believe that such a platform can play a pivotal role in automating chemistry and chemical engineering research, as well as assist in drug discovery and material design tasks. A demo of our platform is provided at \url{www.ibm.biz/molecular_demo}.

Yingheng Wang, Yair Schiff, Aaron Gokaslan et al.

While diffusion models excel at generating high-quality samples, their latent variables typically lack semantic meaning and are not suitable for representation learning. Here, we propose InfoDiffusion, an algorithm that augments diffusion models with low-dimensional latent variables that capture high-level factors of variation in the data. InfoDiffusion relies on a learning objective regularized with the mutual information between observed and hidden variables, which improves latent space quality and prevents the latents from being ignored by expressive diffusion-based decoders. Empirically, we find that InfoDiffusion learns disentangled and human-interpretable latent representations that are competitive with state-of-the-art generative and contrastive methods, while retaining the high sample quality of diffusion models. Our method enables manipulating the attributes of generated images and has the potential to assist tasks that require exploring a learned latent space to generate quality samples, e.g., generative design.

Richa Rastogi, Yair Schiff, Alon Hacohen et al. · allen-ai

We introduce semi-parametric inducing point networks (SPIN), a general-purpose architecture that can query the training set at inference time in a compute-efficient manner. Semi-parametric architectures are typically more compact than parametric models, but their computational complexity is often quadratic. In contrast, SPIN attains linear complexity via a cross-attention mechanism between datapoints inspired by inducing point methods. Querying large training sets can be particularly useful in meta-learning, as it unlocks additional training signal, but often exceeds the scaling limits of existing models. We use SPIN as the basis of the Inducing Point Neural Process, a probabilistic model which supports large contexts in meta-learning and achieves high accuracy where existing models fail. In our experiments, SPIN reduces memory requirements, improves accuracy across a range of meta-learning tasks, and improves state-of-the-art performance on an important practical problem, genotype imputation.

Brian Belgodere, Pierre Dognin, Adam Ivankay et al. · ibm-research

Real-world data often exhibits bias, imbalance, and privacy risks. Synthetic datasets have emerged to address these issues. This paradigm relies on generative AI models to generate unbiased, privacy-preserving data while maintaining fidelity to the original data. However, assessing the trustworthiness of synthetic datasets and models is a critical challenge. We introduce a holistic auditing framework that comprehensively evaluates synthetic datasets and AI models. It focuses on preventing bias and discrimination, ensures fidelity to the source data, assesses utility, robustness, and privacy preservation. We demonstrate the framework's effectiveness by auditing various generative models across diverse use cases like education, healthcare, banking, and human resources, spanning different data modalities such as tabular, time-series, vision, and natural language. This holistic assessment is essential for compliance with regulatory safeguards. We introduce a trustworthiness index to rank synthetic datasets based on their safeguards trade-offs. Furthermore, we present a trustworthiness-driven model selection and cross-validation process during training, exemplified with "TrustFormers" across various data types. This approach allows for controllable trustworthiness trade-offs in synthetic data creation. Our auditing framework fosters collaboration among stakeholders, including data scientists, governance experts, internal reviewers, external certifiers, and regulators. This transparent reporting should become a standard practice to prevent bias, discrimination, and privacy violations, ensuring compliance with policies and providing accountability, safety, and performance guarantees.

Phillip Si, Zeyi Chen, Subham Sekhar Sahoo et al.

Training normalizing flow generative models can be challenging due to the need to calculate computationally expensive determinants of Jacobians. This paper studies the likelihood-free training of flows and proposes the energy objective, an alternative sample-based loss based on proper scoring rules. The energy objective is determinant-free and supports flexible model architectures that are not easily compatible with maximum likelihood training, including semi-autoregressive energy flows, a novel model family that interpolates between fully autoregressive and non-autoregressive models. Energy flows feature competitive sample quality, posterior inference, and generation speed relative to likelihood-based flows; this performance is decorrelated from the quality of log-likelihood estimates, which are generally very poor. Our findings question the use of maximum likelihood as an objective or a metric, and contribute to a scientific study of its role in generative modeling.

Carles Domingo-Enrich, Yair Schiff, Youssef Mroueh

Learning high-dimensional distributions is often done with explicit likelihood modeling or implicit modeling via minimizing integral probability metrics (IPMs). In this paper, we expand this learning paradigm to stochastic orders, namely, the convex or Choquet order between probability measures. Towards this end, exploiting the relation between convex orders and optimal transport, we introduce the Choquet-Toland distance between probability measures, that can be used as a drop-in replacement for IPMs. We also introduce the Variational Dominance Criterion (VDC) to learn probability measures with dominance constraints, that encode the desired stochastic order between the learned measure and a known baseline. We analyze both quantities and show that they suffer from the curse of dimensionality and propose surrogates via input convex maxout networks (ICMNs), that enjoy parametric rates. We provide a min-max framework for learning with stochastic orders and validate it experimentally on synthetic and high-dimensional image generation, with promising results. Finally, our ICMNs class of convex functions and its derived Rademacher Complexity are of independent interest beyond their application in convex orders.

