Yixin Wang

Binxu Li, Tiankai Yan, Yuanting Pan et al.

Multi-Modal Large Language Models (MLLMs), despite being successful, exhibit limited generality and often fall short when compared to specialized models. Recently, LLM-based agents have been developed to address these challenges by selecting appropriate specialized models as tools based on user inputs. However, such advancements have not been extensively explored within the medical domain. To bridge this gap, this paper introduces the first agent explicitly designed for the medical field, named \textbf{M}ulti-modal \textbf{Med}ical \textbf{Agent} (MMedAgent). We curate an instruction-tuning dataset comprising six medical tools solving seven tasks across five modalities, enabling the agent to choose the most suitable tools for a given task. Comprehensive experiments demonstrate that MMedAgent achieves superior performance across a variety of medical tasks compared to state-of-the-art open-source methods and even the closed-source model, GPT-4o. Furthermore, MMedAgent exhibits efficiency in updating and integrating new medical tools. Codes and models are all available.

Cameron Gruich, Varun Madhavan, Yixin Wang et al.

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.

Kevin Christian Wibisono, Yixin Wang

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.

Kevin Christian Wibisono, Yixin Wang

The self-attention mechanism is the backbone of the transformer neural network underlying most large language models. It can capture complex word patterns and long-range dependencies in natural language. This paper introduces exponential family attention (EFA), a probabilistic generative model that extends self-attention to handle high-dimensional sequence, spatial, or spatial-temporal data of mixed data types, including both discrete and continuous observations. The key idea of EFA is to model each observation conditional on all other existing observations, called the context, whose relevance is learned in a data-driven way via an attention-based latent factor model. In particular, unlike static latent embeddings, EFA uses the self-attention mechanism to capture dynamic interactions in the context, where the relevance of each context observations depends on other observations. We establish an identifiability result and provide a generalization guarantee on excess loss for EFA. Across real-world and synthetic data sets -- including U.S. city temperatures, Instacart shopping baskets, and MovieLens ratings -- we find that EFA consistently outperforms existing models in capturing complex latent structures and reconstructing held-out data.

Hunter Nisonoff, Yixin Wang, Jennifer Listgarten

The need for function estimation in label-limited settings is common in the natural sciences. At the same time, prior knowledge of function values is often available in these domains. For example, data-free biophysics-based models can be informative on protein properties, while quantum-based computations can be informative on small molecule properties. How can we coherently leverage such prior knowledge to help improve a neural network model that is quite accurate in some regions of input space -- typically near the training data -- but wildly wrong in other regions? Bayesian neural networks (BNN) enable the user to specify prior information only on the neural network weights, not directly on the function values. Moreover, there is in general no clear mapping between these. Herein, we tackle this problem by developing an approach to augment BNNs with prior information on the function values themselves. Our probabilistic approach yields predictions that rely more heavily on the prior information when the epistemic uncertainty is large, and more heavily on the neural network when the epistemic uncertainty is small.

Matthew Lakier, Dimcho Karakashev, Yixin Wang et al.

Smartphones store a significant amount of personal and private information, and are playing an increasingly important role in people's lives. It is important for authentication techniques to be more resistant against two known attacks called shoulder surfing and smudge attacks. In this work, we propose a new technique called 3D Pattern. Our 3D Pattern technique takes advantage of a new input paradigm called pre-touch, which could soon allow smartphones to sense a user's finger position at some distance from the screen. We implement the technique and evaluate it in a pilot study (n=6) by comparing it to PIN and pattern locks. Our results show that although our prototype takes about 8 seconds to authenticate, it is immune to smudge attacks and promises to be more resistant to shoulder surfing.

Wesley Tansey, Yixin Wang, David M. Blei et al.

Analyzing large-scale, multi-experiment studies requires scientists to test each experimental outcome for statistical significance and then assess the results as a whole. We present Black Box FDR (BB-FDR), an empirical-Bayes method for analyzing multi-experiment studies when many covariates are gathered per experiment. BB-FDR learns a series of black box predictive models to boost power and control the false discovery rate (FDR) at two stages of study analysis. In Stage 1, it uses a deep neural network prior to report which experiments yielded significant outcomes. In Stage 2, a separate black box model of each covariate is used to select features that have significant predictive power across all experiments. In benchmarks, BB-FDR outperforms competing state-of-the-art methods in both stages of analysis. We apply BB-FDR to two real studies on cancer drug efficacy. For both studies, BB-FDR increases the proportion of significant outcomes discovered and selects variables that reveal key genomic drivers of drug sensitivity and resistance in cancer.