Grounding Language Models for Visual Entity Recognition

We introduce AutoVER, an Autoregressive model for Visual Entity Recognition. Our model extends an autoregressive Multi-modal Large Language Model by employing retrieval augmented constrained generation. It mitigates low performance on out-of-domain entities while excelling in queries that require visually-situated reasoning. Our method learns to distinguish similar entities within a vast label space by contrastively training on hard negative pairs in parallel with a sequence-to-sequence objective without an external retriever. During inference, a list of retrieved candidate answers explicitly guides language generation by removing invalid decoding paths. The proposed method achieves significant improvements across different dataset splits in the recently proposed Oven-Wiki benchmark. Accuracy on the Entity seen split rises from 32.7% to 61.5%. It also demonstrates superior performance on the unseen and query splits by a substantial double-digit margin.

MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning

Large Language Models (LLMs), despite their remarkable progress across various general domains, encounter significant barriers in medicine and healthcare. This field faces unique challenges such as domain-specific terminologies and the reasoning over specialized knowledge. To address these obstinate issues, we propose a novel Multi-disciplinary Collaboration (MC) framework for the medical domain that leverages role-playing LLM-based agents who participate in a collaborative multi-round discussion, thereby enhancing LLM proficiency and reasoning capabilities. This training-free and interpretable framework encompasses five critical steps: gathering domain experts, proposing individual analyses, summarising these analyses into a report, iterating over discussions until a consensus is reached, and ultimately making a decision. Our work particularly focuses on the zero-shot scenario, our results on nine data sets (MedQA, MedMCQA, PubMedQA, and six subtasks from MMLU) establish that our proposed MC framework excels at mining and harnessing the medical expertise in LLMs, as well as extending its reasoning abilities. Based on these outcomes, we further conduct a human evaluation to pinpoint and categorize common errors within our method, as well as ablation studies aimed at understanding the impact of various factors on overall performance. Our code can be found at \url{https://github.com/gersteinlab/MedAgents}.

Coherent Entity Disambiguation via Modeling Topic and Categorical Dependency

Previous entity disambiguation (ED) methods adopt a discriminative paradigm, where prediction is made based on matching scores between mention context and candidate entities using length-limited encoders. However, these methods often struggle to capture explicit discourse-level dependencies, resulting in incoherent predictions at the abstract level (e.g. topic or category). We propose CoherentED, an ED system equipped with novel designs aimed at enhancing the coherence of entity predictions. Our method first introduces an unsupervised variational autoencoder (VAE) to extract latent topic vectors of context sentences. This approach not only allows the encoder to handle longer documents more effectively, conserves valuable input space, but also keeps a topic-level coherence. Additionally, we incorporate an external category memory, enabling the system to retrieve relevant categories for undecided mentions. By employing step-by-step entity decisions, this design facilitates the modeling of entity-entity interactions, thereby maintaining maximum coherence at the category level. We achieve new state-of-the-art results on popular ED benchmarks, with an average improvement of 1.3 F1 points. Our model demonstrates particularly outstanding performance on challenging long-text scenarios.

Instructed Language Models with Retrievers Are Powerful Entity Linkers

Generative approaches powered by large language models (LLMs) have demonstrated emergent abilities in tasks that require complex reasoning abilities. Yet the generative nature still makes the generated content suffer from hallucinations, thus unsuitable for entity-centric tasks like entity linking (EL) requiring precise entity predictions over a large knowledge base. We present Instructed Generative Entity Linker (INSGENEL), the first approach that enables casual language models to perform entity linking over knowledge bases. Several methods to equip language models with EL capability were proposed in this work, including (i) a sequence-to-sequence training EL objective with instruction-tuning, (ii) a novel generative EL framework based on a light-weight potential mention retriever that frees the model from heavy and non-parallelizable decoding, achieving 4$\times$ speedup without compromise on linking metrics. INSGENEL outperforms previous generative alternatives with +6.8 F1 points gain on average, also with a huge advantage in training data efficiency and training compute consumption. In addition, our skillfully engineered in-context learning (ICL) framework for EL still lags behind INSGENEL significantly, reaffirming that the EL task remains a persistent hurdle for general LLMs.

JaxPruner: A concise library for sparsity research

This paper introduces JaxPruner, an open-source JAX-based pruning and sparse training library for machine learning research. JaxPruner aims to accelerate research on sparse neural networks by providing concise implementations of popular pruning and sparse training algorithms with minimal memory and latency overhead. Algorithms implemented in JaxPruner use a common API and work seamlessly with the popular optimization library Optax, which, in turn, enables easy integration with existing JAX based libraries. We demonstrate this ease of integration by providing examples in four different codebases: Scenic, t5x, Dopamine and FedJAX and provide baseline experiments on popular benchmarks.

