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PubMedDate not supplied

Using lexical disambiguation and named-entity recognition to improve spelling correction in the electronic patient record.

In this article, we show how a set of natural language processing (NLP) tools can be combined to improve the processing of clinical records. The study concentrates on improving spelling correction, which is of major importance for quality control in the electronic patient record (EPR). As first task, we report on the design of an improved interactive tool for correcting spelling errors. Unlike traditional systems, the linguistic context (both semantic and syntactic) is used to improve the correction strategy. The system is organized along three modules. Module 1 is based on a classical spelling checker, it means that it is context-independent and simply measures a string-edit-distance between a misspelled word and a list of well-formed words. Module 2 attempts to rank more relevantly the set of candidates provided by the first module using morpho-syntactic disambiguation tools. Module 3 processes words with the same part-of-speech (POS) and apply word-sense (WS) disambiguation in order to rerank the set of candidates. As second task, we show how this improved interactive spell checker can be cast as a fully automatic system by adjunction of another NLP module: a named-entity (NE) extractor, i.e. a tool able to identify words as such patient and physician names. This module is used to avoid replacement of named-entities when the system is not used in an interactive mode. Results confirm that using the linguistic context can improve interactive spelling correction, and justify the use of named-entity recognizer to conduct fully automatic spelling correction. It is concluded that NLP is mature enough to help information processing in EPR.

Artificial Intelligence↗
PubMed1997

The Colorectal Cancer Recurrence Support (CARES) System.

Colorectal cancer has risen in incidence to become the second commonest form of cancer in Singapore. The primary treatment is surgery but up to 50% of patients still suffer from recurrence of the cancer after surgery. Early identification of recurrence will increase the effectiveness of therapy and the survival of patients. This paper describes the CARES (Cancer Recurrence Support) System, whose objective is to predict the recurrence of colorectal cancer, using Case-based Reasoning (CBR), and supported by other techniques such as data mining and natural language processing. The CARES System employs CBR to compare and contrast between the new and past colorectal cancer patient cases, and makes inferences based on those comparisons to determine the high risk patient groups. The features and functionality of the system are described.

Artificial Intelligence↗
PubMed1998

Dependency parsing for medical language and concept representation.

The theory of conceptual structures serves as a common basis for natural language processing and medical concept representation. We present a PROLOG-based formalization of dependency grammar that can accommodate conceptual structures in its dependency rules. First results indicate that this formalization provides an operational basis for the implementation of medical language parsers and for the design of medical concept representation languages.

Artificial Intelligence↗
PubMed2002

Breakfast in the Pacific.

The Sixth Natural Language Processing Pacific Rim Symposium was held on 27--30 November 2001, at the National Center of Science, Tokyo, Japan.

Journal Article↗
PubMed2003

Context-based ontology building support in clinical domains using formal concept analysis.

OBJECTIVE: Ontology in clinical domains is becoming a core research field in the realm of medical informatics. The objective of this study is to explore the potential role of formal concept analysis (FCA) in a context-based ontology building support in a clinical domain (e.g. cardiovascular medicine here). METHODOLOGY: We developed an ontology building support system that integrated an FCA module with a natural language processing (NLP) module. The user interface of the system was developed as a Protégé-2000 JAVA tab plug-in. A collection of 368 textual discharge summaries and a standard dictionary of Japanese diagnostic terms (MEDIS ver2.0) were used as the main knowledge sources. A preliminary evaluation was taken to show the usefulness of the system. RESULTS: Stability was shown on the MEDIS-based medical concept extraction with high precision. 73+/-14% (mean+/-S.D.) of the compound medical phrases extracted were sufficiently meaningful to form a medical concept from a clinical perspective. Also, 57.7% of attribute implication pairs (i.e. medical concept pairs) extracted were identified as positive from a clinical perspective. CONCLUSION: Under the framework of our ontology building support system using FCA, the clinical experts could reach a mass of both linguistic information and context-based knowledge that was demonstrated as useful to support their ontology building tasks.

Decision Support Systems, Clinical↗
PubMedDate not supplied

Automatically identifying gene/protein terms in MEDLINE abstracts.

