The field of deep generative modeling has grown rapidly and consistently over the years. With the availability of massive amounts of training data coupled with advances in scalable unsupervised learning paradigms, recent large-scale generative models show tremendous promise in synthesizing high-resolution images and text, as well as structured data such as videos and molecules. However, we argue that current large-scale generative AI models do not sufficiently address several fundamental issues that hinder their widespread adoption across domains. In this work, we aim to identify key unresolved challenges in modern generative AI paradigms that should be tackled to further enhance their capabilities, versatility, and reliability. By identifying these challenges, we aim to provide researchers with valuable insights for exploring fruitful research directions, thereby fostering the development of more robust and accessible generative AI solutions.
Causal representation learning has emerged as the center of action in causal machine learning research. In particular, multi-domain datasets present a natural opportunity for showcasing the advantages of causal representation learning over standard unsupervised representation learning. While recent works have taken crucial steps towards learning causal representations, they often lack applicability to multi-domain datasets due to over-simplifying assumptions about the data; e.g. each domain comes from a different single-node perfect intervention. In this work, we relax these assumptions and capitalize on the following observation: there often exists a subset of latents whose certain distributional properties (e.g., support, variance) remain stable across domains; this property holds when, for example, each domain comes from a multi-node imperfect intervention. Leveraging this observation, we show that autoencoders that incorporate such invariances can provably identify the stable set of latents from the rest across different settings.
Publicly available data sets of structural MRIs might not contain specific measurements of brain Regions of Interests (ROIs) that are important for training machine learning models. For example, the curvature scores computed by Freesurfer are not released by the Adolescent Brain Cognitive Development (ABCD) Study. One can address this issue by simply reapplying Freesurfer to the data set. However, this approach is generally computationally and labor intensive (e.g., requiring quality control). An alternative is to impute the missing measurements via a deep learning approach. However, the state-of-the-art is designed to estimate randomly missing values rather than entire measurements. We therefore propose to re-frame the imputation problem as a prediction task on another (public) data set that contains the missing measurements and shares some ROI measurements with the data sets of interest. A deep learning model is then trained to predict the missing measurements from the shared ones and afterwards is applied to the other data sets. Our proposed algorithm models the dependencies between ROI measurements via a graph neural network (GNN) and accounts for demographic differences in brain measurements (e.g. sex) by feeding the graph encoding into a parallel architecture. The architecture simultaneously optimizes a graph decoder to impute values and a classifier in predicting demographic factors. We test the approach, called Demographic Aware Graph-based Imputation (DAGI), on imputing those missing Freesurfer measurements of ABCD (N=3760) by training the predictor on those publicly released by the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA, N=540)...
Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyperparameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods, but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.
Knowledge Graph (KG) plays a crucial role in Medical Report Generation (MRG) because it reveals the relations among diseases and thus can be utilized to guide the generation process. However, constructing a comprehensive KG is labor-intensive and its applications on the MRG process are under-explored. In this study, we establish a complete KG on chest X-ray imaging that includes 137 types of diseases and abnormalities. Based on this KG, we find that the current MRG data sets exhibit a long-tailed problem in disease distribution. To mitigate this problem, we introduce a novel augmentation strategy that enhances the representation of disease types in the tail-end of the distribution. We further design a two-stage MRG approach, where a classifier is first trained to detect whether the input images exhibit any abnormalities. The classified images are then independently fed into two transformer-based generators, namely, ``disease-specific generator" and ``disease-free generator" to generate the corresponding reports. To enhance the clinical evaluation of whether the generated reports correctly describe the diseases appearing in the input image, we propose diverse sensitivity (DS), a new metric that checks whether generated diseases match ground truth and measures the diversity of all generated diseases. Results show that the proposed two-stage generation framework and augmentation strategies improve DS by a considerable margin, indicating a notable reduction in the long-tailed problem associated with under-represented diseases.