Shift-BNN: Highly-Efficient Probabilistic Bayesian Neural Network Training via Memory-Friendly Pattern Retrieving

Bayesian Neural Networks (BNNs) that possess a property of uncertainty estimation have been increasingly adopted in a wide range of safety-critical AI applications which demand reliable and robust decision making, e.g., self-driving, rescue robots, medical image diagnosis. The training procedure of a probabilistic BNN model involves training an ensemble of sampled DNN models, which induces orders of magnitude larger volume of data movement than training a single DNN model. In this paper, we reveal that the root cause for BNN training inefficiency originates from the massive off-chip data transfer by Gaussian Random Variables (GRVs). To tackle this challenge, we propose a novel design that eliminates all the off-chip data transfer by GRVs through the reversed shifting of Linear Feedback Shift Registers (LFSRs) without incurring any training accuracy loss. To efficiently support our LFSR reversion strategy at the hardware level, we explore the design space of the current DNN accelerators and identify the optimal computation mapping scheme to best accommodate our strategy. By leveraging this finding, we design and prototype the first highly efficient BNN training accelerator, named Shift-BNN, that is low-cost and scalable. Extensive evaluation on five representative BNN models demonstrates that Shift-BNN achieves an average of 4.9x (up to 10.8x) boost in energy efficiency and 1.6x (up to 2.8x) speedup over the baseline DNN training accelerator.

Randomness In Neural Network Training: Characterizing The Impact of Tooling

The quest for determinism in machine learning has disproportionately focused on characterizing the impact of noise introduced by algorithmic design choices. In this work, we address a less well understood and studied question: how does our choice of tooling introduce randomness to deep neural network training. We conduct large scale experiments across different types of hardware, accelerators, state of art networks, and open-source datasets, to characterize how tooling choices contribute to the level of non-determinism in a system, the impact of said non-determinism, and the cost of eliminating different sources of noise. Our findings are surprising, and suggest that the impact of non-determinism in nuanced. While top-line metrics such as top-1 accuracy are not noticeably impacted, model performance on certain parts of the data distribution is far more sensitive to the introduction of randomness. Our results suggest that deterministic tooling is critical for AI safety. However, we also find that the cost of ensuring determinism varies dramatically between neural network architectures and hardware types, e.g., with overhead up to $746\%$, $241\%$, and $196\%$ on a spectrum of widely used GPU accelerator architectures, relative to non-deterministic training. The source code used in this paper is available at https://github.com/usyd-fsalab/NeuralNetworkRandomness.

A Graph Representation of Semi-structured Data for Web Question Answering

The abundant semi-structured data on the Web, such as HTML-based tables and lists, provide commercial search engines a rich information source for question answering (QA). Different from plain text passages in Web documents, Web tables and lists have inherent structures, which carry semantic correlations among various elements in tables and lists. Many existing studies treat tables and lists as flat documents with pieces of text and do not make good use of semantic information hidden in structures. In this paper, we propose a novel graph representation of Web tables and lists based on a systematic categorization of the components in semi-structured data as well as their relations. We also develop pre-training and reasoning techniques on the graph model for the QA task. Extensive experiments on several real datasets collected from a commercial engine verify the effectiveness of our approach. Our method improves F1 score by 3.90 points over the state-of-the-art baselines.

DeepEnroll: Patient-Trial Matching with Deep Embedding and Entailment Prediction

Clinical trials are essential for drug development but often suffer from expensive, inaccurate and insufficient patient recruitment. The core problem of patient-trial matching is to find qualified patients for a trial, where patient information is stored in electronic health records (EHR) while trial eligibility criteria (EC) are described in text documents available on the web. How to represent longitudinal patient EHR? How to extract complex logical rules from EC? Most existing works rely on manual rule-based extraction, which is time consuming and inflexible for complex inference. To address these challenges, we proposed DeepEnroll, a cross-modal inference learning model to jointly encode enrollment criteria (text) and patients records (tabular data) into a shared latent space for matching inference. DeepEnroll applies a pre-trained Bidirectional Encoder Representations from Transformers(BERT) model to encode clinical trial information into sentence embedding. And uses a hierarchical embedding model to represent patient longitudinal EHR. In addition, DeepEnroll is augmented by a numerical information embedding and entailment module to reason over numerical information in both EC and EHR. These encoders are trained jointly to optimize patient-trial matching score. We evaluated DeepEnroll on the trial-patient matching task with demonstrated on real world datasets. DeepEnroll outperformed the best baseline by up to 12.4% in average F1.