MOTIVATION: Natural language processing (NLP) techniques are used to extract information automatically from computer-readable literature. In biology, the identification of terms corresponding to biological substances (e.g., genes and proteins) is a necessary step that precedes the application of other NLP systems that extract biological information (e.g., protein-protein interactions, gene regulation events, and biochemical pathways). We have developed GPmarkup (for "gene/protein-full name mark up"), a software system that automatically identifies gene/protein terms (i.e., symbols or full names) in MEDLINE abstracts. As a part of marking up process, we also generated automatically a knowledge source of paired gene/protein symbols and full names (e.g., LARD for lymphocyte associated receptor of death) from MEDLINE. We found that many of the pairs in our knowledge source do not appear in the current GenBank database. Therefore our methods may also be used for automatic lexicon generation. RESULTS: GPmarkup has 73% recall and 93% precision in identifying and marking up gene/protein terms in MEDLINE abstracts. AVAILABILITY: A random sample of gene/protein symbols and full names and a sample set of marked up abstracts can be viewed at http://www.cpmc.columbia.edu/homepages/yuh9001/GPmarkup/. Contact. hy52@columbia.edu. Voice: 212-939-7028; fax: 212-666-0140.

Abstracting and Indexing↗
PubMed1990

Suffix interference in the recall of linguistically coherent speech.

Four experiments are presented that address the stimulus suffix effect for linguistically coherent spoken materials. In Experiment 1, definitions of low-frequency words were presented for online written recall. Each definition was followed by a nonword speech suffix presented in the same voice as the definition, the same nonword presented in a different voice, or a tone. The results yielded a significant reduction in the recall of the terminal words of the definitions in the speech suffix conditions compared with the tone control. This general pattern was replicated in Experiment 2, in which subjects did not begin their recall until the suffix item or tone was presented, although the magnitude of the suffix effect was reduced in this experiment. In Experiment 3, sentences that were part of a cohesive story were presented for on-line recall. Here, the suffix effect was considerably reduced compared with the suffix effect found with the definitions presented in Experiments 1 and 2. This pattern was replicated in Experiment 4, in which subjects did not begin their recall of the story sentences until the speech suffix or tone was presented. Overall, the results suggest that auditory memory interference can take place for linguistically coherent speech, although the magnitude of the interference decreases as one increases the level of linguistic structure in the to-be-recalled materials. Implications of the present results for current models of natural language processing are discussed.

Adult↗
PubMed2026

Predicting genome-wide functional constraints with GPN-Star.

Genomic language models have emerged as a powerful approach for learning genome-wide functional constraints directly from DNA sequences1. However, standard genomic language models adapted from natural language processing often require large model sizes and computational resources, yet still fall short of classical evolutionary models in predictive tasks2-4. Here we introduce a genomic pretrained network with species tree and alignment representations (GPN-Star), which is a biologically grounded genomic language model featuring a phylogeny-aware architecture that leverages whole-genome alignments and species trees to model evolutionary relationships explicitly. Trained on alignments spanning vertebrate, mammal and primate evolutionary timescales, GPN-Star achieves state-of-the-art performance across a wide range of variant effect prediction tasks in both coding and non-coding regions of the human genome. Analyses across timescales show task-dependent advantages of modelling more recent versus deeper evolution. To demonstrate its potential to advance human genetics, we show that GPN-Star substantially outperforms previous methods in prioritizing pathogenic and fine-mapped genome-wide association study variants, yields strong enrichments of complex trait heritability and improves power in rare variant association testing5. Extending beyond humans, we train GPN-Star for five model organisms-Mus musculus, Gallus gallus, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana-demonstrating the robustness and generalizability of the framework. Taken together, these results position GPN-Star as a scalable, powerful and flexible tool for genome interpretation, well suited to leverage the growing abundance of comparative genomics data.

Journal Article↗
PubMed1995

Commercial applications of speech interface technology: an industry at the threshold.

Speech interface technology, which includes automatic speech recognition, synthetic speech, and natural language processing, is beginning to have a significant impact on business and personal computer use. Today, powerful and inexpensive microprocessors and improved algorithms are driving commercial applications in computer command, consumer, data entry, speech-to-text, telephone, and voice verification. Robust speaker-independent recognition systems for command and navigation in personal computers are now available; telephone-based transaction and database inquiry systems using both speech synthesis and recognition are coming into use. Large-vocabulary speech interface systems for document creation and read-aloud proofing are expanding beyond niche markets. Today's applications represent a small preview of a rich future for speech interface technology that will eventually replace keyboards with microphones and loud-speakers to give easy accessibility to increasingly intelligent machines.

Computers↗
PubMed2003

Pathway studio--the analysis and navigation of molecular networks.

SUMMARY: PathwayAssist is a software application developed for navigation and analysis of biological pathways, gene regulation networks and protein interaction maps. It comes with the built-in natural language processing module MedScan and the comprehensive database describing more than 100 000 events of regulation, interaction and modification between proteins, cell processes and small molecules. AVAILABILITY: PathwayAssist is available for commercial licensing from Ariadne Genomics, Inc. The light version with limited functionality will be available for free for academic users at www.ariadnegenomics.com/downloads/.

