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Results for “Large Language Models”

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PubMed1979

Liaison psychiatry as a systems approach to behavior.

In this overview, the psychosomatic theory is discussed from an evolutionary perspective. From its initial concern with relationship between emotions and physiology through psychopathology and anatomo-physio-pathology to socio-psycho-pathophysiology, psychosomatic medicine and its theory is presently viewed as an empiric science utilizing a number of conceptual approaches derived from developmental psychology, classical psychiatry, physiology, sociology and anthropology. These are applied to the study and care of patients in ambulatory and inpatient settings, which are the arenas of the consultation-liaison activity and may be viewed as the clinical laboratories of psychosomatic medicine. In these laboratories, a new language has developed which is largely phenomenological and which attempts to utilize theoretical concepts from several disciplines in explaining the illness illness phenomenon in the present. As such, the practitioner of Liaison Psychiatry is a general systems analyst who analyzes the illness situation of the patient and his attendants in an attempt to decipher the identified problem, explaining it by utilizing selected theoretical concepts from the basic sciences of behavior. Psychosomatic theory is seen as an evolving and bridging science attempting to integrate and combine particulate theory into a more comprehensive synthesis.

Adaptation, Psychological↗

PubMedDate not supplied

Pseudocolor display of regional organ blood flow determined by means of the radioactive microsphere technique.

The measurement of regional blood flow (RBF) by means of the radioactive microsphere method yields large sets of raw data. In order to display this large volume of data, we have developed a program which provides the user with a graphical illustration of RBF in different organs (e.g., heart, kidney, brain) using various projections and sections. RBF is visualized by a pseudocolor representation. This set-up enables the user to perform a semiquantitative analysis of RBF and provides a tool for the compact representation of the spatial distribution of RBF values in different parts and layers of the organs being studied. The program runs on a standard microcomputer.

Animals↗

PubMed2002

Microarray databases: standards and ontologies.

A single microarray can provide information on the expression of tens of thousands of genes. The amount of information generated by a microarray-based experiment is sufficiently large that no single study can be expected to mine each nugget of scientific information. As a consequence, the scale and complexity of microarray experiments require that computer software programs do much of the data processing, storage, visualization, analysis and transfer. The adoption of common standards and ontologies for the management and sharing of microarray data is essential and will provide immediate benefit to the research community.

Database Management Systems↗

PubMed2026

Is a Win-Win possible? Achieving pareto-optimal privacy-utility balance in fine-tuned genome language model embeddings against embedding reconstruction attacks.

MOTIVATION: Genomic data is among the most sensitive categories of personal information, and the growing adoption of language models for sequence analysis raises significant privacy concerns. Prior work demonstrated that embeddings from general-purpose language models adapted for genomic sequences leak substantial single-nucleotide information under reconstruction attacks, and that fine-tuning embeddings can reduce this vulnerability at certain positions. However, three critical questions remain unaddressed: (i) whether privacy-utility tradeoffs are inherent constraints or configuration-dependent phenomena; (ii) whether genomic-specialized models such as DNABERT-base and Nucleotide Transformer exhibit different vulnerabilities than adapted general-purpose models; and (iii) how to statistically validate whether observed privacy improvements represent meaningful gains. Addressing these gaps is essential for guiding model selection in privacy-sensitive genomic applications. RESULTS: We systematically evaluated 13 transformer architectures, 9 general-purpose and 4 genomic-specialized, under position-specific embedding reconstruction attacks. We assessed the vulnerabilities of both pre-trained and fine-tuned models to the single-nucleotide inference-reconstruction attack using our new metrics, including error-based privacy gain and Pareto dominance scores, and statistically validated the results via paired t-tests. XLNet-Large achieved the best observed privacy protection among all evaluated models (+19.5% mean privacy gain) while maintaining competitive prediction performance. General-purpose models outperformed genomic-specialized models in 56% of pairwise comparisons. Tokenization strategy, rather than domain specialization, emerged as the primary determinant of the privacy-utility balance. These findings provide evidence-based guidance for selecting models in privacy-sensitive short-window genomic applications. All privacy claims in this work are specific to position-wise embedding reconstruction attacks and do not extend to other privacy risks, such as membership inference or training data extraction, which may respond differently to fine-tuning. AVAILABILITY AND IMPLEMENTATION: The code is publicly available at https://github.com/AnonymousISCBConf/Win-Win-Privacy-Utility-Analysis.

