Subhashini Venugopalan

Haoyu Guo, Maria Tikhanovskaya, Paul Raccuglia et al.

Large Language Models (LLMs) show great promise as a powerful tool for scientific literature exploration. However, their effectiveness in providing scientifically accurate and comprehensive answers to complex questions within specialized domains remains an active area of research. Using the field of high-temperature cuprates as an exemplar, we evaluate the ability of LLM systems to understand the literature at the level of an expert. We construct an expert-curated database of 1,726 scientific papers that covers the history of the field, and a set of 67 expert-formulated questions that probe deep understanding of the literature. We then evaluate six different LLM-based systems for answering these questions, including both commercially available closed models and a custom retrieval-augmented generation (RAG) system capable of retrieving images alongside text. Experts then evaluate the answers of these systems against a rubric that assesses balanced perspectives, factual comprehensiveness, succinctness, and evidentiary support. Among the six systems two using RAG on curated literature outperformed existing closed models across key metrics, particularly in providing comprehensive and well-supported answers. We discuss promising aspects of LLM performances as well as critical short-comings of all the models. The set of expert-formulated questions and the rubric will be valuable for assessing expert level performance of LLM based reasoning systems.

Nayantara Mudur, Hao Cui, Subhashini Venugopalan et al.

Building precise simulations of the real world and invoking numerical solvers to answer quantitative problems is an essential requirement in engineering and science. We present FEABench, a benchmark to evaluate the ability of large language models (LLMs) and LLM agents to simulate and solve physics, mathematics and engineering problems using finite element analysis (FEA). We introduce a comprehensive evaluation scheme to investigate the ability of LLMs to solve these problems end-to-end by reasoning over natural language problem descriptions and operating COMSOL Multiphysics$^\circledR$, an FEA software, to compute the answers. We additionally design a language model agent equipped with the ability to interact with the software through its Application Programming Interface (API), examine its outputs and use tools to improve its solutions over multiple iterations. Our best performing strategy generates executable API calls 88% of the time. LLMs that can successfully interact with and operate FEA software to solve problems such as those in our benchmark would push the frontiers of automation in engineering. Acquiring this capability would augment LLMs' reasoning skills with the precision of numerical solvers and advance the development of autonomous systems that can tackle complex problems in the real world. The code is available at https://github.com/google/feabench

Mina Lee, Katy Ilonka Gero, John Joon Young Chung et al. · allen-ai, deepmind

In our era of rapid technological advancement, the research landscape for writing assistants has become increasingly fragmented across various research communities. We seek to address this challenge by proposing a design space as a structured way to examine and explore the multidimensional space of intelligent and interactive writing assistants. Through a large community collaboration, we explore five aspects of writing assistants: task, user, technology, interaction, and ecosystem. Within each aspect, we define dimensions (i.e., fundamental components of an aspect) and codes (i.e., potential options for each dimension) by systematically reviewing 115 papers. Our design space aims to offer researchers and designers a practical tool to navigate, comprehend, and compare the various possibilities of writing assistants, and aid in the envisioning and design of new writing assistants.

Subham Sekhar Sahoo, Subhashini Venugopalan, Li Li et al.

Symbolic techniques based on Satisfiability Modulo Theory (SMT) solvers have been proposed for analyzing and verifying neural network properties, but their usage has been fairly limited owing to their poor scalability with larger networks. In this work, we propose a technique for combining gradient-based methods with symbolic techniques to scale such analyses and demonstrate its application for model explanation. In particular, we apply this technique to identify minimal regions in an input that are most relevant for a neural network's prediction. Our approach uses gradient information (based on Integrated Gradients) to focus on a subset of neurons in the first layer, which allows our technique to scale to large networks. The corresponding SMT constraints encode the minimal input mask discovery problem such that after masking the input, the activations of the selected neurons are still above a threshold. After solving for the minimal masks, our approach scores the mask regions to generate a relative ordering of the features within the mask. This produces a saliency map which explains "where a model is looking" when making a prediction. We evaluate our technique on three datasets - MNIST, ImageNet, and Beer Reviews, and demonstrate both quantitatively and qualitatively that the regions generated by our approach are sparser and achieve higher saliency scores compared to the gradient-based methods alone. Code and examples are at - https://github.com/google-research/google-research/tree/master/smug_saliency

Haining Pan, Nayantara Mudur, Will Taranto et al.