Yair Schiff, Omer Belhasin, Roy Uziel et al.

Masked diffusion models (MDMs) have emerged as a promising alternative to autoregressive models, enabling parallel token generation while achieving competitive performance. Despite these advantages, MDMs face a fundamental limitation: once tokens are unmasked, they remain fixed, leading to error accumulation and ultimately degrading sample quality. We address this by proposing a framework that trains a model to perform both unmasking and correction. By reusing outputs from the MDM denoising network as inputs for corrector training, we train a model to recover from potential mistakes. During generation we apply additional corrective refinement steps between unmasking ones in order to change decoded tokens and improve outputs. We name our training and sampling method Progressive Self-Correction (ProSeCo) for its unique ability to iteratively refine an entire sequence, including already generated tokens. We conduct extensive experimental validation across multiple conditional and unconditional tasks, demonstrating that ProSeCo yields better quality-efficiency trade-offs (up to ~2-3x faster sampling) and enables inference-time compute scaling to further increase sample quality beyond standard MDMs (up to ~1.3x improvement on benchmarks).

Yair Schiff, Chia-Hsiang Kao, Aaron Gokaslan et al.

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance.

Inkit Padhi, Yair Schiff, Igor Melnyk et al.

Tabular datasets are ubiquitous in data science applications. Given their importance, it seems natural to apply state-of-the-art deep learning algorithms in order to fully unlock their potential. Here we propose neural network models that represent tabular time series that can optionally leverage their hierarchical structure. This results in two architectures for tabular time series: one for learning representations that is analogous to BERT and can be pre-trained end-to-end and used in downstream tasks, and one that is akin to GPT and can be used for generation of realistic synthetic tabular sequences. We demonstrate our models on two datasets: a synthetic credit card transaction dataset, where the learned representations are used for fraud detection and synthetic data generation, and on a real pollution dataset, where the learned encodings are used to predict atmospheric pollutant concentrations. Code and data are available at https://github.com/IBM/TabFormer.

Guanghan Wang, Yair Schiff, Subham Sekhar Sahoo et al.

Part of the success of diffusion models stems from their ability to perform iterative refinement, i.e., repeatedly correcting outputs during generation. However, modern masked discrete diffusion lacks this capability: when a token is generated, it cannot be updated again, even when it introduces an error. Here, we address this limitation by introducing the remasking diffusion model (ReMDM) sampler, a method that can be applied to pretrained masked diffusion models in a principled way and that is derived from a discrete diffusion model with a custom remasking backward process. Most interestingly, ReMDM endows discrete diffusion with a form of inference-time compute scaling. By increasing the number of sampling steps, ReMDM generates natural language outputs that approach the quality of autoregressive models, whereas when the computation budget is limited, ReMDM better maintains quality. ReMDM also improves sample quality of masked diffusion models for discretized images, and in scientific domains such as molecule design, ReMDM facilitates diffusion guidance and pushes the Pareto frontier of controllability relative to classical masking and uniform noise diffusion. We provide the code along with a blog post on the project page: https://remdm.github.io

Yair Schiff, Subham Sekhar Sahoo, Hao Phung et al.

Diffusion models for continuous data gained widespread adoption owing to their high quality generation and control mechanisms. However, controllable diffusion on discrete data faces challenges given that continuous guidance methods do not directly apply to discrete diffusion. Here, we provide a straightforward derivation of classifier-free and classifier-based guidance for discrete diffusion, as well as a new class of diffusion models that leverage uniform noise and that are more guidable because they can continuously edit their outputs. We improve the quality of these models with a novel continuous-time variational lower bound that yields state-of-the-art performance, especially in settings involving guidance or fast generation. Empirically, we demonstrate that our guidance mechanisms combined with uniform noise diffusion improve controllable generation relative to autoregressive and diffusion baselines on several discrete data domains, including genomic sequences, small molecule design, and discretized image generation.

Yair Schiff, Zhong Yi Wan, Jeffrey B. Parker et al.

Learning dynamics from dissipative chaotic systems is notoriously difficult due to their inherent instability, as formalized by their positive Lyapunov exponents, which exponentially amplify errors in the learned dynamics. However, many of these systems exhibit ergodicity and an attractor: a compact and highly complex manifold, to which trajectories converge in finite-time, that supports an invariant measure, i.e., a probability distribution that is invariant under the action of the dynamics, which dictates the long-term statistical behavior of the system. In this work, we leverage this structure to propose a new framework that targets learning the invariant measure as well as the dynamics, in contrast with typical methods that only target the misfit between trajectories, which often leads to divergence as the trajectories' length increases. We use our framework to propose a tractable and sample efficient objective that can be used with any existing learning objectives. Our Dynamics Stable Learning by Invariant Measure (DySLIM) objective enables model training that achieves better point-wise tracking and long-term statistical accuracy relative to other learning objectives. By targeting the distribution with a scalable regularization term, we hope that this approach can be extended to more complex systems exhibiting slowly-variant distributions, such as weather and climate models.