Genomics↗

PubMed2004

GOstat: find statistically overrepresented Gene Ontologies within a group of genes.

SUMMARY: Modern experimental techniques, as for example DNA microarrays, as a result usually produce a long list of genes, which are potentially interesting in the analyzed process. In order to gain biological understanding from this type of data, it is necessary to analyze the functional annotations of all genes in this list. The Gene-Ontology (GO) database provides a useful tool to annotate and analyze the functions of a large number of genes. Here, we introduce a tool that utilizes this information to obtain an understanding of which annotations are typical for the analyzed list of genes. This program automatically obtains the GO annotations from a database and generates statistics of which annotations are overrepresented in the analyzed list of genes. This results in a list of GO terms sorted by their specificity. AVAILABILITY: Our program GOstat is accessible via the Internet at http://gostat.wehi.edu.au

Abstracting and Indexing↗

PubMed2004

From birdsong to speech: a plea for comparative approaches.

Human language and speech are unique accomplishments. Nevertheless, they share a number of characteristics with other systems of communication, and investigators have thus compared them to birdsong and the vocal signaling of nonhuman primates. Particular interesting parallels concern the development of singing and speaking. These behaviors rely on auditory perception, subsequent memorization and finally, the generation of vocal imitations. Several mechanisms help young individuals to deal with the various challenges during the time of signal development. Specific differences aside, astounding parallels can be found also in how a human and a particularly accomplished bird like the Common Nightingale Luscinia megarhynchos treat the experience of many different sound patterns or songs. As a consequence of such exposure, both human infants and young birds eventually acquire large repertoires of verbal or vocal signals. These achievements, however, require access to specific memory mechanisms which are well adapted to the purposes they serve, thereby allowing them to fulfil their species typical roles. With such aspects as a reference, birdsong is an excellent biological model for memory research and also an appropriate system for the study of evolutionary strategies in a very successful class of organisms.

Animals↗

PubMed2005

PentaPlot: a software tool for the illustration of genome mosaicism.

BACKGROUND: Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree. In particular, the generated maps focus attention on those gene families that significantly deviate from the consensus or plurality phylogeny. PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix. RESULTS: The visualization with dekapentagonal maps critically depends on the optimal layout of unrooted tree topologies representing different evolutionary relationships among five organisms along the vertices of the dekapentagon. This is a difficult optimization problem given the large number of possible layouts. At its core our tool utilizes a genetic algorithm with demes and a local search strategy to search for the optimal layout. The hybrid genetic algorithm performs satisfactorily even in those cases where the chosen genomes are so divergent that little phylogenetic information has survived in the individual gene families. CONCLUSION: PentaPlot is being made publicly available as an open source project at http://pentaplot.sourceforge.net.

Algorithms↗

PubMed2005

Automatic assignment of biomedical categories: toward a generic approach.

MOTIVATION: We report on the development of a generic text categorization system designed to automatically assign biomedical categories to any input text. Unlike usual automatic text categorization systems, which rely on data-intensive models extracted from large sets of training data, our categorizer is largely data-independent. METHODS: In order to evaluate the robustness of our approach we test the system on two different biomedical terminologies: the Medical Subject Headings (MeSH) and the Gene Ontology (GO). Our lightweight categorizer, based on two ranking modules, combines a pattern matcher and a vector space retrieval engine, and uses both stems and linguistically-motivated indexing units. RESULTS AND CONCLUSION: Results show the effectiveness of phrase indexing for both GO and MeSH categorization, but we observe the categorization power of the tool depends on the controlled vocabulary: precision at high ranks ranges from above 90% for MeSH to <20% for GO, establishing a new baseline for categorizers based on retrieval methods.