Database Management Systems↗
PubMed2005

Sign language recognition and translation: a multidisciplined approach from the field of artificial intelligence.

In recent years, research has progressed steadily in regard to the use of computers to recognize and render sign language. This paper reviews significant projects in the field beginning with finger-spelling hands such as "Ralph" (robotics), CyberGloves (virtual reality sensors to capture isolated and continuous signs), camera-based projects such as the CopyCat interactive American Sign Language game (computer vision), and sign recognition software (Hidden Markov Modeling and neural network systems). Avatars such as "Tessa" (Text and Sign Support Assistant; three-dimensional imaging) and spoken language to sign language translation systems such as Poland's project entitled "THETOS" (Text into Sign Language Automatic Translator, which operates in Polish; natural language processing) are addressed. The application of this research to education is also explored. The "ICICLE" (Interactive Computer Identification and Correction of Language Errors) project, for example, uses intelligent computer-aided instruction to build a tutorial system for deaf or hard-of-hearing children that analyzes their English writing and makes tailored lessons and recommendations. Finally, the article considers synthesized sign, which is being added to educational material and has the potential to be developed by students themselves.

Artificial Intelligence↗
PubMed2026

Artificial Intelligence for Colorectal Surgeons-Part II: Research Applications, Challenges in Adoption, and Practical Resources.

BACKGROUND: This is part II of a 2-part series examining artificial intelligence in colorectal surgery. Part I established foundational concepts and clinical applications. Implementation, however, requires understanding research methodologies, available resources, and the specific challenges currently limiting widespread adoption. These topics are the focus of part II. OBJECTIVE: To examine artificial intelligence's transformation of surgical research, provide practical implementation resources, address adoption challenges, and explore future directions in colorectal surgery. METHODS: Comprehensive literature review focusing on artificial intelligence research methodology, implementation barriers, educational resources, and emerging technologies relevant to colorectal surgeons. RESULTS: Artificial intelligence streamlines clinical trial design through predictive modeling and natural language processing, reducing enrollment challenges that contribute to failed or inadequate trial accrual. Machine learning enables heterogeneity analysis within clinical trials, identifying treatment-responsive subgroups. Foundation models unlock analysis of unstructured electronic health record data at scale. Professional societies and universities offer specialized artificial intelligence education programs, with open-access data sets facilitating research participation. However, implementation faces multifaceted challenges: technical infrastructure demands, with real-time processing requiring dedicated graphics processing unit clusters; regulatory frameworks struggling with continuously evolving algorithms; undefined liability distribution for artificial intelligence-assisted decisions; algorithmic bias risking health care disparities; and the "black box" problem limiting clinical trust. Economic barriers include substantial initial costs without clear reimbursement pathways. Future directions include multimodal artificial intelligence integrating imaging, genomics, and histopathology; cognitive robotic systems with real-time decision support; digital twin technology for patient-specific surgical simulation; and global surgical artificial intelligence networks enabling distributed learning across institutions. CONCLUSIONS: Although artificial intelligence offers transformative potential for colorectal surgery research and practice, successful implementation requires addressing technical, regulatory, ethical, and economic challenges. The surgeon's evolving role demands both traditional expertise and computational fluency. Future advances in multimodal integration, autonomous systems, and global collaboration will fundamentally reshape surgical practice but will require thoughtful implementation prioritizing patient benefit and clinical value.

Humans↗
PubMed2025

Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models.

Genomic language models (gLMs) have emerged as a powerful approach for learning genome-wide functional constraints directly from DNA sequences. However, standard gLMs adapted from natural language processing often require extremely large model sizes and computational resources, yet still fall short of classical evolutionary models in predictive tasks. Here, we introduce GPN-Star (Genomic Pretrained Network with Species Tree and Alignment Representation), a biologically grounded gLM featuring a phylogeny-aware architecture that leverages whole-genome alignments and species trees to model evolutionary relationships explicitly. Trained on alignments spanning vertebrate, mammalian, and primate evolutionary timescales, GPN-Star achieves state-of-the-art performance across a wide range of variant effect prediction tasks in both coding and non-coding regions of the human genome. Analyses across timescales reveal task-dependent advantages of modeling more recent versus deeper evolution. To demonstrate its potential to advance human genetics, we show that GPN-Star substantially outperforms prior methods in prioritizing pathogenic and fine-mapped GWAS variants; yields unprecedented enrichments of complex trait heritability; and improves power in rare variant association testing. Extending beyond humans, we train GPN-Star for five model organisms - Mus musculus, Gallus gallus, Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana - demonstrating the robustness and generalizability of the framework. Taken together, these results position GPN-Star as a scalable, powerful, and flexible new tool for genome interpretation, well suited to leverage the growing abundance of comparative genomics data.

