Using Functional Programming to recognize Named Structure in an Optimization Problem: Application to Pooling

Branch-and-cut optimization solvers typically apply generic algorithms, e.g., cutting planes or primal heuristics, to expedite performance for many mathematical optimization problems. But solver software receives an input optimization problem as vectors of equations and constraints containing no structural information. This article proposes automatically detecting named special structure using the pattern matching features of functional programming. Specifically, we deduce the industrially-relevant nonconvex nonlinear Pooling Problem within a mixed-integer nonlinear optimization problem and show that we can uncover pooling structure in optimization problems which are not pooling problems. Previous work has shown that preprocessing heuristics can find network structures; we show that we can additionally detect nonlinear pooling patterns. Finding named structures allows us to apply, to generic optimization problems, cutting planes or primal heuristics developed for the named structure. To demonstrate the recognition algorithm, we use the recognized structure to apply primal heuristics to a test set of standard pooling problems

Label-efficient Contrastive Learning-based model for nuclei detection and classification in 3D Cardiovascular Immunofluorescent Images

Recently, deep learning-based methods achieved promising performance in nuclei detection and classification applications. However, training deep learning-based methods requires a large amount of pixel-wise annotated data, which is time-consuming and labor-intensive, especially in 3D images. An alternative approach is to adapt weak-annotation methods, such as labeling each nucleus with a point, but this method does not extend from 2D histopathology images (for which it was originally developed) to 3D immunofluorescent images. The reason is that 3D images contain multiple channels (z-axis) for nuclei and different markers separately, which makes training using point annotations difficult. To address this challenge, we propose the Label-efficient Contrastive learning-based (LECL) model to detect and classify various types of nuclei in 3D immunofluorescent images. Previous methods use Maximum Intensity Projection (MIP) to convert immunofluorescent images with multiple slices to 2D images, which can cause signals from different z-stacks to falsely appear associated with each other. To overcome this, we devised an Extended Maximum Intensity Projection (EMIP) approach that addresses issues using MIP. Furthermore, we performed a Supervised Contrastive Learning (SCL) approach for weakly supervised settings. We conducted experiments on cardiovascular datasets and found that our proposed framework is effective and efficient in detecting and classifying various types of nuclei in 3D immunofluorescent images.Comment: 11 pages, 5 figures, MICCAI Workshop Conference 202

GLM-130B: An Open Bilingual Pre-trained Model

We introduce GLM-130B, a bilingual (English and Chinese) pre-trained language model with 130 billion parameters. It is an attempt to open-source a 100B-scale model at least as good as GPT-3 (davinci) and unveil how models of such a scale can be successfully pre-trained. Over the course of this effort, we face numerous unexpected technical and engineering challenges, particularly on loss spikes and divergence. In this paper, we introduce the training process of GLM-130B including its design choices, training strategies for both efficiency and stability, and engineering efforts. The resultant GLM-130B model offers significant outperformance over GPT-3 175B (davinci) on a wide range of popular English benchmarks while the performance advantage is not observed in OPT-175B and BLOOM-176B. It also consistently and significantly outperforms ERNIE TITAN 3.0 260B -- the largest Chinese language model -- across related benchmarks. Finally, we leverage a unique scaling property of GLM-130B to reach INT4 quantization without post training, with almost no performance loss, making it the first among 100B-scale models and more importantly, allowing its effective inference on 4$\times$RTX 3090 (24G) or 8$\times$RTX 2080 Ti (11G) GPUs, the most affordable GPUs required for using 100B-scale models. The GLM-130B model weights are publicly accessible and its code, training logs, related toolkit, and lessons learned are open-sourced at \url{https://github.com/THUDM/GLM-130B/}.Comment: Accepted to ICLR 202

Revisiting Binary Code Similarity Analysis using Interpretable Feature Engineering and Lessons Learned