Large language models (LLMs) have demonstrated an unprecedented ability to perform complex tasks in multiple domains, including mathematical and scientific reasoning. We demonstrate that with carefully designed prompts, LLMs can accurately carry out key calculations in research papers in theoretical physics. We focus on a broadly used approximation method in quantum physics: the Hartree-Fock method, requiring an analytic multi-step calculation deriving approximate Hamiltonian and corresponding self-consistency equations. To carry out the calculations using LLMs, we design multi-step prompt templates that break down the analytic calculation into standardized steps with placeholders for problem-specific information. We evaluate GPT-4's performance in executing the calculation for 15 research papers from the past decade, demonstrating that, with correction of intermediate steps, it can correctly derive the final Hartree-Fock Hamiltonian in 13 cases and makes minor errors in 2 cases. Aggregating across all research papers, we find an average score of 87.5 (out of 100) on the execution of individual calculation steps. Overall, the requisite skill for doing these calculations is at the graduate level in quantum condensed matter theory. We further use LLMs to mitigate the two primary bottlenecks in this evaluation process: (i) extracting information from papers to fill in templates and (ii) automatic scoring of the calculation steps, demonstrating good results in both cases. The strong performance is the first step for developing algorithms that automatically explore theoretical hypotheses at an unprecedented scale.

Katrin Tomanek, Shanqing Cai, Subhashini Venugopalan

Abbreviation expansion is a strategy used to speed up communication by limiting the amount of typing and using a language model to suggest expansions. Here we look at personalizing a Large Language Model's (LLM) suggestions based on prior conversations to enhance the relevance of predictions, particularly when the user data is small (~1000 samples). Specifically, we compare fine-tuning, prompt-tuning, and retrieval augmented generation of expanded text suggestions for abbreviated inputs. Our case study with a deployed 8B parameter LLM on a real user living with ALS, and experiments on movie character personalization indicates that (1) customization may be necessary in some scenarios and prompt-tuning generalizes well to those, (2) fine-tuning on in-domain data (with as few as 600 samples) still shows some gains, however (3) retrieval augmented few-shot selection also outperforms fine-tuning. (4) Parameter efficient tuning allows for efficient and scalable personalization. For prompt-tuning, we also find that initializing the learned "soft-prompts" to user relevant concept tokens leads to higher accuracy than random initialization.

Katy Blumer, Subhashini Venugopalan, Michael P. Brenner et al.

We analyze a dataset of retinal images using linear probes: linear regression models trained on some "target" task, using embeddings from a deep convolutional (CNN) model trained on some "source" task as input. We use this method across all possible pairings of 93 tasks in the UK Biobank dataset of retinal images, leading to ~164k different models. We analyze the performance of these linear probes by source and target task and by layer depth. We observe that representations from the middle layers of the network are more generalizable. We find that some target tasks are easily predicted irrespective of the source task, and that some other target tasks are more accurately predicted from correlated source tasks than from embeddings trained on the same task.

Andrei Kapishnikov, Subhashini Venugopalan, Besim Avci et al.

Integrated Gradients (IG) is a commonly used feature attribution method for deep neural networks. While IG has many desirable properties, the method often produces spurious/noisy pixel attributions in regions that are not related to the predicted class when applied to visual models. While this has been previously noted, most existing solutions are aimed at addressing the symptoms by explicitly reducing the noise in the resulting attributions. In this work, we show that one of the causes of the problem is the accumulation of noise along the IG path. To minimize the effect of this source of noise, we propose adapting the attribution path itself -- conditioning the path not just on the image but also on the model being explained. We introduce Adaptive Path Methods (APMs) as a generalization of path methods, and Guided IG as a specific instance of an APM. Empirically, Guided IG creates saliency maps better aligned with the model's prediction and the input image that is being explained. We show through qualitative and quantitative experiments that Guided IG outperforms other, related methods in nearly every experiment.