Guanghan Wang, Yair Schiff, Gilad Turok et al.

While diffusion language models (DLMs) have achieved competitive performance in text generation, improving their reasoning ability with reinforcement learning remains an active research area. Here, we introduce d2, a reasoning framework tailored for masked DLMs. Central to our framework is a new policy gradient algorithm that relies on properties of masking to accurately estimate the likelihoods of sampling trajectories. Our estimators trade off computation for approximation accuracy in an analytically tractable manner, and are particularly effective for DLMs that support any-order likelihood estimation. We characterize and study this property in popular DLMs and show that it is key for efficient diffusion-based reasoning. Empirically, d2 significantly improves over previous diffusion reasoning frameworks using only RL (without relying on supervised fine-tuning), and sets a new state-of-the-art performance for DLMs on logical reasoning tasks (Countdown and Sudoku) and math reasoning benchmarks (GSM8K and MATH500).

Marianne Arriola, Yair Schiff, Hao Phung et al.

Discrete diffusion models enable parallel token sampling for faster inference than autoregressive approaches. However, prior diffusion models use a decoder-only architecture, which requires sampling algorithms that invoke the full network at every denoising step and incur high computational cost. Our key insight is that discrete diffusion models perform two types of computation: 1) representing clean tokens and 2) denoising corrupted tokens, which enables us to use separate modules for each task. We propose an encoder-decoder architecture to accelerate discrete diffusion inference, which relies on an encoder to represent clean tokens and a lightweight decoder to iteratively refine a noised sequence. We also show that this architecture enables faster training of block diffusion models, which partition sequences into blocks for better quality and are commonly used in diffusion language model inference. We introduce a framework for Efficient Encoder-Decoder Diffusion (E2D2), consisting of an architecture with specialized training and sampling algorithms, and we show that E2D2 achieves superior trade-offs between generation quality and inference throughput on summarization, translation, and mathematical reasoning tasks. We provide the code, model weights, and blog post on the project page: https://m-arriola.com/e2d2

Subham Sekhar Sahoo, Marianne Arriola, Yair Schiff et al.

While diffusion models excel at generating high-quality images, prior work reports a significant performance gap between diffusion and autoregressive (AR) methods in language modeling. In this work, we show that simple masked discrete diffusion is more performant than previously thought. We apply an effective training recipe that improves the performance of masked diffusion models and derive a simplified, Rao-Blackwellized objective that results in additional improvements. Our objective has a simple form -- it is a mixture of classical masked language modeling losses -- and can be used to train encoder-only language models that admit efficient samplers, including ones that can generate arbitrary lengths of text semi-autoregressively like a traditional language model. On language modeling benchmarks, a range of masked diffusion models trained with modern engineering practices achieves a new state-of-the-art among diffusion models, and approaches AR perplexity. We provide the code, along with a blog post and video tutorial on the project page: https://s-sahoo.com/mdlm

Yair Schiff, Brian Quanz, Payel Das et al.

The field of Deep Learning is rich with empirical evidence of human-like performance on a variety of prediction tasks. However, despite these successes, the recent Predicting Generalization in Deep Learning (PGDL) NeurIPS 2020 competition suggests that there is a need for more robust and efficient measures of network generalization. In this work, we propose a new framework for evaluating the generalization capabilities of trained networks. We use perturbation response (PR) curves that capture the accuracy change of a given network as a function of varying levels of training sample perturbation. From these PR curves, we derive novel statistics that capture generalization capability. Specifically, we introduce two new measures for accurately predicting generalization gaps: the Gi-score and Pal-score, which are inspired by the Gini coefficient and Palma ratio (measures of income inequality), that accurately predict generalization gaps. Using our framework applied to intra and inter-class sample mixup, we attain better predictive scores than the current state-of-the-art measures on a majority of tasks in the PGDL competition. In addition, we show that our framework and the proposed statistics can be used to capture to what extent a trained network is invariant to a given parametric input transformation, such as rotation or translation. Therefore, these generalization gap prediction statistics also provide a useful means for selecting optimal network architectures and hyperparameters that are invariant to a certain perturbation.

Yair Schiff, Vijil Chenthamarakshan, Samuel Hoffman et al.