Abstracting and Indexing↗

PubMed2006

Clearcut: a fast implementation of relaxed neighbor joining.

SUMMARY: Clearcut is an open source implementation for the relaxed neighbor joining (RNJ) algorithm. While traditional neighbor joining (NJ) remains a popular method for distance-based phylogenetic tree reconstruction, it suffers from a O(N(3)) time complexity, where N represents the number of taxa in the input. Due to this steep asymptotic time complexity, NJ cannot reasonably handle very large datasets. In contrast, RNJ realizes a typical-case time complexity on the order of N(2)logN without any significant qualitative difference in output. RNJ is particularly useful when inferring a very large tree or a large number of trees. In addition, RNJ retains the desirable property that it will always reconstruct the true tree given a matrix of additive pairwise distances. Clearcut implements RNJ as a C program, which takes either a set of aligned sequences or a pre-computed distance matrix as input and produces a phylogenetic tree. Alternatively, Clearcut can reconstruct phylogenies using an extremely fast standard NJ implementation. AVAILABILITY: Clearcut source code is available for download at: http://bioinformatics.hungry.com/clearcut

Algorithms↗

PubMed2003

Imince: an unrestricted factor-analysis-based program for assessing measurement invariance.

In this article, a Windows program for analyzing measurement invariance in two different populations is described. Factor analysis is a common way of assessing measurement invariance, and restricted factor analysis is now the most popular method. However, applied researchers have usually found that the theoretical advantages of restricted factor analysis do not always apply in practical situations. For example, when the participant sample is large, as is the case in Internet-based questionnaires, the available software for restricted factor analysis might fail to converge on a solution. Our program is based on unrestricted factor analysis and considers the three parameters that define factor invariance: difficulties, discriminations, and residual variances. The statistical significance of the tests for evaluating invariance is obtained using Bootstrap resampling procedures. A real-life example demonstrates the usefulness of the program.

Adult↗

PubMed1995

Molecular and pathologic markers in stage I non-small-cell carcinoma of the lung.

PURPOSE: Although standard treatment of stage I non-small-cell lung cancer (NSCLC) consists of surgical resection alone, approximately 50% of clinical stage I and 30% to 40% of pathologic stage I patients have disease recurrence and die following curative resection. A large number of traditional pathologic and newer molecular markers have been identified, which appear to have important prognostic significance in this population. This review attempts to summarize these data comprehensively. METHODS: Criteria for study selection were English-language reports, identified using Medline and Cancerline, through the fall of 1994. Abstracts from the American Society of Clinical Oncology (ASCO) and the International Association for the Study of Lung Cancer (IASLG) were also reviewed. RESULTS: Molecular markers are classified as molecular genetic markers, differentiation markers, proliferation markers, and markers of metastatic propensity. A number of these markers have been reported to be highly predictive of outcome in stage I NSCLC, and several reports conclude that a specific biomarker may be, aside from clinical stage, the most powerful determinant of prognosis in NSCLC. However, little has been done to clarify the relationships between these newer biologic markers, classic clinicopathologic variables, and clinical outcome. CONCLUSION: At present, a firm conclusion regarding which biomarkers are most important in predicting outcome is not possible, and a model that reliably integrates all independent prognostic variables cannot be developed. A prospective trial is mandatory to address this issue, and a study design is suggested that would facilitate the development of a prognostic index, while simultaneously asking a therapeutic question. The development of a prognostic index would facilitate future trials in which only high-risk stage I patients could be targeted for investigation of postresection adjuvant treatment strategies.

Biomarkers↗

PubMed2002

Opiate treatment for opiate withdrawal in newborn infants.