Shawn Xu, Subhashini Venugopalan, Mukund Sundararajan

We study the attribution problem [28] for deep networks applied to perception tasks. For vision tasks, attribution techniques attribute the prediction of a network to the pixels of the input image. We propose a new technique called \emph{Blur Integrated Gradients}. This technique has several advantages over other methods. First, it can tell at what scale a network recognizes an object. It produces scores in the scale/frequency dimension, that we find captures interesting phenomena. Second, it satisfies the scale-space axioms [14], which imply that it employs perturbations that are free of artifact. We therefore produce explanations that are cleaner and consistent with the operation of deep networks. Third, it eliminates the need for a 'baseline' parameter for Integrated Gradients [31] for perception tasks. This is desirable because the choice of baseline has a significant effect on the explanations. We compare the proposed technique against previous techniques and demonstrate application on three tasks: ImageNet object recognition, Diabetic Retinopathy prediction, and AudioSet audio event identification.

Subhashini Venugopalan, Arunachalam Narayanaswamy, Samuel Yang et al.

Confounding variables are a well known source of nuisance in biomedical studies. They present an even greater challenge when we combine them with black-box machine learning techniques that operate on raw data. This work presents two case studies. In one, we discovered biases arising from systematic errors in the data generation process. In the other, we found a spurious source of signal unrelated to the prediction task at hand. In both cases, our prediction models performed well but under careful examination hidden confounders and biases were revealed. These are cautionary tales on the limits of using machine learning techniques on raw data from scientific experiments.

Akinori Mitani, Yun Liu, Abigail Huang et al.

Despite its high prevalence, anemia is often undetected due to the invasiveness and cost of screening and diagnostic tests. Though some non-invasive approaches have been developed, they are less accurate than invasive methods, resulting in an unmet need for more accurate non-invasive methods. Here, we show that deep learning-based algorithms can detect anemia and quantify several related blood measurements using retinal fundus images both in isolation and in combination with basic metadata such as patient demographics. On a validation dataset of 11,388 patients from the UK Biobank, our algorithms achieved a mean absolute error of 0.63 g/dL (95% confidence interval (CI) 0.62-0.64) in quantifying hemoglobin concentration and an area under receiver operating characteristic curve (AUC) of 0.88 (95% CI 0.86-0.89) in detecting anemia. This work shows the potential of automated non-invasive anemia screening based on fundus images, particularly in diabetic patients, who may have regular retinal imaging and are at increased risk of further morbidity and mortality from anemia.

Yun Liu, Krishna Gadepalli, Mohammad Norouzi et al.

Each year, the treatment decisions for more than 230,000 breast cancer patients in the U.S. hinge on whether the cancer has metastasized away from the breast. Metastasis detection is currently performed by pathologists reviewing large expanses of biological tissues. This process is labor intensive and error-prone. We present a framework to automatically detect and localize tumors as small as 100 x 100 pixels in gigapixel microscopy images sized 100,000 x 100,000 pixels. Our method leverages a convolutional neural network (CNN) architecture and obtains state-of-the-art results on the Camelyon16 dataset in the challenging lesion-level tumor detection task. At 8 false positives per image, we detect 92.4% of the tumors, relative to 82.7% by the previous best automated approach. For comparison, a human pathologist attempting exhaustive search achieved 73.2% sensitivity. We achieve image-level AUC scores above 97% on both the Camelyon16 test set and an independent set of 110 slides. In addition, we discover that two slides in the Camelyon16 training set were erroneously labeled normal. Our approach could considerably reduce false negative rates in metastasis detection.

Ronghang Hu, Marcus Rohrbach, Subhashini Venugopalan et al.

Image segmentation from referring expressions is a joint vision and language modeling task, where the input is an image and a textual expression describing a particular region in the image; and the goal is to localize and segment the specific image region based on the given expression. One major difficulty to train such language-based image segmentation systems is the lack of datasets with joint vision and text annotations. Although existing vision datasets such as MS COCO provide image captions, there are few datasets with region-level textual annotations for images, and these are often smaller in scale. In this paper, we explore how existing large scale vision-only and text-only datasets can be utilized to train models for image segmentation from referring expressions. We propose a method to address this problem, and show in experiments that our method can help this joint vision and language modeling task with vision-only and text-only data and outperforms previous results.