Journal Article↗
PubMed2002

Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature.

Functional characterizations of thousands of gene products from many species are described in the published literature. These discussions are extremely valuable for characterizing the functions not only of these gene products, but also of their homologs in other organisms. The Gene Ontology (GO) is an effort to create a controlled terminology for labeling gene functions in a more precise, reliable, computer-readable manner. Currently, the best annotations of gene function with the GO are performed by highly trained biologists who read the literature and select appropriate codes. In this study, we explored the possibility that statistical natural language processing techniques can be used to assign GO codes. We compared three document classification methods (maximum entropy modeling, naïve Bayes classification, and nearest-neighbor classification) to the problem of associating a set of GO codes (for biological process) to literature abstracts and thus to the genes associated with the abstracts. We showed that maximum entropy modeling outperforms the other methods and achieves an accuracy of 72% when ascertaining the function discussed within an abstract. The maximum entropy method provides confidence measures that correlate well with performance. We conclude that statistical methods may be used to assign GO codes and may be useful for the difficult task of reassignment as terminology standards evolve over time.

Algorithms↗
PubMed2005

Semantics-based information modeling for the health-care administration sector: the citation platform.

An information brokerage environment for effective information structuring, indexing, and retrieval in the health-care administration sector is presented. The system is based on ontology modeling, natural language processing, extensible markup language, semantics analysis, and behavioral description. Semantics-based information acquisition is achieved through the uniform modeling, representation, and handling of domain-specific knowledge, both content-based and procedural. The system has been validated using information located on several repositories in the web and its performance is reported in terms of precision and recall.

Artificial Intelligence↗
PubMed2004

An instance of coincidence detection architecture relying on temporal coding.

Although time and space are interrelated in every occurrence of real-world events, only spatial codes are used at the basic level of most computational architectures. Inspired by neurobiological facts and hypotheses that assign a primordial coding role to the temporal dimension, and developed to address both cognitive and engineering applications, guided propagation networks (GPNs) are aimed at a generic real-time machine, based on time-space coincidence testing. The involved temporal parameters are gradually introduced, in relation with complementary applications in the field of human-machine communication: sensori-motor modeling, pattern recognition and natural language processing.

Action Potentials↗
PubMed2006

The influence of perceived sexual orientation on fricative identification.

Listeners are more likely to hear a synthetic fricative ambiguous between /s/ and /integral/ as /integral/ if it is appended to a woman's voice than a man's voice [Strand and Johnson, in Natural Language Processing and Speech Technology: Results of the 3rd KONVENS Conference (Mouton de Gruyter, Berlin, 1996), pp. 14-26]. This study expanded on this finding by replicating the result with a much larger group of male and female talkers than had been examined previously, by examining whether phonetic context mediates the influence of talker sex on fricative identification, and by examining whether talkers' perceived sexual orientation influences fricative identification. Stimuli were created by pairing a synthetic nine-step /s/-/integral/ continuum with tokens of /ae k/ and /Ip/ taken from productions of shack and ship by 44 talkers whose perceived sexual orientation had been reported previously [Munson et al., J. Phonetics (in press)]. Listeners participated in a series of two-alternative sack-shack and sip-ship identification experiments. Listeners identified more /integral/ tokens for women's voices than for men's voices for both continua. Lesbian/bisexual-sounding women elicited more sack and sip responses than heterosexual-sounding women. No consistent influence of perceived sexual orientation on fricative identification was noted for men's voices. Results suggest that listeners are sensitive to the association between fricatives' center frequencies and perceived sexual orientation in women's voices, but not in men's voices.

Adult↗
PubMed2002

Predicting the sub-cellular location of proteins from text using support vector machines.

We present an automatic method to classify the sub-cellular location of proteins based on the text of relevant medline abstracts. For each protein, a vector of terms is generated from medline abstracts in which the protein/gene's name or synonym occurs. A Support Vector Machine (SVM) is used to automatically partition the term space and to thus discriminate the textual features that define sub-cellular location. The method is benchmarked on a set of proteins of known sub-cellular location from S. cerevisiae. No prior knowledge of the problem domain nor any natural language processing is used at any stage. The method out-performs support vector machines trained on amino acid composition and has comparable performance to rule-based text classifiers. Combining text with protein amino-acid composition improves recall for some sub-cellular locations. We discuss the generality of the method and its potential application to a variety of biological classification problems.

Automation↗