Bidirectional attention $\unicode{x2013}$ composed of self-attention with positional encodings and the masked language model (MLM) objective $\unicode{x2013}$ has emerged as a key component of modern large language models (LLMs). Despite its empirical success, few studies have examined its statistical underpinnings: What statistical model is bidirectional attention implicitly fitting? What sets it apart from its non-attention predecessors? We explore these questions in this paper. The key observation is that fitting a single-layer single-head bidirectional attention, upon reparameterization, is equivalent to fitting a continuous bag of words (CBOW) model with mixture-of-experts (MoE) weights. Further, bidirectional attention with multiple heads and multiple layers is equivalent to stacked MoEs and a mixture of MoEs, respectively. This statistical viewpoint reveals the distinct use of MoE in bidirectional attention, which aligns with its practical effectiveness in handling heterogeneous data. It also suggests an immediate extension to categorical tabular data, if we view each word location in a sentence as a tabular feature. Across empirical studies, we find that this extension outperforms existing tabular extensions of transformers in out-of-distribution (OOD) generalization. Finally, this statistical perspective of bidirectional attention enables us to theoretically characterize when linear word analogies are present in its word embeddings. These analyses show that bidirectional attention can require much stronger assumptions to exhibit linear word analogies than its non-attention predecessors.
Identifiability of latent variable models has recently gained interest in terms of its applications to interpretability or out of distribution generalisation. In this work, we study identifiability of Markov Switching Models as a first step towards extending recent results to sequential latent variable models. We present identifiability conditions within first-order Markov dependency structures, and parametrise the transition distribution via non-linear Gaussians. Our experiments showcase the applicability of our approach for regime-dependent causal discovery and high-dimensional time series segmentation.
The impacts of link recommendations on social networks are challenging to evaluate, and so far they have been studied in limited settings. Observational studies are restricted in the kinds of causal questions they can answer and naive A/B tests often lead to biased evaluations due to unaccounted network interference. Furthermore, evaluations in simulation settings are often limited to static network models that do not take into account the potential feedback loops between link recommendation and organic network evolution. To this end, we study the impacts of recommendations on social networks in dynamic settings. Adopting a simulation-based approach, we consider an explicit dynamic formation model -- an extension of the celebrated Jackson-Rogers model -- and investigate how link recommendations affect network evolution over time. Empirically, we find that link recommendations have surprising delayed and indirect effects on the structural properties of networks. Specifically, we find that link recommendations can exhibit considerably different impacts in the immediate term and in the long term. For instance, we observe that friend-of-friend recommendations can have an immediate effect in decreasing degree inequality, but in the long term, they can make the degree distribution substantially more unequal. Moreover, we show that the effects of recommendations can persist in networks, in part due to their indirect impacts on natural dynamics even after recommendations are turned off. We show that, in counterfactual simulations, removing the indirect effects of link recommendations can make the network trend faster toward what it would have been under natural growth dynamics.
It is critical that machine learning (ML) model predictions be trustworthy for high-throughput catalyst discovery approaches. Uncertainty quantification (UQ) methods allow estimation of the trustworthiness of an ML model, but these methods have not been well explored in the field of heterogeneous catalysis. Herein, we investigate different UQ methods applied to a crystal graph convolutional neural network (CGCNN) to predict adsorption energies of molecules on alloys from the Open Catalyst 2020 (OC20) dataset, the largest existing heterogeneous catalyst dataset. We apply three UQ methods to the adsorption energy predictions, namely k-fold ensembling, Monte Carlo dropout, and evidential regression. The effectiveness of each UQ method is assessed based on accuracy, sharpness, dispersion, calibration, and tightness. Evidential regression is demonstrated to be a powerful approach for rapidly obtaining tunable, competitively trustworthy UQ estimates for heterogeneous catalysis applications when using neural networks. Recalibration of model uncertainties is shown to be essential in practical screening applications of catalysts using uncertainties.