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1. Can NLI Provide Proper Indirect Supervision for Low-resource Biomedical Relation Extraction?

   https://doi.org/10.18653/v1/2023.acl-long.138  

   Xu, Jiashu ; Ma, Mingyu Derek ; Chen, Muhao ( January 2023 , Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics)

   Two key obstacles in biomedical relation extraction (RE) are the scarcity of annotations and the prevalence of instances without explicitly pre-defined labels due to low annotation coverage. Existing approaches, which treat biomedical RE as a multi-class classification task, often result in poor generalization in low-resource settings and do not have the ability to make selective prediction on unknown cases but give a guess from seen relations, hindering the applicability of those approaches. We present NBR, which converts biomedical RE as natural language inference formulation through indirect supervision. By converting relations to natural language hypotheses, NBR is capable of exploiting semantic cues to alleviate annotation scarcity. By incorporating a ranking-based loss that implicitly calibrates abstinent instances, NBR learns a clearer decision boundary and is instructed to abstain on uncertain instances. Extensive experiments on three widely-used biomedical RE benchmarks, namely ChemProt, DDI and GAD, verify the effectiveness of NBR in both full-set and low-resource regimes. Our analysis demonstrates that indirect supervision benefits biomedical RE even when a domain gap exists, and combining NLI knowledge with biomedical knowledge leads to the best performance gains. 

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2. New Frontiers of Information Extraction

   https://doi.org/10.18653/v1/2022.naacl-tutorials.3  

   Chen, Muhao ; Huang, Lifu ; Li, Manling ; Zhou, Ben ; Ji, Heng ; Roth, Dan ( January 2022 , Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: Tutorials)

   This tutorial targets researchers and practitioners who are interested in AI and ML technologies for structural information extraction (IE) from unstructured textual sources. Particularly, this tutorial will provide audience with a systematic introduction to recent advances of IE, by answering several important research questions. These questions include (i) how to develop an robust IE system from noisy, insufficient training data, while ensuring the reliability of its prediction? (ii) how to foster the generalizability of IE through enhancing the system’s cross-lingual, cross-domain, cross-task and cross-modal transferability? (iii) how to precisely support extracting structural information with extremely fine-grained, diverse and boundless labels? (iv) how to further improve IE by leveraging indirect supervision from other NLP tasks, such as NLI, QA or summarization, and pre-trained language models? (v) how to acquire knowledge to guide the inference of IE systems? We will discuss several lines of frontier research that tackle those challenges, and will conclude the tutorial by outlining directions for further investigation. 

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3. Subset Selection and Summarization in Sequential Data

   Elhamifar, E. ; De Paolis Kaluza, M. C. ( January 2017 , Neural Information Processing Systems)

   Subset selection, which is the task of finding a small subset of representative items from a large ground set, finds numerous applications in different areas. Sequential data, including time-series and ordered data, contain important structural relation- ships among items, imposed by underlying dynamic models of data, that should play a vital role in the selection of representatives. However, nearly all existing subset selection techniques ignore underlying dynamics of data and treat items independently, leading to incompatible sets of representatives. In this paper, we develop a new framework for sequential subset selection that finds a set of represen- tatives compatible with the dynamic models of data. To do so, we equip items with transition dynamic models and pose the problem as an integer binary optimization over assignments of sequential items to representatives, that leads to high encoding, diversity and transition potentials. Our formulation generalizes the well-known facility location objective to deal with sequential data, incorporating transition dynamics among facilities. As the proposed formulation is non-convex, we derive a max-sum message passing algorithm to solve the problem efficiently. Experiments on synthetic and real data, including instructional video summarization, show that our sequential subset selection framework not only achieves better encoding and diversity than the state of the art, but also successfully incorporates dynamics of data, leading to compatible representatives. 

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4. Issues in the Reproducibility of Deep Learning Results

   https://doi.org/10.1109/SPMB47826.2019.9037840  

   Jean-Paul, S. ; Elseify, T. ; Obeid, I. ; Picone, J. ( December 2019 , IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. ; Selesnik, I. ; Picone, J. (Ed.)