BACKGROUND: Neonatal abstinence syndrome (NAS) due to opiate withdrawal may result in disruption of the mother-infant relationship, sleep-wake abnormalities, feeding difficulties, weight loss and seizures. Treatments used to ameliorate symptoms and reduce morbidity include opiates, sedatives and non-pharmacological treatments. OBJECTIVES: To assess the effectiveness and safety of using an opiate, compared to a sedative or non-pharmacological treatment, for treatment of NAS due to withdrawal from opiates. The evidence for use of different opiates was assessed in subgroup analyses. SEARCH STRATEGY: The standard search strategy of the Cochrane Neonatal Review Group including searches (up to March 2002) of the Oxford Database of Perinatal Trials, Cochrane Controlled Trials Register (The Cochrane Library, Issue 1, 2002), MEDLINE (1966-March 2002), previous reviews including cross references, abstracts, conferences and symposia proceedings, expert informants, journal handsearching mainly in the English language. SELECTION CRITERIA: Trials enrolling infants with NAS born to mothers with an opiate dependence, with > 80% follow up and using random or quasi-random allocation to opiate or control. Control could include an opiate, sedative or non-pharmacological treatment. DATA COLLECTION AND ANALYSIS: Each author assessed study quality and extracted data independently. Primary outcomes included control of symptoms, seizure occurrence, mortality and neurodevelopment. Treatment effect was expressed using relative risk (RR), risk difference (RD), mean difference (MD) and weighted mean difference (WMD). Meta-analysis was performed using a fixed effect model. MAIN RESULTS: Six studies enrolling a total of 511 infants met inclusion criteria (Carin 1983, Finnegan 1984, Kaltenbach 1986, Kandall 1983, Khoo 1995, Madden 1977); however, two (Finnegan 1984, Kaltenbach 1986) may be sequential reports that include some identical patients. The studies enrolled infants of mothers who had used opiates with or without other drugs during pregnancy. Methodological concerns included the use of quasi-random rather than random patient allocation methods in three studies, and sizeable, largely unexplained differences in reported numbers allocated to each group in four studies. Opiate (morphine) vs supportive care only: One study (Khoo 1995) found no significant effect on treatment failure (RR 1.29, 95% CI 0.41, 4.07), a significant increase in hospital stay (MD 15.0 days, 95% CI 8.9, 21.1) and significant reductions in time to regain birthweight (MD -2.8 days, 95% -5.3, -0.3) and duration of supportive care (MD -197.2 minutes/day, 95% CI -274.2, -120.3). Opiate vs phenobarbital: Meta-analysis of three studies found no significant difference in treatment failure (typical RR 0.78, 95% CI 0.46, 1.32). One of these studies (Finnegan 1984) reported that opiate treatment resulted in a significant reduction in treatment failure among infants of mothers who had used only opiates; however, as this was a post-hoc analysis, this result should be interpreted with caution. One study (Kandall 1983) reported a reduction in seizures, of borderline statistical significance, with the use of opiate. Opiate vs diazepam: Meta-analysis of two studies found a significant reduction in treatment failure (RR 0.43, 95% CI 0.23, 0.80) with the use of opiate. No study reported neurodevelopment by allocated treatment group. REVIEWER'S CONCLUSIONS: Opiates, as compared to supportive care only, appear to reduce the time to regain birth weight and reduce the duration of supportive care, but increase the duration of hospital stay; there is no evidence of effect on treatment failure. When compared to phenobarbital, opiates may reduce the incidence of seizures but, overall, there is no evidence of effect on treatment failure. When compared to diazepam, opiates reduce the incidence of treatment failure. A post-hoc analysis generates the hypothesis that treatment effects may vary according to whether the population includes infants born to all opiate users (i.e. with or without other drug exposure) or is restricted to infants of mothers who used opiates only. In view of the methodologic limitations of the included studies the conclusions of this review should be treated with caution. Further research is needed.

Humans↗

PubMed2005

Voting and catalytic processes with inhomogeneities.