Subhashini Venugopalan, Lisa Anne Hendricks, Marcus Rohrbach et al.

Recent captioning models are limited in their ability to scale and describe concepts unseen in paired image-text corpora. We propose the Novel Object Captioner (NOC), a deep visual semantic captioning model that can describe a large number of object categories not present in existing image-caption datasets. Our model takes advantage of external sources -- labeled images from object recognition datasets, and semantic knowledge extracted from unannotated text. We propose minimizing a joint objective which can learn from these diverse data sources and leverage distributional semantic embeddings, enabling the model to generalize and describe novel objects outside of image-caption datasets. We demonstrate that our model exploits semantic information to generate captions for hundreds of object categories in the ImageNet object recognition dataset that are not observed in MSCOCO image-caption training data, as well as many categories that are observed very rarely. Both automatic evaluations and human judgements show that our model considerably outperforms prior work in being able to describe many more categories of objects.

Lisa Anne Hendricks, Subhashini Venugopalan, Marcus Rohrbach et al.

While recent deep neural network models have achieved promising results on the image captioning task, they rely largely on the availability of corpora with paired image and sentence captions to describe objects in context. In this work, we propose the Deep Compositional Captioner (DCC) to address the task of generating descriptions of novel objects which are not present in paired image-sentence datasets. Our method achieves this by leveraging large object recognition datasets and external text corpora and by transferring knowledge between semantically similar concepts. Current deep caption models can only describe objects contained in paired image-sentence corpora, despite the fact that they are pre-trained with large object recognition datasets, namely ImageNet. In contrast, our model can compose sentences that describe novel objects and their interactions with other objects. We demonstrate our model's ability to describe novel concepts by empirically evaluating its performance on MSCOCO and show qualitative results on ImageNet images of objects for which no paired image-caption data exist. Further, we extend our approach to generate descriptions of objects in video clips. Our results show that DCC has distinct advantages over existing image and video captioning approaches for generating descriptions of new objects in context.

Huijuan Xu, Subhashini Venugopalan, Vasili Ramanishka et al.

Generating natural language descriptions for in-the-wild videos is a challenging task. Most state-of-the-art methods for solving this problem borrow existing deep convolutional neural network (CNN) architectures (AlexNet, GoogLeNet) to extract a visual representation of the input video. However, these deep CNN architectures are designed for single-label centered-positioned object classification. While they generate strong semantic features, they have no inherent structure allowing them to detect multiple objects of different sizes and locations in the frame. Our paper tries to solve this problem by integrating the base CNN into several fully convolutional neural networks (FCNs) to form a multi-scale network that handles multiple receptive field sizes in the original image. FCNs, previously applied to image segmentation, can generate class heat-maps efficiently compared to sliding window mechanisms, and can easily handle multiple scales. To further handle the ambiguity over multiple objects and locations, we incorporate the Multiple Instance Learning mechanism (MIL) to consider objects in different positions and at different scales simultaneously. We integrate our multi-scale multi-instance architecture with a sequence-to-sequence recurrent neural network to generate sentence descriptions based on the visual representation. Ours is the first end-to-end trainable architecture that is capable of multi-scale region processing. Evaluation on a Youtube video dataset shows the advantage of our approach compared to the original single-scale whole frame CNN model. Our flexible and efficient architecture can potentially be extended to support other video processing tasks.

Subhashini Venugopalan, Marcus Rohrbach, Jeff Donahue et al.

Real-world videos often have complex dynamics; and methods for generating open-domain video descriptions should be sensitive to temporal structure and allow both input (sequence of frames) and output (sequence of words) of variable length. To approach this problem, we propose a novel end-to-end sequence-to-sequence model to generate captions for videos. For this we exploit recurrent neural networks, specifically LSTMs, which have demonstrated state-of-the-art performance in image caption generation. Our LSTM model is trained on video-sentence pairs and learns to associate a sequence of video frames to a sequence of words in order to generate a description of the event in the video clip. Our model naturally is able to learn the temporal structure of the sequence of frames as well as the sequence model of the generated sentences, i.e. a language model. We evaluate several variants of our model that exploit different visual features on a standard set of YouTube videos and two movie description datasets (M-VAD and MPII-MD).