   The Neuronix high-performance computing cluster allows us to conduct extensive machine learning experiments on big data [1]. This heterogeneous cluster uses innovative scheduling technology, Slurm [2], that manages a network of CPUs and graphics processing units (GPUs). The GPU farm consists of a variety of processors ranging from low-end consumer grade devices such as the Nvidia GTX 970 to higher-end devices such as the GeForce RTX 2080. These GPUs are essential to our research since they allow extremely compute-intensive deep learning tasks to be executed on massive data resources such as the TUH EEG Corpus [2]. We use TensorFlow [3] as the core machine learning library for our deep learning systems, and routinely employ multiple GPUs to accelerate the training process. Reproducible results are essential to machine learning research. Reproducibility in this context means the ability to replicate an existing experiment – performance metrics such as error rates should be identical and floating-point calculations should match closely. Three examples of ways we typically expect an experiment to be replicable are: (1) The same job run on the same processor should produce the same results each time it is run. (2) A job run on a CPU and GPU should produce identical results. (3) A job should produce comparable results if the data is presented in a different order. System optimization requires an ability to directly compare error rates for algorithms evaluated under comparable operating conditions. However, it is a difficult task to exactly reproduce the results for large, complex deep learning systems that often require more than a trillion calculations per experiment [5]. This is a fairly well-known issue and one we will explore in this poster. Researchers must be able to replicate results on a specific data set to establish the integrity of an implementation. They can then use that implementation as a baseline for comparison purposes. A lack of reproducibility makes it very difficult to debug algorithms and validate changes to the system. Equally important, since many results in deep learning research are dependent on the order in which the system is exposed to the data, the specific processors used, and even the order in which those processors are accessed, it becomes a challenging problem to compare two algorithms since each system must be individually optimized for a specific data set or processor. This is extremely time-consuming for algorithm research in which a single run often taxes a computing environment to its limits. Well-known techniques such as cross-validation [5,6] can be used to mitigate these effects, but this is also computationally expensive. These issues are further compounded by the fact that most deep learning algorithms are susceptible to the way computational noise propagates through the system. GPUs are particularly notorious for this because, in a clustered environment, it becomes more difficult to control which processors are used at various points in time. Another equally frustrating issue is that upgrades to the deep learning package, such as the transition from TensorFlow v1.9 to v1.13, can also result in large fluctuations in error rates when re-running the same experiment. Since TensorFlow is constantly updating functions to support GPU use, maintaining an historical archive of experimental results that can be used to calibrate algorithm research is quite a challenge. This makes it very difficult to optimize the system or select the best configurations. The overall impact of all of these issues described above is significant as error rates can fluctuate by as much as 25% due to these types of computational issues. Cross-validation is one technique used to mitigate this, but that is expensive since you need to do multiple runs over the data, which further taxes a computing infrastructure already running at max capacity. GPUs are preferred when training a large network since these systems train at least two orders of magnitude faster than CPUs [7]. Large-scale experiments are simply not feasible without using GPUs. However, there is a tradeoff to gain this performance. Since all our GPUs use the NVIDIA CUDA® Deep Neural Network library (cuDNN) [8], a GPU-accelerated library of primitives for deep neural networks, it adds an element of randomness into the experiment. When a GPU is used to train a network in TensorFlow, it automatically searches for a cuDNN implementation. NVIDIA’s cuDNN implementation provides algorithms that increase the performance and help the model train quicker, but they are non-deterministic algorithms [9,10]. Since our networks have many complex layers, there is no easy way to avoid this randomness. Instead of comparing each epoch, we compare the average performance of the experiment because it gives us a hint of how our model is performing per experiment, and if the changes we make are efficient. In this poster, we will discuss a variety of issues related to reproducibility and introduce ways we mitigate these effects. For example, TensorFlow uses a random number generator (RNG) which is not seeded by default. TensorFlow determines the initialization point and how certain functions execute using the RNG. The solution for this is seeding all the necessary components before training the model. This forces TensorFlow to use the same initialization point and sets how certain layers work (e.g., dropout layers). However, seeding all the RNGs will not guarantee a controlled experiment. Other variables can affect the outcome of the experiment such as training using GPUs, allowing multi-threading on CPUs, using certain layers, etc. To mitigate our problems with reproducibility, we first make sure that the data is processed in the same order during training. Therefore, we save the data from the last experiment and to make sure the newer experiment follows the same order. If we allow the data to be shuffled, it can affect the performance due to how the model was exposed to the data. We also specify the float data type to be 32-bit since Python defaults to 64-bit. We try to avoid using 64-bit precision because the numbers produced by a GPU can vary significantly depending on the GPU architecture [11-13]. Controlling precision somewhat reduces differences due to computational noise even though technically it increases the amount of computational noise. We are currently developing more advanced techniques for preserving the efficiency of our training process while also maintaining the ability to reproduce models. In our poster presentation we will demonstrate these issues using some novel visualization tools, present several examples of the extent to which these issues influence research results on electroencephalography (EEG) and digital pathology experiments and introduce new ways to manage such computational issues. 

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5. Improving Zero-shot Relation Classification via Automatically-acquired Entailment Templates

   Rahimi Mahdi and Surdeanu Mihai ( July 2023 , Proceedings of the 8th Workshop on Representation Learning for NLP (RepL4NLP))

   While fully supervised relation classification (RC) models perform well on large-scale datasets, their performance drops drastically in low-resource settings. As generating annotated examples are expensive, recent zero-shot methods have been proposed that reformulate RC into other NLP tasks for which supervision exists such as textual entailment. However, these methods rely on templates that are manually created which is costly and requires domain expertise. In this paper, we present a novel strategy for template generation for relation classification, which is based on adapting Harris’ distributional similarity principle to templates encoded using contextualized representations. Further, we perform empirical evaluation of different strategies for combining the automatically acquired templates with manual templates. The experimental results on TACRED show that our approach not only performs better than the zero-shot RC methods that only use manual templates, but also that it achieves state-of-the-art performance for zero-shot TACRED at 64.3 F1 score. 

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