We consider the dynamics of the voter model and of the monomer-monomer catalytic process in the presence of many "competing" inhomogeneities and show, through exact calculations and numerical simulations, that their presence results in a non-trivial fluctuating steady state whose properties are studied and turn out to specifically depend on the dimensionality of the system, the strength of the inhomogeneities, and their separating distances. In fact, in arbitrary dimensions, we obtain an exact (yet formal) expression of the order parameters (magnetization and concentration of adsorbed particles) in the presence of an arbitrary number n of inhomogeneities ("zealots" in the voter language) and formal similarities with suitable electrostatic systems are pointed out. In the non-trivial cases n = 1,2, we explicitly compute the static and long-time properties of the order parameters and therefore capture the generic features of the systems. When n > 2 , the problems are studied through numerical simulations. In one spatial dimension, we also compute the expressions of the stationary order parameters in the completely disordered case, where n is arbitrary large. Particular attention is paid to the spatial dependence of the stationary order parameters and formal connections with electrostatics.

Journal Article↗

PubMed2005

Lexical frequency and acoustic reduction in spoken Dutch.

This study investigates the effects of lexical frequency on the durational reduction of morphologically complex words in spoken Dutch. The hypothesis that high-frequency words are more reduced than low-frequency words was tested by comparing the durations of affixes occurring in different carrier words. Four Dutch affixes were investigated, each occurring in a large number of words with different frequencies. The materials came from a large database of face-to-face conversations. For each word containing a target affix, one token was randomly selected for acoustic analysis. Measurements were made of the duration of the affix as a whole and the durations of the individual segments in the affix. For three of the four affixes, a higher frequency of the carrier word led to shorter realizations of the affix as a whole, individual segments in the affix, or both. Other relevant factors were the sex and age of the speaker, segmental context, and speech rate. To accommodate for these findings, models of speech production should allow word frequency to affect the acoustic realizations of lower-level units, such as individual speech sounds occurring in affixes.

Humans↗

PubMed2005

CT colonography in the detection of colorectal polyps and cancer: systematic review, meta-analysis, and proposed minimum data set for study level reporting.

PURPOSE: To assess the methodologic quality of available data in published reports of computed tomographic (CT) colonography by performing systematic review and meta-analysis. MATERIALS AND METHODS: The MEDLINE database was searched for colonography reports published between 1994 and 2003, without language restriction. The terms colonography, colography, CT colonoscopy, CT pneumocolon, virtual colonoscopy, and virtual endoscopy were used. Studies were selected if the focus was detection of colorectal polyps verified with within-subject reference colonoscopy by using key methodologic criteria based on information presented at the Fourth International Symposium on Virtual Colonoscopy (Boston, Mass). Two reviewers independently abstracted methodologic characteristics. Per-patient and per-polyp detection rates were extracted, and authors were contacted, when necessary. Per-patient sensitivity and specificity were calculated for different lesion size categories, and Forest plots were produced. Meta-analysis of paired sensitivity and specificity was conducted by using a hierarchical model that enabled estimation of summary receiver operating characteristic curves allowing for variation in diagnostic threshold, and the average operating point was calculated. Per-polyp sensitivity was also calculated. RESULTS: Of 1398 studies considered for inclusion, 24 met our criteria. There were 4181 patients with a study prevalence of abnormality of 15%-72%. Meta-analysis of 2610 patients, 206 of whom had large polyps, showed high per-patient average sensitivity (93%; 95% confidence interval [CI]: 73%, 98%) and specificity (97%; 95% CI: 95%, 99%) for colonography; sensitivity and specificity decreased to 86% (95% CI: 75%, 93%) and 86% (95% CI: 76%, 93%), respectively, when the threshold was lowered to include medium polyps. When polyps of all sizes were included, studies were too heterogeneous in sensitivity (range, 45%-97%) and specificity (range, 26%-97%) to allow meaningful meta-analysis. Of 150 cancers, 144 were detected (sensitivity, 95.9%; 95% CI: 91.4%, 98.5%). Data reporting was frequently incomplete, with no generally accepted format. CONCLUSION: CT colonography seems sufficiently sensitive and specific in the detection of large and medium polyps; it is especially sensitive in the detection of symptomatic cancer. Studies are poorly reported, however, and the authors propose a minimum data set for study reporting.