Binary code similarity analysis (BCSA) is widely used for diverse security applications such as plagiarism detection, software license violation detection, and vulnerability discovery. Despite the surging research interest in BCSA, it is significantly challenging to perform new research in this field for several reasons. First, most existing approaches focus only on the end results, namely, increasing the success rate of BCSA, by adopting uninterpretable machine learning. Moreover, they utilize their own benchmark sharing neither the source code nor the entire dataset. Finally, researchers often use different terminologies or even use the same technique without citing the previous literature properly, which makes it difficult to reproduce or extend previous work. To address these problems, we take a step back from the mainstream and contemplate fundamental research questions for BCSA. Why does a certain technique or a feature show better results than the others? Specifically, we conduct the first systematic study on the basic features used in BCSA by leveraging interpretable feature engineering on a large-scale benchmark. Our study reveals various useful insights on BCSA. For example, we show that a simple interpretable model with a few basic features can achieve a comparable result to that of recent deep learning-based approaches. Furthermore, we show that the way we compile binaries or the correctness of underlying binary analysis tools can significantly affect the performance of BCSA. Lastly, we make all our source code and benchmark public and suggest future directions in this field to help further research.Comment: 22 pages, under revision to Transactions on Software Engineering (July 2021

Positive emotion broadens attention focus through decreased position-specific spatial encoding in early visual cortex: evidence from ERPs

Recent evidence has suggested that not only stimulus-specific attributes or top-down expectations can modulate attention selection processes, but also the actual mood state of the participant. In this study, we tested the prediction that the induction of positive mood can dynamically influence attention allocation and, in turn, modulate early stimulus sensory processing in primary visual cortex (V1). High-density visual event-related potentials (ERPs) were recorded while participants performed a demanding task at fixation and were presented with peripheral irrelevant visual textures, whose position was systematically varied in the upper visual field (close, medium, or far relative to fixation). Either a neutral or a positive mood was reliably induced and maintained throughout the experimental session. The ERP results showed that the earliest retinotopic component following stimulus onset (C1) strongly varied in topography as a function of the position of the peripheral distractor, in agreement with a near-far spatial gradient. However, this effect was altered for participants in a positive relative to a neutral mood. On the contrary, positive mood did not modulate attention allocation for the central (task-relevant) stimuli, as reflected by the P300 component. We ran a control behavioral experiment confirming that positive emotion selectively impaired attention allocation to the peripheral distractors. These results suggest a mood-dependent tuning of position-specific encoding in V1 rapidly following stimulus onset. We discuss these results against the dominant broaden-and-build theory

Overview of BioASQ 2021-MESINESP track. Evaluation of advance hierarchical classification techniques for scientific literature, patents and clinical trials

CLEF 2021 – Conference and Labs of the Evaluation Forum, September 21–24, 2021, Bucharest, Romania,There is a pressing need to exploit recent advances in natural language processing technologies, in particular language models and deep learning approaches, to enable improved retrieval, classification and ultimately access to information contained in multiple, heterogeneous types of documents. This is particularly true for the field of biomedicine and clinical research, where medical experts and scientists need to carry out complex search queries against a variety of document collections, including literature, patents, clinical trials or other kind of content like EHRs. Indexing documents with structured controlled vocabularies used for semantic search engines and query expansion purposes is a critical task for enabling sophisticated user queries and even cross-language retrieval. Due to the complexity of the medical domain and the use of very large hierarchical indexing terminologies, implementing efficient automatic systems to aid manual indexing is extremely difficult. This paper provides a summary of the MESINESP task results on medical semantic indexing in Spanish (BioASQ/ CLEF 2021 Challenge). MESINESP was carried out in direct collaboration with literature content databases and medical indexing experts using the DeCS vocabulary, a similar resource as MeSH terms. Seven participating teams used advanced technologies including extreme multilabel classification and deep language models to solve this challenge which can be viewed as a multi-label classification problem. MESINESP resources, we have released a Gold Standard collection of 243,000 documents with a total of 2179 manual annotations divided in train, development and test subsets covering literature, patents as well as clinical trial summaries, under a cross-genre training and data labeling scenario. Manual indexing of the evaluation subsets was carried out by three independent experts using a specially developed indexing interface called ASIT. Additionally, we have published a collection of large-scale automatic semantic annotations based on NER systems of these documents with mentions of drugs/medications (170,000), symptoms (137,000), diseases (840,000) and clinical procedures (415,000). In addition to a summary of the used technologies by the teams, this paperS