Deep generative models have emerged as a powerful tool for learning useful molecular representations and designing novel molecules with desired properties, with applications in drug discovery and material design. However, most existing deep generative models are restricted due to lack of spatial information. Here we propose augmentation of deep generative models with topological data analysis (TDA) representations, known as persistence images, for robust encoding of 3D molecular geometry. We show that the TDA augmentation of a character-based Variational Auto-Encoder (VAE) outperforms state-of-the-art generative neural nets in accurately modeling the structural composition of the QM9 benchmark. Generated molecules are valid, novel, and diverse, while exhibiting distinct electronic property distribution, namely higher sample population with small HOMO-LUMO gap. These results demonstrate that TDA features indeed provide crucial geometric signal for learning abstract structures, which is non-trivial for existing generative models operating on string, graph, or 3D point sets to capture.

David Alvarez-Melis, Yair Schiff, Youssef Mroueh

Gradient flows are a powerful tool for optimizing functionals in general metric spaces, including the space of probabilities endowed with the Wasserstein metric. A typical approach to solving this optimization problem relies on its connection to the dynamic formulation of optimal transport and the celebrated Jordan-Kinderlehrer-Otto (JKO) scheme. However, this formulation involves optimization over convex functions, which is challenging, especially in high dimensions. In this work, we propose an approach that relies on the recently introduced input-convex neural networks (ICNN) to parametrize the space of convex functions in order to approximate the JKO scheme, as well as in designing functionals over measures that enjoy convergence guarantees. We derive a computationally efficient implementation of this JKO-ICNN framework and experimentally demonstrate its feasibility and validity in approximating solutions of low-dimensional partial differential equations with known solutions. We also demonstrate its viability in high-dimensional applications through an experiment in controlled generation for molecular discovery.

Yair Schiff, Brian Quanz, Payel Das et al.

The field of Deep Learning is rich with empirical evidence of human-like performance on a variety of regression, classification, and control tasks. However, despite these successes, the field lacks strong theoretical error bounds and consistent measures of network generalization and learned invariances. In this work, we introduce two new measures, the Gi-score and Pal-score, that capture a deep neural network's generalization capabilities. Inspired by the Gini coefficient and Palma ratio, measures of income inequality, our statistics are robust measures of a network's invariance to perturbations that accurately predict generalization gaps, i.e., the difference between accuracy on training and test sets.

Pierre Dognin, Igor Melnyk, Youssef Mroueh et al.

Image captioning has recently demonstrated impressive progress largely owing to the introduction of neural network algorithms trained on curated dataset like MS-COCO. Often work in this field is motivated by the promise of deployment of captioning systems in practical applications. However, the scarcity of data and contexts in many competition datasets renders the utility of systems trained on these datasets limited as an assistive technology in real-world settings, such as helping visually impaired people navigate and accomplish everyday tasks. This gap motivated the introduction of the novel VizWiz dataset, which consists of images taken by the visually impaired and captions that have useful, task-oriented information. In an attempt to help the machine learning computer vision field realize its promise of producing technologies that have positive social impact, the curators of the VizWiz dataset host several competitions, including one for image captioning. This work details the theory and engineering from our winning submission to the 2020 captioning competition. Our work provides a step towards improved assistive image captioning systems.

Pierre Dognin, Igor Melnyk, Youssef Mroueh et al.

Image captioning systems have made substantial progress, largely due to the availability of curated datasets like Microsoft COCO or Vizwiz that have accurate descriptions of their corresponding images. Unfortunately, scarce availability of such cleanly labeled data results in trained algorithms producing captions that can be terse and idiosyncratically specific to details in the image. We propose a new technique, cooperative distillation that combines clean curated datasets with the web-scale automatically extracted captions of the Google Conceptual Captions dataset (GCC), which can have poor descriptions of images, but is abundant in size and therefore provides a rich vocabulary resulting in more expressive captions.

Yair Schiff, Vijil Chenthamarakshan, Karthikeyan Natesan Ramamurthy et al.

Deep generative models are increasingly becoming integral parts of the in silico molecule design pipeline and have dual goals of learning the chemical and structural features that render candidate molecules viable while also being flexible enough to generate novel designs. Specifically, Variational Auto Encoders (VAEs) are generative models in which encoder-decoder network pairs are trained to reconstruct training data distributions in such a way that the latent space of the encoder network is smooth. Therefore, novel candidates can be found by sampling from this latent space. However, the scope of architectures and hyperparameters is vast and choosing the best combination for in silico discovery has important implications for downstream success. Therefore, it is important to develop a principled methodology for distinguishing how well a given generative model is able to learn salient molecular features. In this work, we propose a method for measuring how well the latent space of deep generative models is able to encode structural and chemical features of molecular datasets by correlating latent space metrics with metrics from the field of topological data analysis (TDA). We apply our evaluation methodology to a VAE trained on SMILES strings and show that 3D topology information is consistently encoded throughout the latent space of the model.