Colonic Polyps↗

PubMed2005

Automatic detection of subsystem/pathway variants in genome analysis.

MOTIVATION: Proteins work together in pathways and networks, collectively comprising the cellular machinery. A subsystem (a generalization of pathway concept) is a group of related functional roles (such as enzymes) jointly involved in a specific aspect of the cellular machinery. Subsystems provide a natural framework for comparative genome analysis and functional annotation. A subsystem may be implemented in a number of different functional variants in individual species. In order to reliably project functional assignments across multiple genomes, we have to be able to identify the variants implemented in each genome. The analysis of such variants across diverse species is an interesting problem by itself and may provide new evolutionary insights. However, no computational techniques are presently available for an automated detection and analysis of subsystem variants. RESULTS: Here we formulate the subsystem variant detection problem as finding the minimum number of subgraphs of a subsystem, which is represented as a graph, and solve the optimization problem by integer programming approach. The performance of our method was tested on subsystems encoded in the SEED, a genomic integration platform developed by the Fellowship for Interpretation of Genomes as a component of a large-scale effort on comparative analysis and annotation of multiple diverse genomes. Here we illustrate the results obtained for two expert-encoded subsystems of the biosynthesis of Coenzyme A and FMN/FAD cofactors. Applications of variant detection, to support genomic annotations and to assess divergence of species, are briefly discussed in the context of these universally conserved and essential metabolic subsystems. SUPPLEMENTARY INFORMATION: The details of the variant detection results are available at http://ffas.burnham.org/svar/supp.html.

Animals↗

PubMed2001

Ultrasound-assisted lipoplasty.

BACKGROUND: Ultrasound-assisted lipoplasty (UAL) has been associated with particular types of complications and uncertain long-term effects arising from interactions between ultrasonic energy and living tissue. The present review seeks to address these issues. METHODS: Search strategy Three search strategies were devised to retrieve literature from Medline, Current Contents, Embase and Cochrane Library databases up until April 2000. Study selection Inclusion of papers was largely determined using a predetermined protocol. English language papers were selected. Acceptable study designs included randomized controlled trials, controlled clinical trials, case series or case reports. Data collection and analysis Thirty-six papers met the inclusion criteria. They were tabulated and critically appraised in terms of methodology and design, outcomes, and the possible influence of bias, confounding and chance. Other papers were also included to provide background material. RESULTS: There was little high-level evidence available comparing UAL and suction-assisted lipoplasty (SAL), with no conclusive evidence that UAL has a safety benefit, although low-quality evidence suggests that UAL is associated with reduced surgeon fatigue as well as increased operating times, slower aspiration rates and an increased learning curve. There is inadequate evidence to determine whether the theoretical potential for DNA damage from ultrasound is realized in the clinical setting. CONCLUSIONS: The evidence base for UAL is inadequate to determine the procedure's safety and efficacy. The potential for DNA damage must be investigated with appropriate in vivo animal models. Recommendations for the safe use of UAL are discussed.

Adipose Tissue↗

PubMed2002

Evaluation and application of a semantic network partition.

Semantic networks (SNs) are excellent knowledge representation structures. However, large semantic networks are hard to comprehend. To overcome this difficulty, several methods of partitioning have been developed that rely on different mixes of structural and semantic methods. However, little has appeared in the literature concerning the question whether a partition of a semantic network creates subnetworks that agree with human insight. We address this issue by presenting a comparison between the results of an algorithmic partitioning method and a partition created by a group of experts. Subsequently, we show how a network partition can be used to generate various partial views of a semantic network, which facilitate user orientation. Examples from the Unified Medical Language System (UMLS) SN are used to demonstrate partial views.

Algorithms↗